# kalarislabs/research-agent-skills

281 Agent Skills for researchers: scientific and research paper writing, journal formats, literature review, citations, data science, ML research and domain science.

- [Plugin page](https://agent-plugins.directory/kalarislabs/research-agent-skills) · [as markdown](https://agent-plugins.directory/kalarislabs/research-agent-skills.md)
- [Versions](https://agent-plugins.directory/kalarislabs/research-agent-skills/versions)
- [Source](https://github.com/KalarisLabs/research-agent-skills/tree/df088027ff233dc511fa74cb7f406b4e87fa438c)

## Skills

- [13c-metabolic-flux](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/13c-metabolic-flux)
- [abstract-and-title](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/abstract-and-title)
- [academic-plotting](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/academic-plotting)
- [acm-sigconf](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/acm-sigconf)
- [adaptyv](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/adaptyv)
- [aeon](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/aeon)
- [alphagenome](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/alphagenome)
- [analytical-method-validation](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/analytical-method-validation)
- [anndata](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/anndata)
- [apa7](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/apa7)
- [ara-compiler](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ara-compiler)
- [ara-research-manager](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ara-research-manager)
- [ara-rigor-reviewer](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ara-rigor-reviewer)
- [arbor](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/arbor)
- [arboreto](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/arboreto)
- [arxiv-submission](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/arxiv-submission)
- [astropy](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/astropy)
- [audiocraft-audio-generation](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/audiocraft-audio-generation)
- [autogpt-agents](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/autogpt-agents)
- [autoresearch](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/autoresearch)
- [autoskill](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/autoskill)
- [awq-quantization](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/awq-quantization)
- [axolotl](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/axolotl)
- [benchling-integration](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/benchling-integration)
- [bgpt-paper-search](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/bgpt-paper-search)
- [bibtex-hygiene](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/bibtex-hygiene)
- [bids](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/bids)
- [biopython](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/biopython)
- [bioservices](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/bioservices)
- [blip-2-vision-language](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/blip-2-vision-language)
- [brainstorming-research-ideas](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/brainstorming-research-ideas)
- [bulk-rnaseq](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/bulk-rnaseq)
- [cell-press](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/cell-press)
- [cellxgene-census](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/cellxgene-census)
- [chroma](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/chroma)
- [cirq](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/cirq)
- [citation-management](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/citation-management)
- [citation-verification](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/citation-verification)
- [clinical-decision-support](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/clinical-decision-support)
- [clinical-reports](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/clinical-reports)
- [clip](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/clip)
- [cobrapy](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/cobrapy)
- [consciousness-council](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/consciousness-council)
- [constitutional-ai](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/constitutional-ai)
- [cover-letter-to-editor](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/cover-letter-to-editor)
- [creative-thinking-for-research](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/creative-thinking-for-research)
- [crewai-multi-agent](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/crewai-multi-agent)
- [dask](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/dask)
- [database-lookup](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/database-lookup)
- [datalad](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/datalad)
- [datamol](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/datamol)
- [deepchem](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/deepchem)
- [deepspeed](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/deepspeed)
- [deeptools](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/deeptools)
- [depmap](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/depmap)
- [dhdna-profiler](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/dhdna-profiler)
- [diffdock](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/diffdock)
- [distributed-llm-pretraining-torchtitan](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/distributed-llm-pretraining-torchtitan)
- [dnanexus-integration](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/dnanexus-integration)
- [dspy](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/dspy)
- [elsevier-cas](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/elsevier-cas)
- [esm](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/esm)
- [etetoolkit](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/etetoolkit)
- [evaluating-code-models](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/evaluating-code-models)
- [evaluating-cosmos-policy](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/evaluating-cosmos-policy)
- [evaluating-llms-harness](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/evaluating-llms-harness)
- [evolving-ai-agents](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/evolving-ai-agents)
- [exa-search](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/exa-search)
- [experiment-tracking-swanlab](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/experiment-tracking-swanlab)
- [experimental-design](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/experimental-design)
- [exploratory-data-analysis](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/exploratory-data-analysis)
- [faiss](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/faiss)
- [fictiv](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/fictiv)
- [fine-tuning-openvla-oft](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/fine-tuning-openvla-oft)
- [fine-tuning-serving-openpi](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/fine-tuning-serving-openpi)
- [fine-tuning-with-trl](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/fine-tuning-with-trl)
- [firecrawl-research-index](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/firecrawl-research-index)
- [flowio](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/flowio)
- [fluidsim](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/fluidsim)
- [folklore-variant-evidence](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/folklore-variant-evidence)
- [generate-image](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/generate-image)
- [geniml](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/geniml)
- [genomic-coordinates](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/genomic-coordinates)
- [genomic-intelligence](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/genomic-intelligence)
- [geomaster](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/geomaster)
- [geopandas](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/geopandas)
- [get-available-resources](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/get-available-resources)
- [gget](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/gget)
- [gguf-quantization](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/gguf-quantization)
- [ginkgo-cloud-lab](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ginkgo-cloud-lab)
- [gptq](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/gptq)
- [grpo-rl-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/grpo-rl-training)
- [gtars](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/gtars)
- [guidance](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/guidance)
- [histolab](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/histolab)
- [hqq-quantization](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/hqq-quantization)
- [hugging-science](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/hugging-science)
- [huggingface-accelerate](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/huggingface-accelerate)
- [huggingface-tokenizers](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/huggingface-tokenizers)
- [hypogenic](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/hypogenic)
- [hypothesis-generation](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/hypothesis-generation)
- [ieee-transactions](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ieee-transactions)
- [imaging-data-commons](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/imaging-data-commons)
- [implementing-llms-litgpt](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/implementing-llms-litgpt)
- [infographics](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/infographics)
- [instructor](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/instructor)
- [iso-standards-readiness](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/iso-standards-readiness)
- [knowledge-distillation](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/knowledge-distillation)
- [lab-hardware-cad](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/lab-hardware-cad)
- [labarchive-integration](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/labarchive-integration)
- [lambda-labs-gpu-cloud](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/lambda-labs-gpu-cloud)
- [lamindb](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/lamindb)
- [langchain](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/langchain)
- [langsmith-observability](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/langsmith-observability)
- [latchbio-integration](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/latchbio-integration)
- [latex-posters](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/latex-posters)
- [liteparse](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/liteparse)
- [literature-review](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/literature-review)
- [llama-cpp](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/llama-cpp)
- [llama-factory](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/llama-factory)
- [llamaguard](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/llamaguard)
- [llamaindex](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/llamaindex)
- [llava](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/llava)
- [long-context](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/long-context)
- [mamba-architecture](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/mamba-architecture)
- [markdown-mermaid-writing](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/markdown-mermaid-writing)
- [market-research-reports](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/market-research-reports)
- [markitdown](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/markitdown)
- [matchms](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/matchms)
- [matlab](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/matlab)
- [matplotlib](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/matplotlib)
- [medchem](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/medchem)
- [miles-rl-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/miles-rl-training)
- [ml-paper-writing](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ml-paper-writing)
- [ml-training-recipes](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ml-training-recipes)
- [mlflow](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/mlflow)
- [modal](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/modal)
- [modal-serverless-gpu](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/modal-serverless-gpu)
- [model-merging](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/model-merging)
- [model-pruning](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/model-pruning)
- [moe-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/moe-training)
- [molecular-dynamics](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/molecular-dynamics)
- [molfeat](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/molfeat)
- [nanogpt](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/nanogpt)
- [nature-portfolio](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/nature-portfolio)
- [ncats-arax](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ncats-arax)
- [nemo-curator](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/nemo-curator)
- [nemo-evaluator-sdk](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/nemo-evaluator-sdk)
- [nemo-guardrails](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/nemo-guardrails)
- [networkx](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/networkx)
- [neurokit2](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/neurokit2)
- [neuropixels-analysis](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/neuropixels-analysis)
- [nextflow](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/nextflow)
- [nnsight-remote-interpretability](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/nnsight-remote-interpretability)
- [omero-integration](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/omero-integration)
- [onekgpd](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/onekgpd)
- [ontology-term-resolution](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ontology-term-resolution)
- [open-notebook](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/open-notebook)
- [openpiv](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/openpiv)
- [openrlhf-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/openrlhf-training)
- [opentrons-integration](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/opentrons-integration)
- [optimize-for-gpu](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/optimize-for-gpu)
- [optimizing-attention-flash](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/optimizing-attention-flash)
- [outlines](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/outlines)
- [pacsomatic](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pacsomatic)
- [paper-corpus-rag](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/paper-corpus-rag)
- [paper-lookup](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/paper-lookup)
- [paperclip](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/paperclip)
- [paperzilla](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/paperzilla)
- [parallel-web](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/parallel-web)
- [pathml](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pathml)
- [pathogen-variant-surveillance](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pathogen-variant-surveillance)
- [pathway-enrichment](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pathway-enrichment)
- [peer-review](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/peer-review)
- [peft-fine-tuning](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/peft-fine-tuning)
- [pennylane](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pennylane)
- [phoenix-observability](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/phoenix-observability)
- [pi-agent](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pi-agent)
- [pinecone](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pinecone)
- [pkpd-modeling](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pkpd-modeling)
- [plos](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/plos)
- [polars](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/polars)
- [polars-bio](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/polars-bio)
- [pptx-posters](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pptx-posters)
- [presenting-conference-talks](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/presenting-conference-talks)
- [prompt-guard](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/prompt-guard)
- [protocolsio-integration](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/protocolsio-integration)
- [pufferlib](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pufferlib)
- [pydeseq2](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pydeseq2)
- [pydicom](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pydicom)
- [pyhealth](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pyhealth)
- [pylabrobot](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pylabrobot)
- [pymatgen](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pymatgen)
- [pymc](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pymc)
- [pymoo](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pymoo)
- [pyopenms](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pyopenms)
- [pysam](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pysam)
- [pytdc](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pytdc)
- [pytorch-fsdp2](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pytorch-fsdp2)
- [pytorch-lightning](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pytorch-lightning)
- [pytorch-lightning-distributed](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pytorch-lightning-distributed)
- [pyvene-interventions](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pyvene-interventions)
- [pyzotero](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/pyzotero)
- [qdrant-vector-search](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/qdrant-vector-search)
- [qiskit](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/qiskit)
- [quantizing-models-bitsandbytes](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/quantizing-models-bitsandbytes)
- [qutip](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/qutip)
- [ray-data](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ray-data)
- [ray-train](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/ray-train)
- [rdkit](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/rdkit)
- [rebuttal-and-response-to-reviewers](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/rebuttal-and-response-to-reviewers)
- [reference-manager-interop](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/reference-manager-interop)
- [relsa-severity-assessment](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/relsa-severity-assessment)
- [reproducibility-statement](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/reproducibility-statement)
- [research-agent-skills](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/research-agent-skills)
- [research-grants](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/research-grants)
- [research-knowledge-graph](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/research-knowledge-graph)
- [research-lookup](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/research-lookup)
- [research-skill-creator](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/research-skill-creator)
- [rowan](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/rowan)
- [rwkv-architecture](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/rwkv-architecture)
- [scanpy](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scanpy)
- [scholar-evaluation](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scholar-evaluation)
- [science-aaas](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/science-aaas)
- [scientific-brainstorming](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scientific-brainstorming)
- [scientific-critical-thinking](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scientific-critical-thinking)
- [scientific-schematics](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scientific-schematics)
- [scientific-slides](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scientific-slides)
- [scientific-visualization](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scientific-visualization)
- [scientific-writing](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scientific-writing)
- [scikit-bio](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scikit-bio)
- [scikit-learn](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scikit-learn)
- [scikit-survival](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scikit-survival)
- [scvelo](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scvelo)
- [scvi-tools](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/scvi-tools)
- [seaborn](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/seaborn)
- [segment-anything-model](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/segment-anything-model)
- [sentence-transformers](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/sentence-transformers)
- [sentencepiece](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/sentencepiece)
- [serving-llms-vllm](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/serving-llms-vllm)
- [sglang](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/sglang)
- [shap](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/shap)
- [simpo-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/simpo-training)
- [simpy](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/simpy)
- [skypilot-multi-cloud-orchestration](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/skypilot-multi-cloud-orchestration)
- [slime-rl-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/slime-rl-training)
- [sparse-autoencoder-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/sparse-autoencoder-training)
- [speculative-decoding](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/speculative-decoding)
- [springer-lncs](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/springer-lncs)
- [stable-baselines3](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/stable-baselines3)
- [stable-diffusion-image-generation](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/stable-diffusion-image-generation)
- [statistical-analysis](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/statistical-analysis)
- [statistical-power](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/statistical-power)
- [statsmodels](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/statsmodels)
- [sympy](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/sympy)
- [systematic-review-prisma](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/systematic-review-prisma)
- [systems-paper-writing](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/systems-paper-writing)
- [tamarind](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/tamarind)
- [tensorboard](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/tensorboard)
- [tensorrt-llm](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/tensorrt-llm)
- [tiledbvcf](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/tiledbvcf)
- [timesfm-forecasting](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/timesfm-forecasting)
- [torch-geometric](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/torch-geometric)
- [torchdrug](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/torchdrug)
- [torchforge-rl-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/torchforge-rl-training)
- [training-llms-megatron](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/training-llms-megatron)
- [transformer-lens-interpretability](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/transformer-lens-interpretability)
- [transformers](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/transformers)
- [treatment-plans](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/treatment-plans)
- [umap-learn](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/umap-learn)
- [uncertainty-and-units](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/uncertainty-and-units)
- [unslop-academic-writing](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/unslop-academic-writing)
- [unsloth](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/unsloth)
- [usfiscaldata](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/usfiscaldata)
- [vaex](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/vaex)
- [venue-templates](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/venue-templates)
- [verl-rl-training](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/verl-rl-training)
- [waypoint-bio](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/waypoint-bio)
- [weights-and-biases](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/weights-and-biases)
- [whisper](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/whisper)
- [zarr-python](https://agent-plugins.directory/kalarislabs/research-agent-skills/skills/zarr-python)

## Documents

- [CHANGELOG.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/CHANGELOG.md)
- [README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/README.md)
- [skills/13c-metabolic-flux/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/13c-metabolic-flux/SKILL.md)
- [skills/13c-metabolic-flux/references/inference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/13c-metabolic-flux/references/inference.md)
- [skills/13c-metabolic-flux/references/input-contract.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/13c-metabolic-flux/references/input-contract.md)
- [skills/abstract-and-title/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/abstract-and-title/SKILL.md)
- [skills/academic-plotting/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/academic-plotting/SKILL.md)
- [skills/academic-plotting/references/data-visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/academic-plotting/references/data-visualization.md)
- [skills/academic-plotting/references/diagram-generation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/academic-plotting/references/diagram-generation.md)
- [skills/academic-plotting/references/style-guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/academic-plotting/references/style-guide.md)
- [skills/acm-sigconf/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/acm-sigconf/SKILL.md)
- [skills/adaptyv/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/adaptyv/SKILL.md)
- [skills/adaptyv/references/api-endpoints.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/adaptyv/references/api-endpoints.md)
- [skills/aeon/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/SKILL.md)
- [skills/aeon/references/anomaly_detection.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/anomaly_detection.md)
- [skills/aeon/references/classification.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/classification.md)
- [skills/aeon/references/clustering.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/clustering.md)
- [skills/aeon/references/datasets_benchmarking.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/datasets_benchmarking.md)
- [skills/aeon/references/distances.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/distances.md)
- [skills/aeon/references/forecasting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/forecasting.md)
- [skills/aeon/references/networks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/networks.md)
- [skills/aeon/references/regression.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/regression.md)
- [skills/aeon/references/segmentation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/segmentation.md)
- [skills/aeon/references/similarity_search.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/similarity_search.md)
- [skills/aeon/references/transformations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/aeon/references/transformations.md)
- [skills/alphagenome/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/alphagenome/SKILL.md)
- [skills/alphagenome/references/atlas.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/alphagenome/references/atlas.md)
- [skills/alphagenome/references/interpretation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/alphagenome/references/interpretation.md)
- [skills/alphagenome/references/model-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/alphagenome/references/model-api.md)
- [skills/analytical-method-validation/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/SKILL.md)
- [skills/analytical-method-validation/assets/validation-protocol-template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/assets/validation-protocol-template.md)
- [skills/analytical-method-validation/assets/validation-report-template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/assets/validation-report-template.md)
- [skills/analytical-method-validation/references/compendial-and-clsi.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/references/compendial-and-clsi.md)
- [skills/analytical-method-validation/references/framework-selection.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/references/framework-selection.md)
- [skills/analytical-method-validation/references/ich-m10-bioanalytical.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/references/ich-m10-bioanalytical.md)
- [skills/analytical-method-validation/references/ich-q2r2.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/references/ich-q2r2.md)
- [skills/analytical-method-validation/references/source-ledger.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/references/source-ledger.md)
- [skills/analytical-method-validation/references/statistics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/analytical-method-validation/references/statistics.md)
- [skills/anndata/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/anndata/SKILL.md)
- [skills/anndata/references/best_practices.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/anndata/references/best_practices.md)
- [skills/anndata/references/concatenation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/anndata/references/concatenation.md)
- [skills/anndata/references/data_structure.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/anndata/references/data_structure.md)
- [skills/anndata/references/io_operations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/anndata/references/io_operations.md)
- [skills/anndata/references/manipulation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/anndata/references/manipulation.md)
- [skills/apa7/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/apa7/SKILL.md)
- [skills/ara-compiler/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-compiler/SKILL.md)
- [skills/ara-compiler/references/ara-schema.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-compiler/references/ara-schema.md)
- [skills/ara-compiler/references/exploration-tree-spec.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-compiler/references/exploration-tree-spec.md)
- [skills/ara-compiler/references/validation-checklist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-compiler/references/validation-checklist.md)
- [skills/ara-research-manager/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-research-manager/SKILL.md)
- [skills/ara-research-manager/references/event-taxonomy.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-research-manager/references/event-taxonomy.md)
- [skills/ara-research-manager/references/provenance-tags.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-research-manager/references/provenance-tags.md)
- [skills/ara-research-manager/references/session-protocol.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-research-manager/references/session-protocol.md)
- [skills/ara-rigor-reviewer/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-rigor-reviewer/SKILL.md)
- [skills/ara-rigor-reviewer/references/review-dimensions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ara-rigor-reviewer/references/review-dimensions.md)
- [skills/arbor/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arbor/SKILL.md)
- [skills/arbor/references/arbor-upstream.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arbor/references/arbor-upstream.md)
- [skills/arbor/references/executor-brief.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arbor/references/executor-brief.md)
- [skills/arbor/references/htr-methodology.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arbor/references/htr-methodology.md)
- [skills/arbor/references/report-template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arbor/references/report-template.md)
- [skills/arboreto/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arboreto/SKILL.md)
- [skills/arboreto/references/algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arboreto/references/algorithms.md)
- [skills/arboreto/references/basic_inference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arboreto/references/basic_inference.md)
- [skills/arboreto/references/distributed_computing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arboreto/references/distributed_computing.md)
- [skills/arxiv-submission/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/arxiv-submission/SKILL.md)
- [skills/astropy/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/astropy/SKILL.md)
- [skills/astropy/references/coordinates.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/astropy/references/coordinates.md)
- [skills/astropy/references/cosmology.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/astropy/references/cosmology.md)
- [skills/astropy/references/fits.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/astropy/references/fits.md)
- [skills/astropy/references/tables.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/astropy/references/tables.md)
- [skills/astropy/references/time.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/astropy/references/time.md)
- [skills/astropy/references/units.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/astropy/references/units.md)
- [skills/astropy/references/wcs_and_other_modules.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/astropy/references/wcs_and_other_modules.md)
- [skills/audiocraft-audio-generation/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/audiocraft-audio-generation/SKILL.md)
- [skills/audiocraft-audio-generation/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/audiocraft-audio-generation/references/advanced-usage.md)
- [skills/audiocraft-audio-generation/references/musicgen-style-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/audiocraft-audio-generation/references/musicgen-style-usage.md)
- [skills/audiocraft-audio-generation/references/musicgen-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/audiocraft-audio-generation/references/musicgen-usage.md)
- [skills/audiocraft-audio-generation/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/audiocraft-audio-generation/references/troubleshooting.md)
- [skills/autogpt-agents/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autogpt-agents/SKILL.md)
- [skills/autogpt-agents/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autogpt-agents/references/advanced-usage.md)
- [skills/autogpt-agents/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autogpt-agents/references/troubleshooting.md)
- [skills/autoresearch/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autoresearch/SKILL.md)
- [skills/autoresearch/references/agent-continuity.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autoresearch/references/agent-continuity.md)
- [skills/autoresearch/references/progress-reporting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autoresearch/references/progress-reporting.md)
- [skills/autoresearch/references/skill-routing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autoresearch/references/skill-routing.md)
- [skills/autoresearch/templates/findings.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autoresearch/templates/findings.md)
- [skills/autoresearch/templates/research-log.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autoresearch/templates/research-log.md)
- [skills/autoskill/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autoskill/SKILL.md)
- [skills/autoskill/references/https-proxy.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/autoskill/references/https-proxy.md)
- [skills/awq-quantization/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/awq-quantization/SKILL.md)
- [skills/awq-quantization/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/awq-quantization/references/advanced-usage.md)
- [skills/awq-quantization/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/awq-quantization/references/troubleshooting.md)
- [skills/axolotl/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/axolotl/SKILL.md)
- [skills/axolotl/references/api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/axolotl/references/api.md)
- [skills/axolotl/references/dataset-formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/axolotl/references/dataset-formats.md)
- [skills/axolotl/references/index.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/axolotl/references/index.md)
- [skills/axolotl/references/other.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/axolotl/references/other.md)
- [skills/benchling-integration/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/benchling-integration/SKILL.md)
- [skills/benchling-integration/references/api_endpoints.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/benchling-integration/references/api_endpoints.md)
- [skills/benchling-integration/references/authentication.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/benchling-integration/references/authentication.md)
- [skills/benchling-integration/references/core_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/benchling-integration/references/core_capabilities.md)
- [skills/benchling-integration/references/eventbridge.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/benchling-integration/references/eventbridge.md)
- [skills/benchling-integration/references/sdk_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/benchling-integration/references/sdk_reference.md)
- [skills/bgpt-paper-search/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bgpt-paper-search/SKILL.md)
- [skills/bibtex-hygiene/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bibtex-hygiene/SKILL.md)
- [skills/bids/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bids/SKILL.md)
- [skills/bids/references/bids_specification.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bids/references/bids_specification.md)
- [skills/bids/references/conversion_tools.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bids/references/conversion_tools.md)
- [skills/bids/references/core_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bids/references/core_workflows.md)
- [skills/bids/references/metadata_fields.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bids/references/metadata_fields.md)
- [skills/biopython/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/SKILL.md)
- [skills/biopython/references/advanced.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/references/advanced.md)
- [skills/biopython/references/alignment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/references/alignment.md)
- [skills/biopython/references/blast.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/references/blast.md)
- [skills/biopython/references/databases.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/references/databases.md)
- [skills/biopython/references/phylogenetics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/references/phylogenetics.md)
- [skills/biopython/references/sequence_io.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/references/sequence_io.md)
- [skills/biopython/references/structure.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/references/structure.md)
- [skills/biopython/references/using-this-skill.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/biopython/references/using-this-skill.md)
- [skills/bioservices/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bioservices/SKILL.md)
- [skills/bioservices/references/identifier_mapping.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bioservices/references/identifier_mapping.md)
- [skills/bioservices/references/services_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bioservices/references/services_reference.md)
- [skills/bioservices/references/workflow_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bioservices/references/workflow_patterns.md)
- [skills/blip-2-vision-language/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/blip-2-vision-language/SKILL.md)
- [skills/blip-2-vision-language/references/advanced-usage-2.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/blip-2-vision-language/references/advanced-usage-2.md)
- [skills/blip-2-vision-language/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/blip-2-vision-language/references/advanced-usage.md)
- [skills/blip-2-vision-language/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/blip-2-vision-language/references/troubleshooting.md)
- [skills/brainstorming-research-ideas/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/brainstorming-research-ideas/SKILL.md)
- [skills/bulk-rnaseq/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bulk-rnaseq/SKILL.md)
- [skills/bulk-rnaseq/references/counts-and-handoff.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bulk-rnaseq/references/counts-and-handoff.md)
- [skills/bulk-rnaseq/references/design-and-qc.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bulk-rnaseq/references/design-and-qc.md)
- [skills/bulk-rnaseq/references/upstream-manual.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bulk-rnaseq/references/upstream-manual.md)
- [skills/bulk-rnaseq/references/upstream-nfcore.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/bulk-rnaseq/references/upstream-nfcore.md)
- [skills/cell-press/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cell-press/SKILL.md)
- [skills/cellxgene-census/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cellxgene-census/SKILL.md)
- [skills/cellxgene-census/references/census_schema.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cellxgene-census/references/census_schema.md)
- [skills/cellxgene-census/references/common_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cellxgene-census/references/common_patterns.md)
- [skills/cellxgene-census/references/core_workflow_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cellxgene-census/references/core_workflow_patterns.md)
- [skills/chroma/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/chroma/SKILL.md)
- [skills/chroma/references/integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/chroma/references/integration.md)
- [skills/cirq/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cirq/SKILL.md)
- [skills/cirq/references/building.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cirq/references/building.md)
- [skills/cirq/references/experiments.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cirq/references/experiments.md)
- [skills/cirq/references/hardware.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cirq/references/hardware.md)
- [skills/cirq/references/noise.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cirq/references/noise.md)
- [skills/cirq/references/simulation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cirq/references/simulation.md)
- [skills/cirq/references/transformation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cirq/references/transformation.md)
- [skills/citation-management/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/SKILL.md)
- [skills/citation-management/assets/citation_checklist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/assets/citation_checklist.md)
- [skills/citation-management/references/best_practices.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/best_practices.md)
- [skills/citation-management/references/bibtex_formatting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/bibtex_formatting.md)
- [skills/citation-management/references/citation_validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/citation_validation.md)
- [skills/citation-management/references/core_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/core_workflow.md)
- [skills/citation-management/references/example_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/example_workflows.md)
- [skills/citation-management/references/google_scholar_search.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/google_scholar_search.md)
- [skills/citation-management/references/metadata_extraction.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/metadata_extraction.md)
- [skills/citation-management/references/pubmed_search.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/pubmed_search.md)
- [skills/citation-management/references/script_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/script_reference.md)
- [skills/citation-management/references/search_strategies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-management/references/search_strategies.md)
- [skills/citation-verification/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/citation-verification/SKILL.md)
- [skills/clinical-decision-support/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/SKILL.md)
- [skills/clinical-decision-support/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/README.md)
- [skills/clinical-decision-support/references/cohort_evaluation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/cohort_evaluation.md)
- [skills/clinical-decision-support/references/decision_logic_traceability.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/decision_logic_traceability.md)
- [skills/clinical-decision-support/references/evidence_profiles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/evidence_profiles.md)
- [skills/clinical-decision-support/references/model_biomarker_evaluation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/model_biomarker_evaluation.md)
- [skills/clinical-decision-support/references/privacy_and_disclosure.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/privacy_and_disclosure.md)
- [skills/clinical-decision-support/references/regulatory_and_governance.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/regulatory_and_governance.md)
- [skills/clinical-decision-support/references/safety_and_scope.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/safety_and_scope.md)
- [skills/clinical-decision-support/references/security_validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/security_validation.md)
- [skills/clinical-decision-support/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/sources.md)
- [skills/clinical-decision-support/references/study_reporting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/study_reporting.md)
- [skills/clinical-decision-support/references/survival_analysis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-decision-support/references/survival_analysis.md)
- [skills/clinical-reports/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/SKILL.md)
- [skills/clinical-reports/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/README.md)
- [skills/clinical-reports/references/case_report_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/case_report_guidelines.md)
- [skills/clinical-reports/references/clinical_trial_reporting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/clinical_trial_reporting.md)
- [skills/clinical-reports/references/data_presentation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/data_presentation.md)
- [skills/clinical-reports/references/diagnostic_reports_standards.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/diagnostic_reports_standards.md)
- [skills/clinical-reports/references/medical_terminology.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/medical_terminology.md)
- [skills/clinical-reports/references/privacy_and_deidentification.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/privacy_and_deidentification.md)
- [skills/clinical-reports/references/professional_review.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/professional_review.md)
- [skills/clinical-reports/references/report_type_routing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/report_type_routing.md)
- [skills/clinical-reports/references/safety_reporting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/safety_reporting.md)
- [skills/clinical-reports/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clinical-reports/references/sources.md)
- [skills/clip/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clip/SKILL.md)
- [skills/clip/references/applications.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/clip/references/applications.md)
- [skills/cobrapy/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cobrapy/SKILL.md)
- [skills/cobrapy/references/api_quick_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cobrapy/references/api_quick_reference.md)
- [skills/cobrapy/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cobrapy/references/workflows.md)
- [skills/consciousness-council/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/consciousness-council/SKILL.md)
- [skills/consciousness-council/references/advanced-configurations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/consciousness-council/references/advanced-configurations.md)
- [skills/constitutional-ai/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/constitutional-ai/SKILL.md)
- [skills/cover-letter-to-editor/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/cover-letter-to-editor/SKILL.md)
- [skills/creative-thinking-for-research/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/creative-thinking-for-research/SKILL.md)
- [skills/crewai-multi-agent/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/crewai-multi-agent/SKILL.md)
- [skills/crewai-multi-agent/references/flows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/crewai-multi-agent/references/flows.md)
- [skills/crewai-multi-agent/references/tools.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/crewai-multi-agent/references/tools.md)
- [skills/crewai-multi-agent/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/crewai-multi-agent/references/troubleshooting.md)
- [skills/crewai-multi-agent/references/yaml-configuration-recommended.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/crewai-multi-agent/references/yaml-configuration-recommended.md)
- [skills/dask/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dask/SKILL.md)
- [skills/dask/references/arrays.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dask/references/arrays.md)
- [skills/dask/references/bags.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dask/references/bags.md)
- [skills/dask/references/best-practices.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dask/references/best-practices.md)
- [skills/dask/references/core-capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dask/references/core-capabilities.md)
- [skills/dask/references/dataframes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dask/references/dataframes.md)
- [skills/dask/references/futures.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dask/references/futures.md)
- [skills/dask/references/schedulers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dask/references/schedulers.md)
- [skills/database-lookup/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/SKILL.md)
- [skills/database-lookup/references/addgene.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/addgene.md)
- [skills/database-lookup/references/alphafold.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/alphafold.md)
- [skills/database-lookup/references/alphavantage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/alphavantage.md)
- [skills/database-lookup/references/bea.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/bea.md)
- [skills/database-lookup/references/bindingdb.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/bindingdb.md)
- [skills/database-lookup/references/biogrid.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/biogrid.md)
- [skills/database-lookup/references/bls.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/bls.md)
- [skills/database-lookup/references/brenda.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/brenda.md)
- [skills/database-lookup/references/cbioportal.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/cbioportal.md)
- [skills/database-lookup/references/census.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/census.md)
- [skills/database-lookup/references/chebi.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/chebi.md)
- [skills/database-lookup/references/chembl.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/chembl.md)
- [skills/database-lookup/references/clinicaltrials.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/clinicaltrials.md)
- [skills/database-lookup/references/clinpgx.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/clinpgx.md)
- [skills/database-lookup/references/clinvar.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/clinvar.md)
- [skills/database-lookup/references/cod.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/cod.md)
- [skills/database-lookup/references/cosmic.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/cosmic.md)
- [skills/database-lookup/references/dailymed.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/dailymed.md)
- [skills/database-lookup/references/database_selection_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/database_selection_guide.md)
- [skills/database-lookup/references/datacommons.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/datacommons.md)
- [skills/database-lookup/references/dbsnp.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/dbsnp.md)
- [skills/database-lookup/references/disgenet.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/disgenet.md)
- [skills/database-lookup/references/drugbank.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/drugbank.md)
- [skills/database-lookup/references/ecb.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/ecb.md)
- [skills/database-lookup/references/emdb.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/emdb.md)
- [skills/database-lookup/references/ena.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/ena.md)
- [skills/database-lookup/references/encode.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/encode.md)
- [skills/database-lookup/references/ensembl.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/ensembl.md)
- [skills/database-lookup/references/epa.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/epa.md)
- [skills/database-lookup/references/eurostat.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/eurostat.md)
- [skills/database-lookup/references/fda.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/fda.md)
- [skills/database-lookup/references/federal-reserve.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/federal-reserve.md)
- [skills/database-lookup/references/fred.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/fred.md)
- [skills/database-lookup/references/gene-ontology.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/gene-ontology.md)
- [skills/database-lookup/references/geo.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/geo.md)
- [skills/database-lookup/references/gnomad.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/gnomad.md)
- [skills/database-lookup/references/gtex.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/gtex.md)
- [skills/database-lookup/references/gwas-catalog.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/gwas-catalog.md)
- [skills/database-lookup/references/hca.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/hca.md)
- [skills/database-lookup/references/hpo.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/hpo.md)
- [skills/database-lookup/references/human-protein-atlas.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/human-protein-atlas.md)
- [skills/database-lookup/references/interpro.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/interpro.md)
- [skills/database-lookup/references/jaspar.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/jaspar.md)
- [skills/database-lookup/references/kegg.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/kegg.md)
- [skills/database-lookup/references/lincs-l1000.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/lincs-l1000.md)
- [skills/database-lookup/references/materials-project.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/materials-project.md)
- [skills/database-lookup/references/metabolomics-workbench.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/metabolomics-workbench.md)
- [skills/database-lookup/references/monarch.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/monarch.md)
- [skills/database-lookup/references/mousemine.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/mousemine.md)
- [skills/database-lookup/references/myvariant.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/myvariant.md)
- [skills/database-lookup/references/nasa-exoplanet-archive.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/nasa-exoplanet-archive.md)
- [skills/database-lookup/references/nasa.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/nasa.md)
- [skills/database-lookup/references/ncbi-gene.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/ncbi-gene.md)
- [skills/database-lookup/references/ncbi-protein.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/ncbi-protein.md)
- [skills/database-lookup/references/ncbi-taxonomy.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/ncbi-taxonomy.md)
- [skills/database-lookup/references/nist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/nist.md)
- [skills/database-lookup/references/noaa.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/noaa.md)
- [skills/database-lookup/references/omim.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/omim.md)
- [skills/database-lookup/references/opentargets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/opentargets.md)
- [skills/database-lookup/references/openweathermap.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/openweathermap.md)
- [skills/database-lookup/references/pdb.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/pdb.md)
- [skills/database-lookup/references/pride.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/pride.md)
- [skills/database-lookup/references/pubchem.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/pubchem.md)
- [skills/database-lookup/references/quickgo.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/quickgo.md)
- [skills/database-lookup/references/reactome.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/reactome.md)
- [skills/database-lookup/references/regulomedb.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/regulomedb.md)
- [skills/database-lookup/references/retrieval-contract.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/retrieval-contract.md)
- [skills/database-lookup/references/rummageo.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/rummageo.md)
- [skills/database-lookup/references/sdss.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/sdss.md)
- [skills/database-lookup/references/sec-edgar.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/sec-edgar.md)
- [skills/database-lookup/references/simbad.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/simbad.md)
- [skills/database-lookup/references/sra.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/sra.md)
- [skills/database-lookup/references/string.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/string.md)
- [skills/database-lookup/references/tcga-gdc.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/tcga-gdc.md)
- [skills/database-lookup/references/treasury.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/treasury.md)
- [skills/database-lookup/references/ucsc-genome.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/ucsc-genome.md)
- [skills/database-lookup/references/uniprot.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/uniprot.md)
- [skills/database-lookup/references/usgs.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/usgs.md)
- [skills/database-lookup/references/uspto.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/uspto.md)
- [skills/database-lookup/references/who.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/who.md)
- [skills/database-lookup/references/worldbank.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/worldbank.md)
- [skills/database-lookup/references/zinc.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/database-lookup/references/zinc.md)
- [skills/datalad/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datalad/SKILL.md)
- [skills/datalad/references/data-access.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datalad/references/data-access.md)
- [skills/datalad/references/provenance.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datalad/references/provenance.md)
- [skills/datalad/references/publishing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datalad/references/publishing.md)
- [skills/datamol/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/SKILL.md)
- [skills/datamol/references/conformers_module.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/references/conformers_module.md)
- [skills/datamol/references/core_api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/references/core_api.md)
- [skills/datamol/references/core_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/references/core_workflows.md)
- [skills/datamol/references/descriptors_viz.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/references/descriptors_viz.md)
- [skills/datamol/references/fragments_scaffolds.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/references/fragments_scaffolds.md)
- [skills/datamol/references/io_module.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/references/io_module.md)
- [skills/datamol/references/reactions_data.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/references/reactions_data.md)
- [skills/datamol/references/workflow_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/datamol/references/workflow_patterns.md)
- [skills/deepchem/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepchem/SKILL.md)
- [skills/deepchem/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepchem/references/api_reference.md)
- [skills/deepchem/references/core_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepchem/references/core_capabilities.md)
- [skills/deepchem/references/typical_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepchem/references/typical_workflows.md)
- [skills/deepchem/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepchem/references/workflows.md)
- [skills/deepspeed/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/SKILL.md)
- [skills/deepspeed/references/08.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/08.md)
- [skills/deepspeed/references/09.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/09.md)
- [skills/deepspeed/references/2020.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/2020.md)
- [skills/deepspeed/references/2023.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/2023.md)
- [skills/deepspeed/references/assets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/assets.md)
- [skills/deepspeed/references/index.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/index.md)
- [skills/deepspeed/references/mii.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/mii.md)
- [skills/deepspeed/references/other.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/other.md)
- [skills/deepspeed/references/tutorials.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deepspeed/references/tutorials.md)
- [skills/deeptools/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deeptools/SKILL.md)
- [skills/deeptools/assets/quick_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deeptools/assets/quick_reference.md)
- [skills/deeptools/references/core_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deeptools/references/core_workflows.md)
- [skills/deeptools/references/effective_genome_sizes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deeptools/references/effective_genome_sizes.md)
- [skills/deeptools/references/normalization_methods.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deeptools/references/normalization_methods.md)
- [skills/deeptools/references/tools_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deeptools/references/tools_reference.md)
- [skills/deeptools/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/deeptools/references/workflows.md)
- [skills/depmap/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/depmap/SKILL.md)
- [skills/depmap/references/dependency_analysis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/depmap/references/dependency_analysis.md)
- [skills/dhdna-profiler/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dhdna-profiler/SKILL.md)
- [skills/dhdna-profiler/references/advanced-profiling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dhdna-profiler/references/advanced-profiling.md)
- [skills/diffdock/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/diffdock/SKILL.md)
- [skills/diffdock/references/confidence_and_limitations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/diffdock/references/confidence_and_limitations.md)
- [skills/diffdock/references/parameters_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/diffdock/references/parameters_reference.md)
- [skills/diffdock/references/workflows_examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/diffdock/references/workflows_examples.md)
- [skills/distributed-llm-pretraining-torchtitan/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/distributed-llm-pretraining-torchtitan/SKILL.md)
- [skills/distributed-llm-pretraining-torchtitan/references/checkpoint.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/distributed-llm-pretraining-torchtitan/references/checkpoint.md)
- [skills/distributed-llm-pretraining-torchtitan/references/custom-models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/distributed-llm-pretraining-torchtitan/references/custom-models.md)
- [skills/distributed-llm-pretraining-torchtitan/references/float8.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/distributed-llm-pretraining-torchtitan/references/float8.md)
- [skills/distributed-llm-pretraining-torchtitan/references/fsdp.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/distributed-llm-pretraining-torchtitan/references/fsdp.md)
- [skills/dnanexus-integration/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/SKILL.md)
- [skills/dnanexus-integration/references/app-development.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/app-development.md)
- [skills/dnanexus-integration/references/authentication.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/authentication.md)
- [skills/dnanexus-integration/references/configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/configuration.md)
- [skills/dnanexus-integration/references/data-operations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/data-operations.md)
- [skills/dnanexus-integration/references/job-execution.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/job-execution.md)
- [skills/dnanexus-integration/references/operations-and-troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/operations-and-troubleshooting.md)
- [skills/dnanexus-integration/references/python-sdk.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/python-sdk.md)
- [skills/dnanexus-integration/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/sources.md)
- [skills/dnanexus-integration/references/workflow-languages.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dnanexus-integration/references/workflow-languages.md)
- [skills/dspy/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dspy/SKILL.md)
- [skills/dspy/references/common-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dspy/references/common-patterns.md)
- [skills/dspy/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dspy/references/examples.md)
- [skills/dspy/references/lm-provider-configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dspy/references/lm-provider-configuration.md)
- [skills/dspy/references/modules.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dspy/references/modules.md)
- [skills/dspy/references/optimizers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/dspy/references/optimizers.md)
- [skills/elsevier-cas/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/elsevier-cas/SKILL.md)
- [skills/esm/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/esm/SKILL.md)
- [skills/esm/references/biohub-platform.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/esm/references/biohub-platform.md)
- [skills/esm/references/esm-c-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/esm/references/esm-c-api.md)
- [skills/esm/references/esm3-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/esm/references/esm3-api.md)
- [skills/esm/references/forge-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/esm/references/forge-api.md)
- [skills/esm/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/esm/references/workflows.md)
- [skills/etetoolkit/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/etetoolkit/SKILL.md)
- [skills/etetoolkit/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/etetoolkit/references/api_reference.md)
- [skills/etetoolkit/references/migration-ete3-to-ete4.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/etetoolkit/references/migration-ete3-to-ete4.md)
- [skills/etetoolkit/references/taxonomy.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/etetoolkit/references/taxonomy.md)
- [skills/etetoolkit/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/etetoolkit/references/visualization.md)
- [skills/etetoolkit/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/etetoolkit/references/workflows.md)
- [skills/evaluating-code-models/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-code-models/SKILL.md)
- [skills/evaluating-code-models/references/benchmarks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-code-models/references/benchmarks.md)
- [skills/evaluating-code-models/references/custom-tasks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-code-models/references/custom-tasks.md)
- [skills/evaluating-code-models/references/issues.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-code-models/references/issues.md)
- [skills/evaluating-cosmos-policy/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-cosmos-policy/SKILL.md)
- [skills/evaluating-cosmos-policy/references/libero-commands.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-cosmos-policy/references/libero-commands.md)
- [skills/evaluating-cosmos-policy/references/robocasa-commands.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-cosmos-policy/references/robocasa-commands.md)
- [skills/evaluating-llms-harness/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-llms-harness/SKILL.md)
- [skills/evaluating-llms-harness/references/api-evaluation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-llms-harness/references/api-evaluation.md)
- [skills/evaluating-llms-harness/references/benchmark-guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-llms-harness/references/benchmark-guide.md)
- [skills/evaluating-llms-harness/references/common-issues.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-llms-harness/references/common-issues.md)
- [skills/evaluating-llms-harness/references/custom-tasks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-llms-harness/references/custom-tasks.md)
- [skills/evaluating-llms-harness/references/distributed-eval.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-llms-harness/references/distributed-eval.md)
- [skills/evaluating-llms-harness/references/hardware-requirements.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evaluating-llms-harness/references/hardware-requirements.md)
- [skills/evolving-ai-agents/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/SKILL.md)
- [skills/evolving-ai-agents/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/references/README.md)
- [skills/evolving-ai-agents/references/api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/references/api.md)
- [skills/evolving-ai-agents/references/architecture.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/references/architecture.md)
- [skills/evolving-ai-agents/references/design-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/references/design-patterns.md)
- [skills/evolving-ai-agents/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/references/examples.md)
- [skills/evolving-ai-agents/references/issues.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/references/issues.md)
- [skills/evolving-ai-agents/references/releases.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/references/releases.md)
- [skills/evolving-ai-agents/references/tutorials.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/evolving-ai-agents/references/tutorials.md)
- [skills/exa-search/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exa-search/SKILL.md)
- [skills/exa-search/references/web-extract.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exa-search/references/web-extract.md)
- [skills/exa-search/references/web-search.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exa-search/references/web-search.md)
- [skills/experiment-tracking-swanlab/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/experiment-tracking-swanlab/SKILL.md)
- [skills/experiment-tracking-swanlab/references/integrations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/experiment-tracking-swanlab/references/integrations.md)
- [skills/experiment-tracking-swanlab/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/experiment-tracking-swanlab/references/visualization.md)
- [skills/experimental-design/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/experimental-design/SKILL.md)
- [skills/experimental-design/references/design_types.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/experimental-design/references/design_types.md)
- [skills/experimental-design/references/factorial_and_doe.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/experimental-design/references/factorial_and_doe.md)
- [skills/experimental-design/references/randomization_and_blocking.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/experimental-design/references/randomization_and_blocking.md)
- [skills/experimental-design/references/sequential_and_adaptive.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/experimental-design/references/sequential_and_adaptive.md)
- [skills/exploratory-data-analysis/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exploratory-data-analysis/SKILL.md)
- [skills/exploratory-data-analysis/assets/report_template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exploratory-data-analysis/assets/report_template.md)
- [skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md)
- [skills/exploratory-data-analysis/references/chemistry_molecular_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md)
- [skills/exploratory-data-analysis/references/general_scientific_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exploratory-data-analysis/references/general_scientific_formats.md)
- [skills/exploratory-data-analysis/references/microscopy_imaging_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md)
- [skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md)
- [skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md)
- [skills/faiss/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/faiss/SKILL.md)
- [skills/faiss/references/index_types.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/faiss/references/index_types.md)
- [skills/fictiv/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fictiv/SKILL.md)
- [skills/fictiv/references/capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fictiv/references/capabilities.md)
- [skills/fictiv/references/checkout-and-payment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fictiv/references/checkout-and-payment.md)
- [skills/fictiv/references/orders-library-teams.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fictiv/references/orders-library-teams.md)
- [skills/fictiv/references/quoting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fictiv/references/quoting.md)
- [skills/fictiv/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fictiv/references/troubleshooting.md)
- [skills/fictiv/references/ui-map.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fictiv/references/ui-map.md)
- [skills/fine-tuning-openvla-oft/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-openvla-oft/SKILL.md)
- [skills/fine-tuning-openvla-oft/references/aloha-workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-openvla-oft/references/aloha-workflow.md)
- [skills/fine-tuning-openvla-oft/references/config-troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-openvla-oft/references/config-troubleshooting.md)
- [skills/fine-tuning-openvla-oft/references/libero-workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-openvla-oft/references/libero-workflow.md)
- [skills/fine-tuning-openvla-oft/references/paper-and-checkpoints.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-openvla-oft/references/paper-and-checkpoints.md)
- [skills/fine-tuning-serving-openpi/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-serving-openpi/SKILL.md)
- [skills/fine-tuning-serving-openpi/references/checkpoints-and-env-map.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-serving-openpi/references/checkpoints-and-env-map.md)
- [skills/fine-tuning-serving-openpi/references/config-recipes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-serving-openpi/references/config-recipes.md)
- [skills/fine-tuning-serving-openpi/references/for-hpc-cluster-users.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-serving-openpi/references/for-hpc-cluster-users.md)
- [skills/fine-tuning-serving-openpi/references/pytorch-gotchas.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-serving-openpi/references/pytorch-gotchas.md)
- [skills/fine-tuning-serving-openpi/references/remote-client-pattern.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-serving-openpi/references/remote-client-pattern.md)
- [skills/fine-tuning-serving-openpi/references/training-debugging.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-serving-openpi/references/training-debugging.md)
- [skills/fine-tuning-with-trl/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-with-trl/SKILL.md)
- [skills/fine-tuning-with-trl/references/dpo-variants.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-with-trl/references/dpo-variants.md)
- [skills/fine-tuning-with-trl/references/online-rl.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-with-trl/references/online-rl.md)
- [skills/fine-tuning-with-trl/references/reward-modeling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-with-trl/references/reward-modeling.md)
- [skills/fine-tuning-with-trl/references/sft-training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fine-tuning-with-trl/references/sft-training.md)
- [skills/firecrawl-research-index/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/firecrawl-research-index/SKILL.md)
- [skills/flowio/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/flowio/SKILL.md)
- [skills/flowio/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/flowio/references/api_reference.md)
- [skills/flowio/references/fcs_semantics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/flowio/references/fcs_semantics.md)
- [skills/flowio/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/flowio/references/sources.md)
- [skills/flowio/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/flowio/references/troubleshooting.md)
- [skills/flowio/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/flowio/references/workflows.md)
- [skills/fluidsim/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fluidsim/SKILL.md)
- [skills/fluidsim/references/advanced_features.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fluidsim/references/advanced_features.md)
- [skills/fluidsim/references/installation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fluidsim/references/installation.md)
- [skills/fluidsim/references/output_analysis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fluidsim/references/output_analysis.md)
- [skills/fluidsim/references/parameters.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fluidsim/references/parameters.md)
- [skills/fluidsim/references/simulation_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fluidsim/references/simulation_workflow.md)
- [skills/fluidsim/references/solvers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/fluidsim/references/solvers.md)
- [skills/folklore-variant-evidence/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/folklore-variant-evidence/SKILL.md)
- [skills/folklore-variant-evidence/references/mcp-contract.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/folklore-variant-evidence/references/mcp-contract.md)
- [skills/generate-image/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/generate-image/SKILL.md)
- [skills/generate-image/references/models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/generate-image/references/models.md)
- [skills/geniml/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geniml/SKILL.md)
- [skills/geniml/references/bedspace.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geniml/references/bedspace.md)
- [skills/geniml/references/consensus_peaks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geniml/references/consensus_peaks.md)
- [skills/geniml/references/region2vec.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geniml/references/region2vec.md)
- [skills/geniml/references/scembed.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geniml/references/scembed.md)
- [skills/geniml/references/utilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geniml/references/utilities.md)
- [skills/genomic-coordinates/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-coordinates/SKILL.md)
- [skills/genomic-coordinates/references/format-conventions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-coordinates/references/format-conventions.md)
- [skills/genomic-coordinates/references/reference-builds.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-coordinates/references/reference-builds.md)
- [skills/genomic-coordinates/references/transcript-coordinates.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-coordinates/references/transcript-coordinates.md)
- [skills/genomic-coordinates/references/variant-representation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-coordinates/references/variant-representation.md)
- [skills/genomic-intelligence/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-intelligence/SKILL.md)
- [skills/genomic-intelligence/references/api-and-auth.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-intelligence/references/api-and-auth.md)
- [skills/genomic-intelligence/references/mcp.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-intelligence/references/mcp.md)
- [skills/genomic-intelligence/references/sequence-acquisition.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-intelligence/references/sequence-acquisition.md)
- [skills/genomic-intelligence/references/tasks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/genomic-intelligence/references/tasks.md)
- [skills/geomaster/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/README.md)
- [skills/geomaster/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/SKILL.md)
- [skills/geomaster/references/advanced-gis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/advanced-gis.md)
- [skills/geomaster/references/big-data.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/big-data.md)
- [skills/geomaster/references/code-examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/code-examples.md)
- [skills/geomaster/references/coordinate-systems.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/coordinate-systems.md)
- [skills/geomaster/references/core-libraries.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/core-libraries.md)
- [skills/geomaster/references/data-sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/data-sources.md)
- [skills/geomaster/references/gis-software.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/gis-software.md)
- [skills/geomaster/references/industry-applications.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/industry-applications.md)
- [skills/geomaster/references/machine-learning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/machine-learning.md)
- [skills/geomaster/references/programming-languages.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/programming-languages.md)
- [skills/geomaster/references/remote-sensing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/remote-sensing.md)
- [skills/geomaster/references/scientific-domains.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/scientific-domains.md)
- [skills/geomaster/references/specialized-topics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/specialized-topics.md)
- [skills/geomaster/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geomaster/references/troubleshooting.md)
- [skills/geopandas/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geopandas/SKILL.md)
- [skills/geopandas/references/crs-management.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geopandas/references/crs-management.md)
- [skills/geopandas/references/data-io.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geopandas/references/data-io.md)
- [skills/geopandas/references/data-structures.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geopandas/references/data-structures.md)
- [skills/geopandas/references/geometric-operations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geopandas/references/geometric-operations.md)
- [skills/geopandas/references/spatial-analysis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geopandas/references/spatial-analysis.md)
- [skills/geopandas/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/geopandas/references/visualization.md)
- [skills/get-available-resources/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/get-available-resources/SKILL.md)
- [skills/get-available-resources/references/resource_semantics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/get-available-resources/references/resource_semantics.md)
- [skills/get-available-resources/references/snapshot_schema.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/get-available-resources/references/snapshot_schema.md)
- [skills/get-available-resources/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/get-available-resources/references/sources.md)
- [skills/gget/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gget/SKILL.md)
- [skills/gget/references/common_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gget/references/common_workflows.md)
- [skills/gget/references/database_info.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gget/references/database_info.md)
- [skills/gget/references/module_catalog.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gget/references/module_catalog.md)
- [skills/gget/references/module_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gget/references/module_reference.md)
- [skills/gget/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gget/references/workflows.md)
- [skills/gguf-quantization/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gguf-quantization/SKILL.md)
- [skills/gguf-quantization/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gguf-quantization/references/advanced-usage.md)
- [skills/gguf-quantization/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gguf-quantization/references/troubleshooting.md)
- [skills/ginkgo-cloud-lab/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/SKILL.md)
- [skills/ginkgo-cloud-lab/references/cell-free-protein-expression-hibit.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-hibit.md)
- [skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md)
- [skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md)
- [skills/ginkgo-cloud-lab/references/cfps-expression-purification-quantification.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/cfps-expression-purification-quantification.md)
- [skills/ginkgo-cloud-lab/references/cfps-strep-purification-thermal-shift.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/cfps-strep-purification-thermal-shift.md)
- [skills/ginkgo-cloud-lab/references/cfps-strep-tag-purification-a280.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/cfps-strep-tag-purification-a280.md)
- [skills/ginkgo-cloud-lab/references/echo-ms-cfps-detection.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/echo-ms-cfps-detection.md)
- [skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md)
- [skills/ginkgo-cloud-lab/references/ecoli-expression-purification-quantification.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/ecoli-expression-purification-quantification.md)
- [skills/ginkgo-cloud-lab/references/ecoli-minibinder-expression-histag-a280.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/ecoli-minibinder-expression-histag-a280.md)
- [skills/ginkgo-cloud-lab/references/ecoli-protein-expression-hibit.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-hibit.md)
- [skills/ginkgo-cloud-lab/references/ecoli-protein-expression-histag-a280.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-histag-a280.md)
- [skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md)
- [skills/ginkgo-cloud-lab/references/ivt-rna-synthesis-qpcr.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/ivt-rna-synthesis-qpcr.md)
- [skills/ginkgo-cloud-lab/references/minibinder-strep-tag-a280.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/minibinder-strep-tag-a280.md)
- [skills/ginkgo-cloud-lab/references/pichia-protein-expression-labchip.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/pichia-protein-expression-labchip.md)
- [skills/ginkgo-cloud-lab/references/spr-target-onboarding.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ginkgo-cloud-lab/references/spr-target-onboarding.md)
- [skills/gptq/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gptq/SKILL.md)
- [skills/gptq/references/calibration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gptq/references/calibration.md)
- [skills/gptq/references/integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gptq/references/integration.md)
- [skills/gptq/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gptq/references/troubleshooting.md)
- [skills/grpo-rl-training/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/grpo-rl-training/README.md)
- [skills/grpo-rl-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/grpo-rl-training/SKILL.md)
- [skills/grpo-rl-training/references/advanced-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/grpo-rl-training/references/advanced-patterns.md)
- [skills/grpo-rl-training/references/critical-training-insights.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/grpo-rl-training/references/critical-training-insights.md)
- [skills/gtars/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gtars/SKILL.md)
- [skills/gtars/references/cli.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gtars/references/cli.md)
- [skills/gtars/references/coverage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gtars/references/coverage.md)
- [skills/gtars/references/overlap.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gtars/references/overlap.md)
- [skills/gtars/references/python-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gtars/references/python-api.md)
- [skills/gtars/references/refget.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gtars/references/refget.md)
- [skills/gtars/references/tokenizers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/gtars/references/tokenizers.md)
- [skills/guidance/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/guidance/SKILL.md)
- [skills/guidance/references/backends.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/guidance/references/backends.md)
- [skills/guidance/references/common-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/guidance/references/common-patterns.md)
- [skills/guidance/references/constraints.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/guidance/references/constraints.md)
- [skills/guidance/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/guidance/references/examples.md)
- [skills/histolab/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/histolab/SKILL.md)
- [skills/histolab/references/core_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/histolab/references/core_capabilities.md)
- [skills/histolab/references/filters_preprocessing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/histolab/references/filters_preprocessing.md)
- [skills/histolab/references/slide_management.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/histolab/references/slide_management.md)
- [skills/histolab/references/tile_extraction.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/histolab/references/tile_extraction.md)
- [skills/histolab/references/tissue_masks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/histolab/references/tissue_masks.md)
- [skills/histolab/references/typical_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/histolab/references/typical_workflows.md)
- [skills/histolab/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/histolab/references/visualization.md)
- [skills/hqq-quantization/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hqq-quantization/SKILL.md)
- [skills/hqq-quantization/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hqq-quantization/references/advanced-usage.md)
- [skills/hqq-quantization/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hqq-quantization/references/troubleshooting.md)
- [skills/hugging-science/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hugging-science/SKILL.md)
- [skills/hugging-science/references/flagship-resources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hugging-science/references/flagship-resources.md)
- [skills/hugging-science/references/topics-and-slugs.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hugging-science/references/topics-and-slugs.md)
- [skills/hugging-science/references/using-datasets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hugging-science/references/using-datasets.md)
- [skills/hugging-science/references/using-models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hugging-science/references/using-models.md)
- [skills/hugging-science/references/using-spaces.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hugging-science/references/using-spaces.md)
- [skills/huggingface-accelerate/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-accelerate/SKILL.md)
- [skills/huggingface-accelerate/references/custom-plugins.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-accelerate/references/custom-plugins.md)
- [skills/huggingface-accelerate/references/megatron-integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-accelerate/references/megatron-integration.md)
- [skills/huggingface-accelerate/references/performance.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-accelerate/references/performance.md)
- [skills/huggingface-tokenizers/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-tokenizers/SKILL.md)
- [skills/huggingface-tokenizers/references/algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-tokenizers/references/algorithms.md)
- [skills/huggingface-tokenizers/references/integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-tokenizers/references/integration.md)
- [skills/huggingface-tokenizers/references/pipeline.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-tokenizers/references/pipeline.md)
- [skills/huggingface-tokenizers/references/tokenization-algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-tokenizers/references/tokenization-algorithms.md)
- [skills/huggingface-tokenizers/references/training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/huggingface-tokenizers/references/training.md)
- [skills/hypogenic/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypogenic/SKILL.md)
- [skills/hypogenic/references/configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypogenic/references/configuration.md)
- [skills/hypogenic/references/datasets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypogenic/references/datasets.md)
- [skills/hypogenic/references/evaluation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypogenic/references/evaluation.md)
- [skills/hypogenic/references/security.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypogenic/references/security.md)
- [skills/hypogenic/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypogenic/references/sources.md)
- [skills/hypogenic/references/upstream.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypogenic/references/upstream.md)
- [skills/hypothesis-generation/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/SKILL.md)
- [skills/hypothesis-generation/assets/preregistration_scaffold_template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/assets/preregistration_scaffold_template.md)
- [skills/hypothesis-generation/references/causal_inference_and_claims.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/causal_inference_and_claims.md)
- [skills/hypothesis-generation/references/concepts_and_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/concepts_and_workflow.md)
- [skills/hypothesis-generation/references/ethics_safety_and_ai.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/ethics_safety_and_ai.md)
- [skills/hypothesis-generation/references/experimental_design_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/experimental_design_patterns.md)
- [skills/hypothesis-generation/references/hypothesis_quality_criteria.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/hypothesis_quality_criteria.md)
- [skills/hypothesis-generation/references/literature_search_strategies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/literature_search_strategies.md)
- [skills/hypothesis-generation/references/preregistration_and_open_science.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/preregistration_and_open_science.md)
- [skills/hypothesis-generation/references/security_validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/security_validation.md)
- [skills/hypothesis-generation/references/source_ledger.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/source_ledger.md)
- [skills/hypothesis-generation/references/tool_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/hypothesis-generation/references/tool_reference.md)
- [skills/ieee-transactions/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ieee-transactions/SKILL.md)
- [skills/imaging-data-commons/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/SKILL.md)
- [skills/imaging-data-commons/references/bigquery_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/bigquery_guide.md)
- [skills/imaging-data-commons/references/cli_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/cli_guide.md)
- [skills/imaging-data-commons/references/clinical_data_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/clinical_data_guide.md)
- [skills/imaging-data-commons/references/cloud_storage_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/cloud_storage_guide.md)
- [skills/imaging-data-commons/references/core-capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/core-capabilities.md)
- [skills/imaging-data-commons/references/dicomweb_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/dicomweb_guide.md)
- [skills/imaging-data-commons/references/digital_pathology_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/digital_pathology_guide.md)
- [skills/imaging-data-commons/references/index_tables_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/index_tables_guide.md)
- [skills/imaging-data-commons/references/licensing_and_citation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/licensing_and_citation.md)
- [skills/imaging-data-commons/references/mcp_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/mcp_guide.md)
- [skills/imaging-data-commons/references/parquet_access_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/parquet_access_guide.md)
- [skills/imaging-data-commons/references/rest_api_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/rest_api_guide.md)
- [skills/imaging-data-commons/references/sql_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/sql_patterns.md)
- [skills/imaging-data-commons/references/use_cases.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/imaging-data-commons/references/use_cases.md)
- [skills/implementing-llms-litgpt/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/implementing-llms-litgpt/SKILL.md)
- [skills/implementing-llms-litgpt/references/custom-models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/implementing-llms-litgpt/references/custom-models.md)
- [skills/implementing-llms-litgpt/references/distributed-training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/implementing-llms-litgpt/references/distributed-training.md)
- [skills/implementing-llms-litgpt/references/supported-models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/implementing-llms-litgpt/references/supported-models.md)
- [skills/implementing-llms-litgpt/references/training-recipes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/implementing-llms-litgpt/references/training-recipes.md)
- [skills/infographics/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/infographics/SKILL.md)
- [skills/infographics/references/color_palettes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/infographics/references/color_palettes.md)
- [skills/infographics/references/design_principles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/infographics/references/design_principles.md)
- [skills/infographics/references/infographic_type_catalog.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/infographics/references/infographic_type_catalog.md)
- [skills/infographics/references/infographic_types.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/infographics/references/infographic_types.md)
- [skills/infographics/references/iterative_refinement.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/infographics/references/iterative_refinement.md)
- [skills/instructor/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/instructor/SKILL.md)
- [skills/instructor/references/advanced-features.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/instructor/references/advanced-features.md)
- [skills/instructor/references/common-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/instructor/references/common-patterns.md)
- [skills/instructor/references/error-handling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/instructor/references/error-handling.md)
- [skills/instructor/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/instructor/references/examples.md)
- [skills/instructor/references/provider-configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/instructor/references/provider-configuration.md)
- [skills/instructor/references/providers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/instructor/references/providers.md)
- [skills/instructor/references/validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/instructor/references/validation.md)
- [skills/iso-standards-readiness/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/SKILL.md)
- [skills/iso-standards-readiness/assets/templates/procedures/CAPA-procedure-template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/assets/templates/procedures/CAPA-procedure-template.md)
- [skills/iso-standards-readiness/assets/templates/procedures/document-control-procedure-template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/assets/templates/procedures/document-control-procedure-template.md)
- [skills/iso-standards-readiness/assets/templates/quality-manual-template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/assets/templates/quality-manual-template.md)
- [skills/iso-standards-readiness/references/assurance-lanes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/assurance-lanes.md)
- [skills/iso-standards-readiness/references/evidence-architecture.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/evidence-architecture.md)
- [skills/iso-standards-readiness/references/gap-analysis-checklist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/gap-analysis-checklist.md)
- [skills/iso-standards-readiness/references/iso-13485.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/iso-13485.md)
- [skills/iso-standards-readiness/references/iso-14971.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/iso-14971.md)
- [skills/iso-standards-readiness/references/iso-15189.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/iso-15189.md)
- [skills/iso-standards-readiness/references/iso-17025.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/iso-17025.md)
- [skills/iso-standards-readiness/references/quality-manual-guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/quality-manual-guide.md)
- [skills/iso-standards-readiness/references/source-ledger.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/iso-standards-readiness/references/source-ledger.md)
- [skills/knowledge-distillation/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/knowledge-distillation/SKILL.md)
- [skills/knowledge-distillation/references/minillm.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/knowledge-distillation/references/minillm.md)
- [skills/lab-hardware-cad/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lab-hardware-cad/SKILL.md)
- [skills/lab-hardware-cad/references/behavior-rigs.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lab-hardware-cad/references/behavior-rigs.md)
- [skills/lab-hardware-cad/references/build123d-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lab-hardware-cad/references/build123d-patterns.md)
- [skills/lab-hardware-cad/references/fabrication-limits.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lab-hardware-cad/references/fabrication-limits.md)
- [skills/lab-hardware-cad/references/labware-adapters.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lab-hardware-cad/references/labware-adapters.md)
- [skills/lab-hardware-cad/references/microfluidics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lab-hardware-cad/references/microfluidics.md)
- [skills/lab-hardware-cad/references/optomechanics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lab-hardware-cad/references/optomechanics.md)
- [skills/lab-hardware-cad/references/validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lab-hardware-cad/references/validation.md)
- [skills/labarchive-integration/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/labarchive-integration/SKILL.md)
- [skills/labarchive-integration/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/labarchive-integration/references/api_reference.md)
- [skills/labarchive-integration/references/authentication_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/labarchive-integration/references/authentication_guide.md)
- [skills/labarchive-integration/references/integrations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/labarchive-integration/references/integrations.md)
- [skills/labarchive-integration/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/labarchive-integration/references/sources.md)
- [skills/lambda-labs-gpu-cloud/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lambda-labs-gpu-cloud/SKILL.md)
- [skills/lambda-labs-gpu-cloud/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lambda-labs-gpu-cloud/references/advanced-usage.md)
- [skills/lambda-labs-gpu-cloud/references/python-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lambda-labs-gpu-cloud/references/python-api.md)
- [skills/lambda-labs-gpu-cloud/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lambda-labs-gpu-cloud/references/troubleshooting.md)
- [skills/lamindb/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lamindb/SKILL.md)
- [skills/lamindb/references/annotation-validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lamindb/references/annotation-validation.md)
- [skills/lamindb/references/core-concepts.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lamindb/references/core-concepts.md)
- [skills/lamindb/references/data-management.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lamindb/references/data-management.md)
- [skills/lamindb/references/integrations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lamindb/references/integrations.md)
- [skills/lamindb/references/ontologies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lamindb/references/ontologies.md)
- [skills/lamindb/references/setup-deployment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/lamindb/references/setup-deployment.md)
- [skills/langchain/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/langchain/SKILL.md)
- [skills/langchain/references/agents.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/langchain/references/agents.md)
- [skills/langchain/references/integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/langchain/references/integration.md)
- [skills/langchain/references/rag-retrieval-augmented-generation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/langchain/references/rag-retrieval-augmented-generation.md)
- [skills/langchain/references/rag.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/langchain/references/rag.md)
- [skills/langsmith-observability/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/langsmith-observability/SKILL.md)
- [skills/langsmith-observability/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/langsmith-observability/references/advanced-usage.md)
- [skills/langsmith-observability/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/langsmith-observability/references/troubleshooting.md)
- [skills/latchbio-integration/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/SKILL.md)
- [skills/latchbio-integration/references/data-management.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/data-management.md)
- [skills/latchbio-integration/references/latch-mcp.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/latch-mcp.md)
- [skills/latchbio-integration/references/nextflow-snakemake.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/nextflow-snakemake.md)
- [skills/latchbio-integration/references/operations-and-debugging.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/operations-and-debugging.md)
- [skills/latchbio-integration/references/registry.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/registry.md)
- [skills/latchbio-integration/references/resource-configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/resource-configuration.md)
- [skills/latchbio-integration/references/ui-and-automation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/ui-and-automation.md)
- [skills/latchbio-integration/references/verified-workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/verified-workflows.md)
- [skills/latchbio-integration/references/workflow-creation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latchbio-integration/references/workflow-creation.md)
- [skills/latex-posters/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/SKILL.md)
- [skills/latex-posters/assets/poster_quality_checklist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/assets/poster_quality_checklist.md)
- [skills/latex-posters/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/README.md)
- [skills/latex-posters/references/ai_graphics_for_posters.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/ai_graphics_for_posters.md)
- [skills/latex-posters/references/compilation_and_quality_control.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/compilation_and_quality_control.md)
- [skills/latex-posters/references/latex_poster_packages.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/latex_poster_packages.md)
- [skills/latex-posters/references/latex_poster_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/latex_poster_reference.md)
- [skills/latex-posters/references/poster_content_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/poster_content_guide.md)
- [skills/latex-posters/references/poster_design_principles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/poster_design_principles.md)
- [skills/latex-posters/references/poster_layout_design.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/poster_layout_design.md)
- [skills/latex-posters/references/poster_patterns_and_presentation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/latex-posters/references/poster_patterns_and_presentation.md)
- [skills/liteparse/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/liteparse/SKILL.md)
- [skills/liteparse/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/liteparse/references/api_reference.md)
- [skills/liteparse/references/choosing_a_parser.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/liteparse/references/choosing_a_parser.md)
- [skills/liteparse/references/cli_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/liteparse/references/cli_reference.md)
- [skills/liteparse/references/ocr_and_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/liteparse/references/ocr_and_formats.md)
- [skills/liteparse/references/output_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/liteparse/references/output_formats.md)
- [skills/literature-review/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/literature-review/SKILL.md)
- [skills/literature-review/assets/review_template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/literature-review/assets/review_template.md)
- [skills/literature-review/references/citation_styles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/literature-review/references/citation_styles.md)
- [skills/literature-review/references/core_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/literature-review/references/core_workflow.md)
- [skills/literature-review/references/database_strategies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/literature-review/references/database_strategies.md)
- [skills/literature-review/references/example_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/literature-review/references/example_workflow.md)
- [skills/literature-review/references/search_and_citation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/literature-review/references/search_and_citation.md)
- [skills/llama-cpp/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-cpp/SKILL.md)
- [skills/llama-cpp/references/optimization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-cpp/references/optimization.md)
- [skills/llama-cpp/references/quantization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-cpp/references/quantization.md)
- [skills/llama-cpp/references/server.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-cpp/references/server.md)
- [skills/llama-factory/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-factory/SKILL.md)
- [skills/llama-factory/references/_images.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-factory/references/_images.md)
- [skills/llama-factory/references/advanced.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-factory/references/advanced.md)
- [skills/llama-factory/references/getting_started.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-factory/references/getting_started.md)
- [skills/llama-factory/references/index.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-factory/references/index.md)
- [skills/llama-factory/references/other.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llama-factory/references/other.md)
- [skills/llamaguard/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llamaguard/SKILL.md)
- [skills/llamaindex/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llamaindex/SKILL.md)
- [skills/llamaindex/references/advanced-rag-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llamaindex/references/advanced-rag-patterns.md)
- [skills/llamaindex/references/agents-with-tools.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llamaindex/references/agents-with-tools.md)
- [skills/llamaindex/references/agents.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llamaindex/references/agents.md)
- [skills/llamaindex/references/data_connectors.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llamaindex/references/data_connectors.md)
- [skills/llamaindex/references/query_engines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llamaindex/references/query_engines.md)
- [skills/llava/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llava/SKILL.md)
- [skills/llava/references/training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/llava/references/training.md)
- [skills/long-context/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/long-context/SKILL.md)
- [skills/long-context/references/extension_methods.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/long-context/references/extension_methods.md)
- [skills/long-context/references/fine_tuning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/long-context/references/fine_tuning.md)
- [skills/long-context/references/implementation-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/long-context/references/implementation-patterns.md)
- [skills/long-context/references/rope.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/long-context/references/rope.md)
- [skills/mamba-architecture/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mamba-architecture/SKILL.md)
- [skills/mamba-architecture/references/architecture-details.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mamba-architecture/references/architecture-details.md)
- [skills/mamba-architecture/references/benchmarks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mamba-architecture/references/benchmarks.md)
- [skills/mamba-architecture/references/training-guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mamba-architecture/references/training-guide.md)
- [skills/markdown-mermaid-writing/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/SKILL.md)
- [skills/markdown-mermaid-writing/assets/examples/example-research-report.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/assets/examples/example-research-report.md)
- [skills/markdown-mermaid-writing/references/diagrams/architecture.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/architecture.md)
- [skills/markdown-mermaid-writing/references/diagrams/block.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/block.md)
- [skills/markdown-mermaid-writing/references/diagrams/c4.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/c4.md)
- [skills/markdown-mermaid-writing/references/diagrams/class.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/class.md)
- [skills/markdown-mermaid-writing/references/diagrams/complex_examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md)
- [skills/markdown-mermaid-writing/references/diagrams/er.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/er.md)
- [skills/markdown-mermaid-writing/references/diagrams/flowchart.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/flowchart.md)
- [skills/markdown-mermaid-writing/references/diagrams/gantt.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/gantt.md)
- [skills/markdown-mermaid-writing/references/diagrams/git_graph.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/git_graph.md)
- [skills/markdown-mermaid-writing/references/diagrams/kanban.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/kanban.md)
- [skills/markdown-mermaid-writing/references/diagrams/mindmap.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/mindmap.md)
- [skills/markdown-mermaid-writing/references/diagrams/packet.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/packet.md)
- [skills/markdown-mermaid-writing/references/diagrams/pie.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/pie.md)
- [skills/markdown-mermaid-writing/references/diagrams/quadrant.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/quadrant.md)
- [skills/markdown-mermaid-writing/references/diagrams/radar.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/radar.md)
- [skills/markdown-mermaid-writing/references/diagrams/requirement.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/requirement.md)
- [skills/markdown-mermaid-writing/references/diagrams/sankey.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/sankey.md)
- [skills/markdown-mermaid-writing/references/diagrams/sequence.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/sequence.md)
- [skills/markdown-mermaid-writing/references/diagrams/state.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/state.md)
- [skills/markdown-mermaid-writing/references/diagrams/timeline.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/timeline.md)
- [skills/markdown-mermaid-writing/references/diagrams/treemap.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/treemap.md)
- [skills/markdown-mermaid-writing/references/diagrams/user_journey.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/user_journey.md)
- [skills/markdown-mermaid-writing/references/diagrams/xy_chart.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md)
- [skills/markdown-mermaid-writing/references/diagrams/zenuml.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/diagrams/zenuml.md)
- [skills/markdown-mermaid-writing/references/markdown_style_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/markdown_style_guide.md)
- [skills/markdown-mermaid-writing/references/mermaid_style_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/references/mermaid_style_guide.md)
- [skills/markdown-mermaid-writing/templates/decision_record.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/decision_record.md)
- [skills/markdown-mermaid-writing/templates/how_to_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/how_to_guide.md)
- [skills/markdown-mermaid-writing/templates/issue.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/issue.md)
- [skills/markdown-mermaid-writing/templates/kanban.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/kanban.md)
- [skills/markdown-mermaid-writing/templates/presentation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/presentation.md)
- [skills/markdown-mermaid-writing/templates/project_documentation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/project_documentation.md)
- [skills/markdown-mermaid-writing/templates/pull_request.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/pull_request.md)
- [skills/markdown-mermaid-writing/templates/research_paper.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/research_paper.md)
- [skills/markdown-mermaid-writing/templates/status_report.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markdown-mermaid-writing/templates/status_report.md)
- [skills/market-research-reports/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/SKILL.md)
- [skills/market-research-reports/assets/FORMATTING_GUIDE.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/assets/FORMATTING_GUIDE.md)
- [skills/market-research-reports/references/data_analysis_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/references/data_analysis_patterns.md)
- [skills/market-research-reports/references/evidence_model.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/references/evidence_model.md)
- [skills/market-research-reports/references/methods_and_ethics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/references/methods_and_ethics.md)
- [skills/market-research-reports/references/official_data_sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/references/official_data_sources.md)
- [skills/market-research-reports/references/report_structure_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/references/report_structure_guide.md)
- [skills/market-research-reports/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/references/sources.md)
- [skills/market-research-reports/references/visual_generation_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/market-research-reports/references/visual_generation_guide.md)
- [skills/markitdown/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markitdown/SKILL.md)
- [skills/markitdown/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markitdown/references/api_reference.md)
- [skills/markitdown/references/cloud_and_ocr.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markitdown/references/cloud_and_ocr.md)
- [skills/markitdown/references/file_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markitdown/references/file_formats.md)
- [skills/markitdown/references/mcp_and_plugins.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markitdown/references/mcp_and_plugins.md)
- [skills/markitdown/references/migration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markitdown/references/migration.md)
- [skills/markitdown/references/security.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markitdown/references/security.md)
- [skills/markitdown/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/markitdown/references/workflows.md)
- [skills/matchms/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matchms/SKILL.md)
- [skills/matchms/references/filtering.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matchms/references/filtering.md)
- [skills/matchms/references/importing_exporting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matchms/references/importing_exporting.md)
- [skills/matchms/references/migration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matchms/references/migration.md)
- [skills/matchms/references/similarity.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matchms/references/similarity.md)
- [skills/matchms/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matchms/references/sources.md)
- [skills/matchms/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matchms/references/workflows.md)
- [skills/matlab/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/SKILL.md)
- [skills/matlab/references/data-import-export.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/references/data-import-export.md)
- [skills/matlab/references/executing-scripts.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/references/executing-scripts.md)
- [skills/matlab/references/graphics-visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/references/graphics-visualization.md)
- [skills/matlab/references/mathematics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/references/mathematics.md)
- [skills/matlab/references/matrices-arrays.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/references/matrices-arrays.md)
- [skills/matlab/references/octave-compatibility.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/references/octave-compatibility.md)
- [skills/matlab/references/programming.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/references/programming.md)
- [skills/matlab/references/python-integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matlab/references/python-integration.md)
- [skills/matplotlib/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matplotlib/SKILL.md)
- [skills/matplotlib/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matplotlib/references/api_reference.md)
- [skills/matplotlib/references/common_issues.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matplotlib/references/common_issues.md)
- [skills/matplotlib/references/plot_types.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matplotlib/references/plot_types.md)
- [skills/matplotlib/references/styling_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/matplotlib/references/styling_guide.md)
- [skills/medchem/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/medchem/SKILL.md)
- [skills/medchem/references/api_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/medchem/references/api_guide.md)
- [skills/medchem/references/rules_catalog.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/medchem/references/rules_catalog.md)
- [skills/miles-rl-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/miles-rl-training/SKILL.md)
- [skills/miles-rl-training/references/api-reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/miles-rl-training/references/api-reference.md)
- [skills/miles-rl-training/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/miles-rl-training/references/troubleshooting.md)
- [skills/ml-paper-writing/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/SKILL.md)
- [skills/ml-paper-writing/references/checklists.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/checklists.md)
- [skills/ml-paper-writing/references/citation-workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/citation-workflow.md)
- [skills/ml-paper-writing/references/from-research-repo.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/from-research-repo.md)
- [skills/ml-paper-writing/references/issues-reviewers-figures.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/issues-reviewers-figures.md)
- [skills/ml-paper-writing/references/latex-templates-and-conversion.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/latex-templates-and-conversion.md)
- [skills/ml-paper-writing/references/reviewer-guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/reviewer-guidelines.md)
- [skills/ml-paper-writing/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/sources.md)
- [skills/ml-paper-writing/references/writing-guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/writing-guide.md)
- [skills/ml-paper-writing/references/writing-philosophy.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/references/writing-philosophy.md)
- [skills/ml-paper-writing/templates/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/templates/README.md)
- [skills/ml-paper-writing/templates/aaai2026/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/templates/aaai2026/README.md)
- [skills/ml-paper-writing/templates/acl/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/templates/acl/README.md)
- [skills/ml-paper-writing/templates/acl/formatting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/templates/acl/formatting.md)
- [skills/ml-paper-writing/templates/colm2025/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-paper-writing/templates/colm2025/README.md)
- [skills/ml-training-recipes/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-training-recipes/SKILL.md)
- [skills/ml-training-recipes/references/architecture.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-training-recipes/references/architecture.md)
- [skills/ml-training-recipes/references/biomedical.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-training-recipes/references/biomedical.md)
- [skills/ml-training-recipes/references/domain-specific.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-training-recipes/references/domain-specific.md)
- [skills/ml-training-recipes/references/experiment-loop.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-training-recipes/references/experiment-loop.md)
- [skills/ml-training-recipes/references/optimizers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-training-recipes/references/optimizers.md)
- [skills/ml-training-recipes/references/scaling-and-selection.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ml-training-recipes/references/scaling-and-selection.md)
- [skills/mlflow/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mlflow/SKILL.md)
- [skills/mlflow/references/autologging.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mlflow/references/autologging.md)
- [skills/mlflow/references/deployment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mlflow/references/deployment.md)
- [skills/mlflow/references/integration-examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mlflow/references/integration-examples.md)
- [skills/mlflow/references/model-registry-2.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mlflow/references/model-registry-2.md)
- [skills/mlflow/references/model-registry.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mlflow/references/model-registry.md)
- [skills/mlflow/references/tracking.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/mlflow/references/tracking.md)
- [skills/modal-serverless-gpu/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal-serverless-gpu/SKILL.md)
- [skills/modal-serverless-gpu/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal-serverless-gpu/references/advanced-usage.md)
- [skills/modal-serverless-gpu/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal-serverless-gpu/references/troubleshooting.md)
- [skills/modal/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/SKILL.md)
- [skills/modal/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/api_reference.md)
- [skills/modal/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/examples.md)
- [skills/modal/references/functions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/functions.md)
- [skills/modal/references/getting-started.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/getting-started.md)
- [skills/modal/references/gpu.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/gpu.md)
- [skills/modal/references/images.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/images.md)
- [skills/modal/references/resources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/resources.md)
- [skills/modal/references/scaling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/scaling.md)
- [skills/modal/references/scheduled-jobs.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/scheduled-jobs.md)
- [skills/modal/references/secrets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/secrets.md)
- [skills/modal/references/volumes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/volumes.md)
- [skills/modal/references/web-endpoints.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/modal/references/web-endpoints.md)
- [skills/model-merging/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-merging/SKILL.md)
- [skills/model-merging/references/coefficient-tuning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-merging/references/coefficient-tuning.md)
- [skills/model-merging/references/evaluation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-merging/references/evaluation.md)
- [skills/model-merging/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-merging/references/examples.md)
- [skills/model-merging/references/merge-methods-guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-merging/references/merge-methods-guide.md)
- [skills/model-merging/references/methods.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-merging/references/methods.md)
- [skills/model-pruning/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-pruning/SKILL.md)
- [skills/model-pruning/references/production-deployment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-pruning/references/production-deployment.md)
- [skills/model-pruning/references/wanda.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/model-pruning/references/wanda.md)
- [skills/moe-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/moe-training/SKILL.md)
- [skills/moe-training/references/advanced-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/moe-training/references/advanced-patterns.md)
- [skills/moe-training/references/architectures.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/moe-training/references/architectures.md)
- [skills/moe-training/references/inference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/moe-training/references/inference.md)
- [skills/moe-training/references/training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/moe-training/references/training.md)
- [skills/molecular-dynamics/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/molecular-dynamics/SKILL.md)
- [skills/molecular-dynamics/references/mdanalysis_analysis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/molecular-dynamics/references/mdanalysis_analysis.md)
- [skills/molfeat/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/molfeat/SKILL.md)
- [skills/molfeat/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/molfeat/references/api_reference.md)
- [skills/molfeat/references/available_featurizers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/molfeat/references/available_featurizers.md)
- [skills/molfeat/references/choosing_a_featurizer.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/molfeat/references/choosing_a_featurizer.md)
- [skills/molfeat/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/molfeat/references/examples.md)
- [skills/nanogpt/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nanogpt/SKILL.md)
- [skills/nanogpt/references/architecture.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nanogpt/references/architecture.md)
- [skills/nanogpt/references/data.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nanogpt/references/data.md)
- [skills/nanogpt/references/training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nanogpt/references/training.md)
- [skills/nature-portfolio/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nature-portfolio/SKILL.md)
- [skills/ncats-arax/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ncats-arax/SKILL.md)
- [skills/ncats-arax/references/output-schema.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ncats-arax/references/output-schema.md)
- [skills/ncats-arax/references/query-contract.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ncats-arax/references/query-contract.md)
- [skills/nemo-curator/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-curator/SKILL.md)
- [skills/nemo-curator/references/deduplication.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-curator/references/deduplication.md)
- [skills/nemo-curator/references/filtering.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-curator/references/filtering.md)
- [skills/nemo-evaluator-sdk/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-evaluator-sdk/SKILL.md)
- [skills/nemo-evaluator-sdk/references/adapter-system.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-evaluator-sdk/references/adapter-system.md)
- [skills/nemo-evaluator-sdk/references/configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-evaluator-sdk/references/configuration.md)
- [skills/nemo-evaluator-sdk/references/custom-benchmarks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-evaluator-sdk/references/custom-benchmarks.md)
- [skills/nemo-evaluator-sdk/references/execution-backends.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-evaluator-sdk/references/execution-backends.md)
- [skills/nemo-evaluator-sdk/references/python-api-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-evaluator-sdk/references/python-api-usage.md)
- [skills/nemo-guardrails/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nemo-guardrails/SKILL.md)
- [skills/networkx/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/networkx/SKILL.md)
- [skills/networkx/references/algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/networkx/references/algorithms.md)
- [skills/networkx/references/generators.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/networkx/references/generators.md)
- [skills/networkx/references/graph-basics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/networkx/references/graph-basics.md)
- [skills/networkx/references/io.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/networkx/references/io.md)
- [skills/networkx/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/networkx/references/visualization.md)
- [skills/neurokit2/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/SKILL.md)
- [skills/neurokit2/references/bio_module.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/bio_module.md)
- [skills/neurokit2/references/complexity.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/complexity.md)
- [skills/neurokit2/references/ecg_cardiac.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/ecg_cardiac.md)
- [skills/neurokit2/references/eda.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/eda.md)
- [skills/neurokit2/references/eeg.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/eeg.md)
- [skills/neurokit2/references/emg.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/emg.md)
- [skills/neurokit2/references/eog.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/eog.md)
- [skills/neurokit2/references/epochs_events.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/epochs_events.md)
- [skills/neurokit2/references/hrv.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/hrv.md)
- [skills/neurokit2/references/ppg.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/ppg.md)
- [skills/neurokit2/references/rsp.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/rsp.md)
- [skills/neurokit2/references/signal_processing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neurokit2/references/signal_processing.md)
- [skills/neuropixels-analysis/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/SKILL.md)
- [skills/neuropixels-analysis/references/AI_CURATION.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/AI_CURATION.md)
- [skills/neuropixels-analysis/references/ANALYSIS.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/ANALYSIS.md)
- [skills/neuropixels-analysis/references/AUTOMATED_CURATION.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md)
- [skills/neuropixels-analysis/references/MOTION_CORRECTION.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/MOTION_CORRECTION.md)
- [skills/neuropixels-analysis/references/PREPROCESSING.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/PREPROCESSING.md)
- [skills/neuropixels-analysis/references/QUALITY_METRICS.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/QUALITY_METRICS.md)
- [skills/neuropixels-analysis/references/SPIKE_SORTING.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/SPIKE_SORTING.md)
- [skills/neuropixels-analysis/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/api_reference.md)
- [skills/neuropixels-analysis/references/plotting_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/plotting_guide.md)
- [skills/neuropixels-analysis/references/standard_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/neuropixels-analysis/references/standard_workflow.md)
- [skills/nextflow/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nextflow/SKILL.md)
- [skills/nextflow/references/configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nextflow/references/configuration.md)
- [skills/nextflow/references/containers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nextflow/references/containers.md)
- [skills/nextflow/references/developing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nextflow/references/developing.md)
- [skills/nextflow/references/language.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nextflow/references/language.md)
- [skills/nextflow/references/nf-core-tools.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nextflow/references/nf-core-tools.md)
- [skills/nextflow/references/running-pipelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nextflow/references/running-pipelines.md)
- [skills/nextflow/references/testing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nextflow/references/testing.md)
- [skills/nnsight-remote-interpretability/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nnsight-remote-interpretability/SKILL.md)
- [skills/nnsight-remote-interpretability/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nnsight-remote-interpretability/references/README.md)
- [skills/nnsight-remote-interpretability/references/api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nnsight-remote-interpretability/references/api.md)
- [skills/nnsight-remote-interpretability/references/tutorials.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/nnsight-remote-interpretability/references/tutorials.md)
- [skills/omero-integration/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/SKILL.md)
- [skills/omero-integration/references/advanced.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/advanced.md)
- [skills/omero-integration/references/connection.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/connection.md)
- [skills/omero-integration/references/data_access.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/data_access.md)
- [skills/omero-integration/references/image_processing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/image_processing.md)
- [skills/omero-integration/references/metadata.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/metadata.md)
- [skills/omero-integration/references/rois.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/rois.md)
- [skills/omero-integration/references/scripts.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/scripts.md)
- [skills/omero-integration/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/sources.md)
- [skills/omero-integration/references/tables.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/omero-integration/references/tables.md)
- [skills/onekgpd/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/onekgpd/SKILL.md)
- [skills/onekgpd/references/annotation_vocabularies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/onekgpd/references/annotation_vocabularies.md)
- [skills/onekgpd/references/onekgpd_commands.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/onekgpd/references/onekgpd_commands.md)
- [skills/ontology-term-resolution/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ontology-term-resolution/SKILL.md)
- [skills/ontology-term-resolution/references/companion-apis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ontology-term-resolution/references/companion-apis.md)
- [skills/ontology-term-resolution/references/curation-rules.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ontology-term-resolution/references/curation-rules.md)
- [skills/ontology-term-resolution/references/ols4-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ontology-term-resolution/references/ols4-api.md)
- [skills/ontology-term-resolution/references/ontology-registry.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ontology-term-resolution/references/ontology-registry.md)
- [skills/open-notebook/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/open-notebook/SKILL.md)
- [skills/open-notebook/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/open-notebook/references/api_reference.md)
- [skills/open-notebook/references/architecture.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/open-notebook/references/architecture.md)
- [skills/open-notebook/references/configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/open-notebook/references/configuration.md)
- [skills/open-notebook/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/open-notebook/references/examples.md)
- [skills/openpiv/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/openpiv/SKILL.md)
- [skills/openpiv/references/advanced_algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/openpiv/references/advanced_algorithms.md)
- [skills/openrlhf-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/openrlhf-training/SKILL.md)
- [skills/openrlhf-training/references/algorithm-comparison.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/openrlhf-training/references/algorithm-comparison.md)
- [skills/openrlhf-training/references/custom-rewards.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/openrlhf-training/references/custom-rewards.md)
- [skills/openrlhf-training/references/hybrid-engine.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/openrlhf-training/references/hybrid-engine.md)
- [skills/openrlhf-training/references/multi-node-training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/openrlhf-training/references/multi-node-training.md)
- [skills/opentrons-integration/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/opentrons-integration/SKILL.md)
- [skills/opentrons-integration/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/opentrons-integration/references/api_reference.md)
- [skills/opentrons-integration/references/liquid_handling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/opentrons-integration/references/liquid_handling.md)
- [skills/opentrons-integration/references/migration-api-2-19-to-2-29.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/opentrons-integration/references/migration-api-2-19-to-2-29.md)
- [skills/opentrons-integration/references/modules_and_deck.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/opentrons-integration/references/modules_and_deck.md)
- [skills/opentrons-integration/references/protocol_authoring.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/opentrons-integration/references/protocol_authoring.md)
- [skills/opentrons-integration/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/opentrons-integration/references/sources.md)
- [skills/opentrons-integration/references/validation_and_operations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/opentrons-integration/references/validation_and_operations.md)
- [skills/optimize-for-gpu/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/SKILL.md)
- [skills/optimize-for-gpu/references/code_transformation_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/code_transformation_patterns.md)
- [skills/optimize-for-gpu/references/cucim.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/cucim.md)
- [skills/optimize-for-gpu/references/cudf.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/cudf.md)
- [skills/optimize-for-gpu/references/cugraph.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/cugraph.md)
- [skills/optimize-for-gpu/references/cuml.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/cuml.md)
- [skills/optimize-for-gpu/references/cupy.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/cupy.md)
- [skills/optimize-for-gpu/references/cuspatial.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/cuspatial.md)
- [skills/optimize-for-gpu/references/cuvs.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/cuvs.md)
- [skills/optimize-for-gpu/references/cuxfilter.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/cuxfilter.md)
- [skills/optimize-for-gpu/references/decision_framework.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/decision_framework.md)
- [skills/optimize-for-gpu/references/installation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/installation.md)
- [skills/optimize-for-gpu/references/kvikio.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/kvikio.md)
- [skills/optimize-for-gpu/references/numba.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/numba.md)
- [skills/optimize-for-gpu/references/raft.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/raft.md)
- [skills/optimize-for-gpu/references/warp.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimize-for-gpu/references/warp.md)
- [skills/optimizing-attention-flash/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimizing-attention-flash/SKILL.md)
- [skills/optimizing-attention-flash/references/benchmarks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimizing-attention-flash/references/benchmarks.md)
- [skills/optimizing-attention-flash/references/transformers-integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/optimizing-attention-flash/references/transformers-integration.md)
- [skills/outlines/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/outlines/SKILL.md)
- [skills/outlines/references/backend-configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/outlines/references/backend-configuration.md)
- [skills/outlines/references/backends.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/outlines/references/backends.md)
- [skills/outlines/references/common-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/outlines/references/common-patterns.md)
- [skills/outlines/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/outlines/references/examples.md)
- [skills/outlines/references/json_generation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/outlines/references/json_generation.md)
- [skills/pacsomatic/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pacsomatic/SKILL.md)
- [skills/pacsomatic/references/agent-playbook.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pacsomatic/references/agent-playbook.md)
- [skills/pacsomatic/references/config-and-output.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pacsomatic/references/config-and-output.md)
- [skills/pacsomatic/references/pacsomatic_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pacsomatic/references/pacsomatic_guide.md)
- [skills/paper-corpus-rag/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-corpus-rag/SKILL.md)
- [skills/paper-lookup/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/SKILL.md)
- [skills/paper-lookup/references/arxiv.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/arxiv.md)
- [skills/paper-lookup/references/biorxiv.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/biorxiv.md)
- [skills/paper-lookup/references/biostudies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/biostudies.md)
- [skills/paper-lookup/references/core.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/core.md)
- [skills/paper-lookup/references/crossref.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/crossref.md)
- [skills/paper-lookup/references/doaj.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/doaj.md)
- [skills/paper-lookup/references/europepmc.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/europepmc.md)
- [skills/paper-lookup/references/figshare.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/figshare.md)
- [skills/paper-lookup/references/medrxiv.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/medrxiv.md)
- [skills/paper-lookup/references/openalex.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/openalex.md)
- [skills/paper-lookup/references/opencitations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/opencitations.md)
- [skills/paper-lookup/references/pmc.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/pmc.md)
- [skills/paper-lookup/references/pubmed.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/pubmed.md)
- [skills/paper-lookup/references/pubtator.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/pubtator.md)
- [skills/paper-lookup/references/ror.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/ror.md)
- [skills/paper-lookup/references/semantic-scholar.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/semantic-scholar.md)
- [skills/paper-lookup/references/unpaywall.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/unpaywall.md)
- [skills/paper-lookup/references/zenodo.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paper-lookup/references/zenodo.md)
- [skills/paperclip/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paperclip/SKILL.md)
- [skills/paperclip/references/cli-reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paperclip/references/cli-reference.md)
- [skills/paperclip/references/installation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paperclip/references/installation.md)
- [skills/paperclip/references/map-reduce.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paperclip/references/map-reduce.md)
- [skills/paperclip/references/python-sdk.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paperclip/references/python-sdk.md)
- [skills/paperclip/references/repos-and-workspace.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paperclip/references/repos-and-workspace.md)
- [skills/paperclip/references/search-and-retrieval.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paperclip/references/search-and-retrieval.md)
- [skills/paperzilla/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/paperzilla/SKILL.md)
- [skills/parallel-web/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/parallel-web/SKILL.md)
- [skills/parallel-web/references/data-enrichment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/parallel-web/references/data-enrichment.md)
- [skills/parallel-web/references/deep-research.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/parallel-web/references/deep-research.md)
- [skills/parallel-web/references/findall.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/parallel-web/references/findall.md)
- [skills/parallel-web/references/monitor.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/parallel-web/references/monitor.md)
- [skills/parallel-web/references/web-extract.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/parallel-web/references/web-extract.md)
- [skills/parallel-web/references/web-search.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/parallel-web/references/web-search.md)
- [skills/pathml/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathml/SKILL.md)
- [skills/pathml/references/data_management.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathml/references/data_management.md)
- [skills/pathml/references/graphs.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathml/references/graphs.md)
- [skills/pathml/references/image_loading.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathml/references/image_loading.md)
- [skills/pathml/references/machine_learning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathml/references/machine_learning.md)
- [skills/pathml/references/multiparametric.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathml/references/multiparametric.md)
- [skills/pathml/references/preprocessing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathml/references/preprocessing.md)
- [skills/pathogen-variant-surveillance/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathogen-variant-surveillance/SKILL.md)
- [skills/pathogen-variant-surveillance/references/lapis-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathogen-variant-surveillance/references/lapis-api.md)
- [skills/pathogen-variant-surveillance/references/lineage-nomenclature.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathogen-variant-surveillance/references/lineage-nomenclature.md)
- [skills/pathogen-variant-surveillance/references/surveillance-caveats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathogen-variant-surveillance/references/surveillance-caveats.md)
- [skills/pathway-enrichment/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathway-enrichment/SKILL.md)
- [skills/pathway-enrichment/references/databases-and-gene-sets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathway-enrichment/references/databases-and-gene-sets.md)
- [skills/pathway-enrichment/references/gseapy.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathway-enrichment/references/gseapy.md)
- [skills/pathway-enrichment/references/interpretation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pathway-enrichment/references/interpretation.md)
- [skills/peer-review/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peer-review/SKILL.md)
- [skills/peer-review/assets/review_scaffold_template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peer-review/assets/review_scaffold_template.md)
- [skills/peer-review/references/common_issues.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peer-review/references/common_issues.md)
- [skills/peer-review/references/ethical_review_practice.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peer-review/references/ethical_review_practice.md)
- [skills/peer-review/references/reporting_standards.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peer-review/references/reporting_standards.md)
- [skills/peer-review/references/security_validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peer-review/references/security_validation.md)
- [skills/peer-review/references/statistical_reproducibility.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peer-review/references/statistical_reproducibility.md)
- [skills/peer-review/references/tool_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peer-review/references/tool_reference.md)
- [skills/peft-fine-tuning/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peft-fine-tuning/SKILL.md)
- [skills/peft-fine-tuning/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peft-fine-tuning/references/advanced-usage.md)
- [skills/peft-fine-tuning/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/peft-fine-tuning/references/troubleshooting.md)
- [skills/pennylane/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pennylane/SKILL.md)
- [skills/pennylane/references/advanced_features.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pennylane/references/advanced_features.md)
- [skills/pennylane/references/devices_backends.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pennylane/references/devices_backends.md)
- [skills/pennylane/references/getting_started.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pennylane/references/getting_started.md)
- [skills/pennylane/references/optimization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pennylane/references/optimization.md)
- [skills/pennylane/references/quantum_chemistry.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pennylane/references/quantum_chemistry.md)
- [skills/pennylane/references/quantum_circuits.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pennylane/references/quantum_circuits.md)
- [skills/pennylane/references/quantum_ml.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pennylane/references/quantum_ml.md)
- [skills/phoenix-observability/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/phoenix-observability/SKILL.md)
- [skills/phoenix-observability/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/phoenix-observability/references/advanced-usage.md)
- [skills/phoenix-observability/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/phoenix-observability/references/troubleshooting.md)
- [skills/pi-agent/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/SKILL.md)
- [skills/pi-agent/references/compaction.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/compaction.md)
- [skills/pi-agent/references/containerization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/containerization.md)
- [skills/pi-agent/references/custom-provider.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/custom-provider.md)
- [skills/pi-agent/references/development.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/development.md)
- [skills/pi-agent/references/environment-variables.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/environment-variables.md)
- [skills/pi-agent/references/extensions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/extensions.md)
- [skills/pi-agent/references/json.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/json.md)
- [skills/pi-agent/references/keybindings.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/keybindings.md)
- [skills/pi-agent/references/llama-cpp.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/llama-cpp.md)
- [skills/pi-agent/references/models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/models.md)
- [skills/pi-agent/references/overview.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/overview.md)
- [skills/pi-agent/references/packages.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/packages.md)
- [skills/pi-agent/references/pi-interview.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/pi-interview.md)
- [skills/pi-agent/references/pi-mcp-adapter.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/pi-mcp-adapter.md)
- [skills/pi-agent/references/pi-subagents.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/pi-subagents.md)
- [skills/pi-agent/references/pi-web-access.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/pi-web-access.md)
- [skills/pi-agent/references/prompt-templates.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/prompt-templates.md)
- [skills/pi-agent/references/providers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/providers.md)
- [skills/pi-agent/references/quickstart.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/quickstart.md)
- [skills/pi-agent/references/rpc.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/rpc.md)
- [skills/pi-agent/references/sdk.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/sdk.md)
- [skills/pi-agent/references/security.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/security.md)
- [skills/pi-agent/references/session-format.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/session-format.md)
- [skills/pi-agent/references/sessions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/sessions.md)
- [skills/pi-agent/references/settings.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/settings.md)
- [skills/pi-agent/references/shell-aliases.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/shell-aliases.md)
- [skills/pi-agent/references/skills.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/skills.md)
- [skills/pi-agent/references/terminal-setup.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/terminal-setup.md)
- [skills/pi-agent/references/termux.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/termux.md)
- [skills/pi-agent/references/themes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/themes.md)
- [skills/pi-agent/references/tmux.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/tmux.md)
- [skills/pi-agent/references/tui.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/tui.md)
- [skills/pi-agent/references/usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/usage.md)
- [skills/pi-agent/references/windows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pi-agent/references/windows.md)
- [skills/pinecone/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pinecone/SKILL.md)
- [skills/pinecone/references/deployment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pinecone/references/deployment.md)
- [skills/pkpd-modeling/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/SKILL.md)
- [skills/pkpd-modeling/assets/nca-reporting-checklist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/assets/nca-reporting-checklist.md)
- [skills/pkpd-modeling/assets/popk-analysis-plan.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/assets/popk-analysis-plan.md)
- [skills/pkpd-modeling/references/antimicrobial-and-tdm.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/antimicrobial-and-tdm.md)
- [skills/pkpd-modeling/references/bioequivalence.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/bioequivalence.md)
- [skills/pkpd-modeling/references/dataset-standards.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/dataset-standards.md)
- [skills/pkpd-modeling/references/ddi-and-qt.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/ddi-and-qt.md)
- [skills/pkpd-modeling/references/nca-conventions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/nca-conventions.md)
- [skills/pkpd-modeling/references/pbpk.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/pbpk.md)
- [skills/pkpd-modeling/references/pd-and-exposure-response.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/pd-and-exposure-response.md)
- [skills/pkpd-modeling/references/population-pk.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/population-pk.md)
- [skills/pkpd-modeling/references/regulatory-guidance.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/regulatory-guidance.md)
- [skills/pkpd-modeling/references/software-ecosystem.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/software-ecosystem.md)
- [skills/pkpd-modeling/references/source-ledger.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/source-ledger.md)
- [skills/pkpd-modeling/references/special-populations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/special-populations.md)
- [skills/pkpd-modeling/references/structural-models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/structural-models.md)
- [skills/pkpd-modeling/references/tmdd-and-biologics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pkpd-modeling/references/tmdd-and-biologics.md)
- [skills/plos/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/plos/SKILL.md)
- [skills/polars-bio/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars-bio/SKILL.md)
- [skills/polars-bio/references/bioframe_migration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars-bio/references/bioframe_migration.md)
- [skills/polars-bio/references/configuration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars-bio/references/configuration.md)
- [skills/polars-bio/references/file_io.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars-bio/references/file_io.md)
- [skills/polars-bio/references/interval_operations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars-bio/references/interval_operations.md)
- [skills/polars-bio/references/pileup_operations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars-bio/references/pileup_operations.md)
- [skills/polars-bio/references/sql_processing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars-bio/references/sql_processing.md)
- [skills/polars/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars/SKILL.md)
- [skills/polars/references/best_practices.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars/references/best_practices.md)
- [skills/polars/references/core_concepts.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars/references/core_concepts.md)
- [skills/polars/references/io_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars/references/io_guide.md)
- [skills/polars/references/operations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars/references/operations.md)
- [skills/polars/references/pandas_migration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars/references/pandas_migration.md)
- [skills/polars/references/transformations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/polars/references/transformations.md)
- [skills/pptx-posters/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/SKILL.md)
- [skills/pptx-posters/assets/poster_quality_checklist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/assets/poster_quality_checklist.md)
- [skills/pptx-posters/references/manifest_spec.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/references/manifest_spec.md)
- [skills/pptx-posters/references/poster_content_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/references/poster_content_guide.md)
- [skills/pptx-posters/references/poster_design_principles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/references/poster_design_principles.md)
- [skills/pptx-posters/references/poster_layout_design.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/references/poster_layout_design.md)
- [skills/pptx-posters/references/pptx_security.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/references/pptx_security.md)
- [skills/pptx-posters/references/security_validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/references/security_validation.md)
- [skills/pptx-posters/references/source_ledger.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pptx-posters/references/source_ledger.md)
- [skills/presenting-conference-talks/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/presenting-conference-talks/SKILL.md)
- [skills/presenting-conference-talks/references/slide-templates.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/presenting-conference-talks/references/slide-templates.md)
- [skills/prompt-guard/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/prompt-guard/SKILL.md)
- [skills/protocolsio-integration/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/protocolsio-integration/SKILL.md)
- [skills/protocolsio-integration/references/additional_features.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/protocolsio-integration/references/additional_features.md)
- [skills/protocolsio-integration/references/authentication.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/protocolsio-integration/references/authentication.md)
- [skills/protocolsio-integration/references/discussions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/protocolsio-integration/references/discussions.md)
- [skills/protocolsio-integration/references/file_manager.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/protocolsio-integration/references/file_manager.md)
- [skills/protocolsio-integration/references/protocols_api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/protocolsio-integration/references/protocols_api.md)
- [skills/protocolsio-integration/references/workspaces.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/protocolsio-integration/references/workspaces.md)
- [skills/pufferlib/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pufferlib/SKILL.md)
- [skills/pufferlib/references/environments.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pufferlib/references/environments.md)
- [skills/pufferlib/references/integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pufferlib/references/integration.md)
- [skills/pufferlib/references/policies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pufferlib/references/policies.md)
- [skills/pufferlib/references/training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pufferlib/references/training.md)
- [skills/pufferlib/references/vectorization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pufferlib/references/vectorization.md)
- [skills/pydeseq2/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pydeseq2/SKILL.md)
- [skills/pydeseq2/references/analysis_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pydeseq2/references/analysis_patterns.md)
- [skills/pydeseq2/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pydeseq2/references/api_reference.md)
- [skills/pydeseq2/references/core_workflow_steps.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pydeseq2/references/core_workflow_steps.md)
- [skills/pydeseq2/references/workflow_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pydeseq2/references/workflow_guide.md)
- [skills/pydicom/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pydicom/SKILL.md)
- [skills/pydicom/references/common_tags.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pydicom/references/common_tags.md)
- [skills/pydicom/references/transfer_syntaxes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pydicom/references/transfer_syntaxes.md)
- [skills/pyhealth/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyhealth/SKILL.md)
- [skills/pyhealth/references/datasets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyhealth/references/datasets.md)
- [skills/pyhealth/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyhealth/references/examples.md)
- [skills/pyhealth/references/installation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyhealth/references/installation.md)
- [skills/pyhealth/references/medcode.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyhealth/references/medcode.md)
- [skills/pyhealth/references/models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyhealth/references/models.md)
- [skills/pyhealth/references/tasks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyhealth/references/tasks.md)
- [skills/pylabrobot/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pylabrobot/SKILL.md)
- [skills/pylabrobot/references/analytical-equipment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pylabrobot/references/analytical-equipment.md)
- [skills/pylabrobot/references/hardware-backends.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pylabrobot/references/hardware-backends.md)
- [skills/pylabrobot/references/liquid-handling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pylabrobot/references/liquid-handling.md)
- [skills/pylabrobot/references/material-handling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pylabrobot/references/material-handling.md)
- [skills/pylabrobot/references/resources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pylabrobot/references/resources.md)
- [skills/pylabrobot/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pylabrobot/references/visualization.md)
- [skills/pymatgen/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymatgen/SKILL.md)
- [skills/pymatgen/references/analysis_modules.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymatgen/references/analysis_modules.md)
- [skills/pymatgen/references/core_classes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymatgen/references/core_classes.md)
- [skills/pymatgen/references/io_formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymatgen/references/io_formats.md)
- [skills/pymatgen/references/materials_project_api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymatgen/references/materials_project_api.md)
- [skills/pymatgen/references/transformations_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymatgen/references/transformations_workflows.md)
- [skills/pymc/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymc/SKILL.md)
- [skills/pymc/references/distributions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymc/references/distributions.md)
- [skills/pymc/references/model_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymc/references/model_patterns.md)
- [skills/pymc/references/sampling_inference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymc/references/sampling_inference.md)
- [skills/pymc/references/standard_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymc/references/standard_workflow.md)
- [skills/pymc/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymc/references/workflows.md)
- [skills/pymoo/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymoo/SKILL.md)
- [skills/pymoo/references/algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymoo/references/algorithms.md)
- [skills/pymoo/references/constraints_mcdm.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymoo/references/constraints_mcdm.md)
- [skills/pymoo/references/operators.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymoo/references/operators.md)
- [skills/pymoo/references/parallelization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymoo/references/parallelization.md)
- [skills/pymoo/references/problems.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymoo/references/problems.md)
- [skills/pymoo/references/quick_start_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymoo/references/quick_start_workflows.md)
- [skills/pymoo/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pymoo/references/visualization.md)
- [skills/pyopenms/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyopenms/SKILL.md)
- [skills/pyopenms/references/data_structures.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyopenms/references/data_structures.md)
- [skills/pyopenms/references/feature_detection.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyopenms/references/feature_detection.md)
- [skills/pyopenms/references/file_io.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyopenms/references/file_io.md)
- [skills/pyopenms/references/identification.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyopenms/references/identification.md)
- [skills/pyopenms/references/metabolomics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyopenms/references/metabolomics.md)
- [skills/pyopenms/references/signal_processing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyopenms/references/signal_processing.md)
- [skills/pysam/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/SKILL.md)
- [skills/pysam/references/alignment_files.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/alignment_files.md)
- [skills/pysam/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/api_reference.md)
- [skills/pysam/references/common_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/common_workflows.md)
- [skills/pysam/references/coordinates_and_indexing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/coordinates_and_indexing.md)
- [skills/pysam/references/cram_and_performance.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/cram_and_performance.md)
- [skills/pysam/references/migration_to_0_24.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/migration_to_0_24.md)
- [skills/pysam/references/sequence_files.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/sequence_files.md)
- [skills/pysam/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/sources.md)
- [skills/pysam/references/variant_files.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pysam/references/variant_files.md)
- [skills/pytdc/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytdc/SKILL.md)
- [skills/pytdc/references/datasets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytdc/references/datasets.md)
- [skills/pytdc/references/oracles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytdc/references/oracles.md)
- [skills/pytdc/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytdc/references/sources.md)
- [skills/pytdc/references/utilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytdc/references/utilities.md)
- [skills/pytorch-fsdp2/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/SKILL.md)
- [skills/pytorch-fsdp2/references/pytorch_dcp_async_recipe.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_dcp_async_recipe.md)
- [skills/pytorch-fsdp2/references/pytorch_dcp_overview.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_dcp_overview.md)
- [skills/pytorch-fsdp2/references/pytorch_dcp_recipe.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_dcp_recipe.md)
- [skills/pytorch-fsdp2/references/pytorch_ddp_notes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_ddp_notes.md)
- [skills/pytorch-fsdp2/references/pytorch_device_mesh_tutorial.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_device_mesh_tutorial.md)
- [skills/pytorch-fsdp2/references/pytorch_examples_fsdp2.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_examples_fsdp2.md)
- [skills/pytorch-fsdp2/references/pytorch_fsdp1_api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_fsdp1_api.md)
- [skills/pytorch-fsdp2/references/pytorch_fsdp2_tutorial.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_fsdp2_tutorial.md)
- [skills/pytorch-fsdp2/references/pytorch_fully_shard_api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_fully_shard_api.md)
- [skills/pytorch-fsdp2/references/pytorch_tp_tutorial.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/pytorch_tp_tutorial.md)
- [skills/pytorch-fsdp2/references/ray_train_fsdp2_example.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/ray_train_fsdp2_example.md)
- [skills/pytorch-fsdp2/references/torchtitan_fsdp_notes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-fsdp2/references/torchtitan_fsdp_notes.md)
- [skills/pytorch-lightning-distributed/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning-distributed/SKILL.md)
- [skills/pytorch-lightning-distributed/references/callbacks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning-distributed/references/callbacks.md)
- [skills/pytorch-lightning-distributed/references/distributed.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning-distributed/references/distributed.md)
- [skills/pytorch-lightning-distributed/references/hyperparameter-tuning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning-distributed/references/hyperparameter-tuning.md)
- [skills/pytorch-lightning/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning/SKILL.md)
- [skills/pytorch-lightning/references/best_practices.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning/references/best_practices.md)
- [skills/pytorch-lightning/references/callbacks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning/references/callbacks.md)
- [skills/pytorch-lightning/references/data_module.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning/references/data_module.md)
- [skills/pytorch-lightning/references/distributed_training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning/references/distributed_training.md)
- [skills/pytorch-lightning/references/lightning_module.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning/references/lightning_module.md)
- [skills/pytorch-lightning/references/logging.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning/references/logging.md)
- [skills/pytorch-lightning/references/trainer.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pytorch-lightning/references/trainer.md)
- [skills/pyvene-interventions/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyvene-interventions/SKILL.md)
- [skills/pyvene-interventions/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyvene-interventions/references/README.md)
- [skills/pyvene-interventions/references/api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyvene-interventions/references/api.md)
- [skills/pyvene-interventions/references/saving-and-sharing-interventions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyvene-interventions/references/saving-and-sharing-interventions.md)
- [skills/pyvene-interventions/references/tutorials.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyvene-interventions/references/tutorials.md)
- [skills/pyzotero/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/SKILL.md)
- [skills/pyzotero/references/authentication.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/authentication.md)
- [skills/pyzotero/references/cli.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/cli.md)
- [skills/pyzotero/references/collections.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/collections.md)
- [skills/pyzotero/references/error-handling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/error-handling.md)
- [skills/pyzotero/references/exports.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/exports.md)
- [skills/pyzotero/references/files-attachments.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/files-attachments.md)
- [skills/pyzotero/references/full-text.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/full-text.md)
- [skills/pyzotero/references/mcp.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/mcp.md)
- [skills/pyzotero/references/pagination.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/pagination.md)
- [skills/pyzotero/references/read-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/read-api.md)
- [skills/pyzotero/references/saved-searches.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/saved-searches.md)
- [skills/pyzotero/references/search-params.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/search-params.md)
- [skills/pyzotero/references/tags.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/tags.md)
- [skills/pyzotero/references/write-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/pyzotero/references/write-api.md)
- [skills/qdrant-vector-search/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qdrant-vector-search/SKILL.md)
- [skills/qdrant-vector-search/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qdrant-vector-search/references/advanced-usage.md)
- [skills/qdrant-vector-search/references/rag-integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qdrant-vector-search/references/rag-integration.md)
- [skills/qdrant-vector-search/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qdrant-vector-search/references/troubleshooting.md)
- [skills/qiskit/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/SKILL.md)
- [skills/qiskit/references/algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/algorithms.md)
- [skills/qiskit/references/backends.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/backends.md)
- [skills/qiskit/references/circuits.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/circuits.md)
- [skills/qiskit/references/migration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/migration.md)
- [skills/qiskit/references/patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/patterns.md)
- [skills/qiskit/references/primitives.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/primitives.md)
- [skills/qiskit/references/setup.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/setup.md)
- [skills/qiskit/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/sources.md)
- [skills/qiskit/references/testing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/testing.md)
- [skills/qiskit/references/transpilation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/transpilation.md)
- [skills/qiskit/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qiskit/references/visualization.md)
- [skills/quantizing-models-bitsandbytes/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/quantizing-models-bitsandbytes/SKILL.md)
- [skills/quantizing-models-bitsandbytes/references/memory-optimization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/quantizing-models-bitsandbytes/references/memory-optimization.md)
- [skills/quantizing-models-bitsandbytes/references/qlora-training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/quantizing-models-bitsandbytes/references/qlora-training.md)
- [skills/quantizing-models-bitsandbytes/references/quantization-formats.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/quantizing-models-bitsandbytes/references/quantization-formats.md)
- [skills/qutip/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qutip/SKILL.md)
- [skills/qutip/references/advanced.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qutip/references/advanced.md)
- [skills/qutip/references/analysis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qutip/references/analysis.md)
- [skills/qutip/references/core_concepts.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qutip/references/core_concepts.md)
- [skills/qutip/references/time_evolution.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qutip/references/time_evolution.md)
- [skills/qutip/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/qutip/references/visualization.md)
- [skills/ray-data/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ray-data/SKILL.md)
- [skills/ray-data/references/integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ray-data/references/integration.md)
- [skills/ray-data/references/transformations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ray-data/references/transformations.md)
- [skills/ray-train/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ray-train/SKILL.md)
- [skills/ray-train/references/multi-node.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/ray-train/references/multi-node.md)
- [skills/rdkit/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rdkit/SKILL.md)
- [skills/rdkit/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rdkit/references/api_reference.md)
- [skills/rdkit/references/core_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rdkit/references/core_capabilities.md)
- [skills/rdkit/references/descriptors_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rdkit/references/descriptors_reference.md)
- [skills/rdkit/references/smarts_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rdkit/references/smarts_patterns.md)
- [skills/rdkit/references/workflows_and_best_practices.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rdkit/references/workflows_and_best_practices.md)
- [skills/rebuttal-and-response-to-reviewers/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rebuttal-and-response-to-reviewers/SKILL.md)
- [skills/reference-manager-interop/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/reference-manager-interop/SKILL.md)
- [skills/relsa-severity-assessment/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/relsa-severity-assessment/SKILL.md)
- [skills/relsa-severity-assessment/references/forecasting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/relsa-severity-assessment/references/forecasting.md)
- [skills/relsa-severity-assessment/references/relsa-method.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/relsa-severity-assessment/references/relsa-method.md)
- [skills/relsa-severity-assessment/references/thresholds-and-zones.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/relsa-severity-assessment/references/thresholds-and-zones.md)
- [skills/reproducibility-statement/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/reproducibility-statement/SKILL.md)
- [skills/research-agent-skills/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-agent-skills/SKILL.md)
- [skills/research-agent-skills/references/catalog.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-agent-skills/references/catalog.md)
- [skills/research-grants/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/SKILL.md)
- [skills/research-grants/assets/budget_justification_template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/assets/budget_justification_template.md)
- [skills/research-grants/assets/nih_specific_aims_template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/assets/nih_specific_aims_template.md)
- [skills/research-grants/assets/nsf_project_summary_template.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/assets/nsf_project_summary_template.md)
- [skills/research-grants/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/README.md)
- [skills/research-grants/references/broader_impacts.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/broader_impacts.md)
- [skills/research-grants/references/core_components.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/core_components.md)
- [skills/research-grants/references/darpa_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/darpa_guidelines.md)
- [skills/research-grants/references/doe_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/doe_guidelines.md)
- [skills/research-grants/references/nih_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/nih_guidelines.md)
- [skills/research-grants/references/nsf_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/nsf_guidelines.md)
- [skills/research-grants/references/nstc_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/nstc_guidelines.md)
- [skills/research-grants/references/proposal_types_and_resubmission.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/proposal_types_and_resubmission.md)
- [skills/research-grants/references/review_criteria.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/review_criteria.md)
- [skills/research-grants/references/specific_aims_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/specific_aims_guide.md)
- [skills/research-grants/references/writing_principles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-grants/references/writing_principles.md)
- [skills/research-knowledge-graph/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-knowledge-graph/SKILL.md)
- [skills/research-lookup/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-lookup/README.md)
- [skills/research-lookup/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-lookup/SKILL.md)
- [skills/research-skill-creator/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/research-skill-creator/SKILL.md)
- [skills/rowan/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rowan/SKILL.md)
- [skills/rowan/references/access_and_pricing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rowan/references/access_and_pricing.md)
- [skills/rowan/references/batch_and_webhooks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rowan/references/batch_and_webhooks.md)
- [skills/rowan/references/end_to_end_example.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rowan/references/end_to_end_example.md)
- [skills/rowan/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rowan/references/troubleshooting.md)
- [skills/rowan/references/workflow_catalog.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rowan/references/workflow_catalog.md)
- [skills/rwkv-architecture/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rwkv-architecture/SKILL.md)
- [skills/rwkv-architecture/references/architecture-details.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rwkv-architecture/references/architecture-details.md)
- [skills/rwkv-architecture/references/rwkv7.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rwkv-architecture/references/rwkv7.md)
- [skills/rwkv-architecture/references/state-management.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/rwkv-architecture/references/state-management.md)
- [skills/scanpy/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scanpy/SKILL.md)
- [skills/scanpy/references/analysis_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scanpy/references/analysis_workflow.md)
- [skills/scanpy/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scanpy/references/api_reference.md)
- [skills/scanpy/references/plotting_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scanpy/references/plotting_guide.md)
- [skills/scanpy/references/r_interop.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scanpy/references/r_interop.md)
- [skills/scanpy/references/standard_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scanpy/references/standard_workflow.md)
- [skills/scholar-evaluation/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scholar-evaluation/SKILL.md)
- [skills/scholar-evaluation/references/evaluation_framework.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scholar-evaluation/references/evaluation_framework.md)
- [skills/scholar-evaluation/references/local_tooling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scholar-evaluation/references/local_tooling.md)
- [skills/scholar-evaluation/references/responsible_assessment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scholar-evaluation/references/responsible_assessment.md)
- [skills/scholar-evaluation/references/security_validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scholar-evaluation/references/security_validation.md)
- [skills/scholar-evaluation/references/source_ledger.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scholar-evaluation/references/source_ledger.md)
- [skills/science-aaas/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/science-aaas/SKILL.md)
- [skills/scientific-brainstorming/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-brainstorming/SKILL.md)
- [skills/scientific-brainstorming/references/brainstorming_methods.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-brainstorming/references/brainstorming_methods.md)
- [skills/scientific-brainstorming/references/facilitation_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-brainstorming/references/facilitation_workflows.md)
- [skills/scientific-brainstorming/references/idea_evaluation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-brainstorming/references/idea_evaluation.md)
- [skills/scientific-brainstorming/references/responsible_ai.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-brainstorming/references/responsible_ai.md)
- [skills/scientific-brainstorming/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-brainstorming/references/sources.md)
- [skills/scientific-critical-thinking/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-critical-thinking/SKILL.md)
- [skills/scientific-critical-thinking/references/common_biases.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-critical-thinking/references/common_biases.md)
- [skills/scientific-critical-thinking/references/core_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-critical-thinking/references/core_capabilities.md)
- [skills/scientific-critical-thinking/references/evidence_hierarchy.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-critical-thinking/references/evidence_hierarchy.md)
- [skills/scientific-critical-thinking/references/experimental_design.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-critical-thinking/references/experimental_design.md)
- [skills/scientific-critical-thinking/references/logical_fallacies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-critical-thinking/references/logical_fallacies.md)
- [skills/scientific-critical-thinking/references/scientific_method.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-critical-thinking/references/scientific_method.md)
- [skills/scientific-critical-thinking/references/statistical_pitfalls.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-critical-thinking/references/statistical_pitfalls.md)
- [skills/scientific-schematics/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-schematics/SKILL.md)
- [skills/scientific-schematics/references/best_practices.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-schematics/references/best_practices.md)
- [skills/scientific-schematics/references/iterative_refinement.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-schematics/references/iterative_refinement.md)
- [skills/scientific-slides/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/SKILL.md)
- [skills/scientific-slides/assets/powerpoint_design_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/assets/powerpoint_design_guide.md)
- [skills/scientific-slides/assets/timing_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/assets/timing_guidelines.md)
- [skills/scientific-slides/references/beamer_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/beamer_guide.md)
- [skills/scientific-slides/references/common_pitfalls.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/common_pitfalls.md)
- [skills/scientific-slides/references/data_visualization_slides.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/data_visualization_slides.md)
- [skills/scientific-slides/references/presentation_structure.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/presentation_structure.md)
- [skills/scientific-slides/references/presentation_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/presentation_workflow.md)
- [skills/scientific-slides/references/prompt_writing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/prompt_writing.md)
- [skills/scientific-slides/references/script_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/script_reference.md)
- [skills/scientific-slides/references/slide_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/slide_capabilities.md)
- [skills/scientific-slides/references/slide_design_principles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/slide_design_principles.md)
- [skills/scientific-slides/references/talk_types_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/talk_types_guide.md)
- [skills/scientific-slides/references/visual_review_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-slides/references/visual_review_workflow.md)
- [skills/scientific-visualization/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-visualization/SKILL.md)
- [skills/scientific-visualization/references/color_palettes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-visualization/references/color_palettes.md)
- [skills/scientific-visualization/references/journal_requirements.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-visualization/references/journal_requirements.md)
- [skills/scientific-visualization/references/matplotlib_examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-visualization/references/matplotlib_examples.md)
- [skills/scientific-visualization/references/publication_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-visualization/references/publication_guidelines.md)
- [skills/scientific-visualization/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-visualization/references/sources.md)
- [skills/scientific-writing/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/SKILL.md)
- [skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md)
- [skills/scientific-writing/assets/manuscript_scaffold.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/assets/manuscript_scaffold.md)
- [skills/scientific-writing/references/authorship_ai_confidentiality.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/authorship_ai_confidentiality.md)
- [skills/scientific-writing/references/citation_styles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/citation_styles.md)
- [skills/scientific-writing/references/cli_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/cli_reference.md)
- [skills/scientific-writing/references/evidence_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/evidence_workflow.md)
- [skills/scientific-writing/references/figures_tables.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/figures_tables.md)
- [skills/scientific-writing/references/imrad_structure.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/imrad_structure.md)
- [skills/scientific-writing/references/journal_policies.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/journal_policies.md)
- [skills/scientific-writing/references/professional_report_formatting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/professional_report_formatting.md)
- [skills/scientific-writing/references/reporting_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/reporting_guidelines.md)
- [skills/scientific-writing/references/research_integrity_open_science.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/research_integrity_open_science.md)
- [skills/scientific-writing/references/source_ledger.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/source_ledger.md)
- [skills/scientific-writing/references/writing_principles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scientific-writing/references/writing_principles.md)
- [skills/scikit-bio/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-bio/SKILL.md)
- [skills/scikit-bio/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-bio/references/api_reference.md)
- [skills/scikit-learn/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/SKILL.md)
- [skills/scikit-learn/references/common_workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/references/common_workflows.md)
- [skills/scikit-learn/references/core_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/references/core_capabilities.md)
- [skills/scikit-learn/references/model_evaluation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/references/model_evaluation.md)
- [skills/scikit-learn/references/pipelines_and_composition.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/references/pipelines_and_composition.md)
- [skills/scikit-learn/references/preprocessing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/references/preprocessing.md)
- [skills/scikit-learn/references/quick_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/references/quick_reference.md)
- [skills/scikit-learn/references/supervised_learning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/references/supervised_learning.md)
- [skills/scikit-learn/references/unsupervised_learning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-learn/references/unsupervised_learning.md)
- [skills/scikit-survival/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-survival/SKILL.md)
- [skills/scikit-survival/references/competing-risks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-survival/references/competing-risks.md)
- [skills/scikit-survival/references/cox-models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-survival/references/cox-models.md)
- [skills/scikit-survival/references/data-handling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-survival/references/data-handling.md)
- [skills/scikit-survival/references/ensemble-models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-survival/references/ensemble-models.md)
- [skills/scikit-survival/references/evaluation-metrics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-survival/references/evaluation-metrics.md)
- [skills/scikit-survival/references/svm-models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scikit-survival/references/svm-models.md)
- [skills/scvelo/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvelo/SKILL.md)
- [skills/scvelo/references/velocity_models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvelo/references/velocity_models.md)
- [skills/scvi-tools/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/SKILL.md)
- [skills/scvi-tools/references/differential-expression.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/references/differential-expression.md)
- [skills/scvi-tools/references/models-atac-seq.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/references/models-atac-seq.md)
- [skills/scvi-tools/references/models-multimodal.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/references/models-multimodal.md)
- [skills/scvi-tools/references/models-scrna-seq.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/references/models-scrna-seq.md)
- [skills/scvi-tools/references/models-spatial.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/references/models-spatial.md)
- [skills/scvi-tools/references/models-specialized.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/references/models-specialized.md)
- [skills/scvi-tools/references/theoretical-foundations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/references/theoretical-foundations.md)
- [skills/scvi-tools/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/scvi-tools/references/workflows.md)
- [skills/seaborn/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/seaborn/SKILL.md)
- [skills/seaborn/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/seaborn/references/examples.md)
- [skills/seaborn/references/function_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/seaborn/references/function_reference.md)
- [skills/seaborn/references/grids_and_levels.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/seaborn/references/grids_and_levels.md)
- [skills/seaborn/references/objects_interface.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/seaborn/references/objects_interface.md)
- [skills/seaborn/references/palettes_and_theming.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/seaborn/references/palettes_and_theming.md)
- [skills/seaborn/references/patterns_and_troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/seaborn/references/patterns_and_troubleshooting.md)
- [skills/seaborn/references/plotting_functions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/seaborn/references/plotting_functions.md)
- [skills/segment-anything-model/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/segment-anything-model/SKILL.md)
- [skills/segment-anything-model/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/segment-anything-model/references/advanced-usage.md)
- [skills/segment-anything-model/references/interactive-segmentation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/segment-anything-model/references/interactive-segmentation.md)
- [skills/segment-anything-model/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/segment-anything-model/references/troubleshooting.md)
- [skills/sentence-transformers/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sentence-transformers/SKILL.md)
- [skills/sentence-transformers/references/models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sentence-transformers/references/models.md)
- [skills/sentencepiece/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sentencepiece/SKILL.md)
- [skills/sentencepiece/references/algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sentencepiece/references/algorithms.md)
- [skills/sentencepiece/references/training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sentencepiece/references/training.md)
- [skills/serving-llms-vllm/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/serving-llms-vllm/SKILL.md)
- [skills/serving-llms-vllm/references/optimization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/serving-llms-vllm/references/optimization.md)
- [skills/serving-llms-vllm/references/quantization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/serving-llms-vllm/references/quantization.md)
- [skills/serving-llms-vllm/references/server-deployment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/serving-llms-vllm/references/server-deployment.md)
- [skills/serving-llms-vllm/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/serving-llms-vllm/references/troubleshooting.md)
- [skills/sglang/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sglang/SKILL.md)
- [skills/sglang/references/deployment.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sglang/references/deployment.md)
- [skills/sglang/references/radix-attention.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sglang/references/radix-attention.md)
- [skills/sglang/references/structured-generation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sglang/references/structured-generation.md)
- [skills/shap/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/SKILL.md)
- [skills/shap/references/data-maskers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/references/data-maskers.md)
- [skills/shap/references/explainers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/references/explainers.md)
- [skills/shap/references/migration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/references/migration.md)
- [skills/shap/references/modalities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/references/modalities.md)
- [skills/shap/references/plots.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/references/plots.md)
- [skills/shap/references/theory.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/references/theory.md)
- [skills/shap/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/references/troubleshooting.md)
- [skills/shap/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/shap/references/workflows.md)
- [skills/simpo-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpo-training/SKILL.md)
- [skills/simpo-training/references/datasets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpo-training/references/datasets.md)
- [skills/simpo-training/references/hyperparameters.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpo-training/references/hyperparameters.md)
- [skills/simpo-training/references/loss-functions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpo-training/references/loss-functions.md)
- [skills/simpy/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/SKILL.md)
- [skills/simpy/references/cli-guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/references/cli-guide.md)
- [skills/simpy/references/events.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/references/events.md)
- [skills/simpy/references/monitoring.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/references/monitoring.md)
- [skills/simpy/references/process-interaction.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/references/process-interaction.md)
- [skills/simpy/references/real-time.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/references/real-time.md)
- [skills/simpy/references/resources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/references/resources.md)
- [skills/simpy/references/simulation-methodology.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/references/simulation-methodology.md)
- [skills/simpy/references/sources.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/simpy/references/sources.md)
- [skills/skypilot-multi-cloud-orchestration/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/skypilot-multi-cloud-orchestration/SKILL.md)
- [skills/skypilot-multi-cloud-orchestration/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/skypilot-multi-cloud-orchestration/references/advanced-usage.md)
- [skills/skypilot-multi-cloud-orchestration/references/sky-serve-model-serving.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/skypilot-multi-cloud-orchestration/references/sky-serve-model-serving.md)
- [skills/skypilot-multi-cloud-orchestration/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/skypilot-multi-cloud-orchestration/references/troubleshooting.md)
- [skills/slime-rl-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/slime-rl-training/SKILL.md)
- [skills/slime-rl-training/references/api-reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/slime-rl-training/references/api-reference.md)
- [skills/slime-rl-training/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/slime-rl-training/references/troubleshooting.md)
- [skills/sparse-autoencoder-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sparse-autoencoder-training/SKILL.md)
- [skills/sparse-autoencoder-training/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sparse-autoencoder-training/references/README.md)
- [skills/sparse-autoencoder-training/references/api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sparse-autoencoder-training/references/api.md)
- [skills/sparse-autoencoder-training/references/tutorials.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sparse-autoencoder-training/references/tutorials.md)
- [skills/speculative-decoding/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/speculative-decoding/SKILL.md)
- [skills/speculative-decoding/references/lookahead.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/speculative-decoding/references/lookahead.md)
- [skills/speculative-decoding/references/medusa.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/speculative-decoding/references/medusa.md)
- [skills/springer-lncs/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/springer-lncs/SKILL.md)
- [skills/stable-baselines3/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-baselines3/SKILL.md)
- [skills/stable-baselines3/references/algorithms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-baselines3/references/algorithms.md)
- [skills/stable-baselines3/references/callbacks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-baselines3/references/callbacks.md)
- [skills/stable-baselines3/references/custom_environments.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-baselines3/references/custom_environments.md)
- [skills/stable-baselines3/references/vectorized_envs.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-baselines3/references/vectorized_envs.md)
- [skills/stable-diffusion-image-generation/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-diffusion-image-generation/SKILL.md)
- [skills/stable-diffusion-image-generation/references/advanced-usage.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-diffusion-image-generation/references/advanced-usage.md)
- [skills/stable-diffusion-image-generation/references/controlnet.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-diffusion-image-generation/references/controlnet.md)
- [skills/stable-diffusion-image-generation/references/generation-parameters.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-diffusion-image-generation/references/generation-parameters.md)
- [skills/stable-diffusion-image-generation/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/stable-diffusion-image-generation/references/troubleshooting.md)
- [skills/statistical-analysis/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-analysis/SKILL.md)
- [skills/statistical-analysis/references/assumptions_and_diagnostics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-analysis/references/assumptions_and_diagnostics.md)
- [skills/statistical-analysis/references/bayesian_statistics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-analysis/references/bayesian_statistics.md)
- [skills/statistical-analysis/references/effect_sizes_and_power.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-analysis/references/effect_sizes_and_power.md)
- [skills/statistical-analysis/references/reporting_standards.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-analysis/references/reporting_standards.md)
- [skills/statistical-analysis/references/test_selection_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-analysis/references/test_selection_guide.md)
- [skills/statistical-power/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-power/SKILL.md)
- [skills/statistical-power/references/closed_form_recipes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-power/references/closed_form_recipes.md)
- [skills/statistical-power/references/effect_sizes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-power/references/effect_sizes.md)
- [skills/statistical-power/references/simulation_based_power.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statistical-power/references/simulation_based_power.md)
- [skills/statsmodels/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/SKILL.md)
- [skills/statsmodels/references/discrete_choice.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/references/discrete_choice.md)
- [skills/statsmodels/references/glm.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/references/glm.md)
- [skills/statsmodels/references/linear_models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/references/linear_models.md)
- [skills/statsmodels/references/model_selection.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/references/model_selection.md)
- [skills/statsmodels/references/modeling_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/references/modeling_capabilities.md)
- [skills/statsmodels/references/quick_start_guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/references/quick_start_guide.md)
- [skills/statsmodels/references/stats_diagnostics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/references/stats_diagnostics.md)
- [skills/statsmodels/references/time_series.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/statsmodels/references/time_series.md)
- [skills/sympy/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sympy/SKILL.md)
- [skills/sympy/references/advanced-topics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sympy/references/advanced-topics.md)
- [skills/sympy/references/code-generation-printing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sympy/references/code-generation-printing.md)
- [skills/sympy/references/core-capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sympy/references/core-capabilities.md)
- [skills/sympy/references/core_capabilities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sympy/references/core_capabilities.md)
- [skills/sympy/references/matrices-linear-algebra.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sympy/references/matrices-linear-algebra.md)
- [skills/sympy/references/physics-mechanics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/sympy/references/physics-mechanics.md)
- [skills/systematic-review-prisma/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/systematic-review-prisma/SKILL.md)
- [skills/systematic-review-prisma/references/prisma-2020-checklist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/systematic-review-prisma/references/prisma-2020-checklist.md)
- [skills/systems-paper-writing/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/systems-paper-writing/SKILL.md)
- [skills/systems-paper-writing/references/checklist.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/systems-paper-writing/references/checklist.md)
- [skills/systems-paper-writing/references/reviewer-guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/systems-paper-writing/references/reviewer-guidelines.md)
- [skills/systems-paper-writing/references/section-blueprints.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/systems-paper-writing/references/section-blueprints.md)
- [skills/systems-paper-writing/references/systems-conferences.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/systems-paper-writing/references/systems-conferences.md)
- [skills/systems-paper-writing/references/writing-patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/systems-paper-writing/references/writing-patterns.md)
- [skills/tamarind/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tamarind/SKILL.md)
- [skills/tamarind/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tamarind/references/api_reference.md)
- [skills/tamarind/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tamarind/references/examples.md)
- [skills/tamarind/references/tool_catalog.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tamarind/references/tool_catalog.md)
- [skills/tamarind/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tamarind/references/workflows.md)
- [skills/tensorboard/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorboard/SKILL.md)
- [skills/tensorboard/references/advanced-features.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorboard/references/advanced-features.md)
- [skills/tensorboard/references/integration-examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorboard/references/integration-examples.md)
- [skills/tensorboard/references/integrations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorboard/references/integrations.md)
- [skills/tensorboard/references/profiling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorboard/references/profiling.md)
- [skills/tensorboard/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorboard/references/visualization.md)
- [skills/tensorrt-llm/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorrt-llm/SKILL.md)
- [skills/tensorrt-llm/references/multi-gpu.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorrt-llm/references/multi-gpu.md)
- [skills/tensorrt-llm/references/optimization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorrt-llm/references/optimization.md)
- [skills/tensorrt-llm/references/serving.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tensorrt-llm/references/serving.md)
- [skills/tiledbvcf/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/tiledbvcf/SKILL.md)
- [skills/timesfm-forecasting/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/SKILL.md)
- [skills/timesfm-forecasting/examples/global-temperature/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/examples/global-temperature/README.md)
- [skills/timesfm-forecasting/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/references/api_reference.md)
- [skills/timesfm-forecasting/references/data_preparation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/references/data_preparation.md)
- [skills/timesfm-forecasting/references/examples_and_validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/references/examples_and_validation.md)
- [skills/timesfm-forecasting/references/output_and_config.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/references/output_and_config.md)
- [skills/timesfm-forecasting/references/performance_tuning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/references/performance_tuning.md)
- [skills/timesfm-forecasting/references/system_requirements.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/references/system_requirements.md)
- [skills/timesfm-forecasting/references/workflows.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/timesfm-forecasting/references/workflows.md)
- [skills/torch-geometric/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torch-geometric/SKILL.md)
- [skills/torch-geometric/references/custom_datasets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torch-geometric/references/custom_datasets.md)
- [skills/torch-geometric/references/explainability.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torch-geometric/references/explainability.md)
- [skills/torch-geometric/references/heterogeneous.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torch-geometric/references/heterogeneous.md)
- [skills/torch-geometric/references/link_prediction.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torch-geometric/references/link_prediction.md)
- [skills/torch-geometric/references/message_passing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torch-geometric/references/message_passing.md)
- [skills/torch-geometric/references/scaling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torch-geometric/references/scaling.md)
- [skills/torchdrug/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/SKILL.md)
- [skills/torchdrug/references/core_concepts.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/references/core_concepts.md)
- [skills/torchdrug/references/datasets.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/references/datasets.md)
- [skills/torchdrug/references/knowledge_graphs.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/references/knowledge_graphs.md)
- [skills/torchdrug/references/models_architectures.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/references/models_architectures.md)
- [skills/torchdrug/references/molecular_generation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/references/molecular_generation.md)
- [skills/torchdrug/references/molecular_property_prediction.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/references/molecular_property_prediction.md)
- [skills/torchdrug/references/protein_modeling.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/references/protein_modeling.md)
- [skills/torchdrug/references/retrosynthesis.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchdrug/references/retrosynthesis.md)
- [skills/torchforge-rl-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchforge-rl-training/SKILL.md)
- [skills/torchforge-rl-training/references/api-reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchforge-rl-training/references/api-reference.md)
- [skills/torchforge-rl-training/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/torchforge-rl-training/references/troubleshooting.md)
- [skills/training-llms-megatron/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/training-llms-megatron/SKILL.md)
- [skills/training-llms-megatron/references/benchmarks.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/training-llms-megatron/references/benchmarks.md)
- [skills/training-llms-megatron/references/parallelism-guide.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/training-llms-megatron/references/parallelism-guide.md)
- [skills/training-llms-megatron/references/production-examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/training-llms-megatron/references/production-examples.md)
- [skills/training-llms-megatron/references/training-recipes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/training-llms-megatron/references/training-recipes.md)
- [skills/transformer-lens-interpretability/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformer-lens-interpretability/SKILL.md)
- [skills/transformer-lens-interpretability/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformer-lens-interpretability/references/README.md)
- [skills/transformer-lens-interpretability/references/api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformer-lens-interpretability/references/api.md)
- [skills/transformer-lens-interpretability/references/tutorials.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformer-lens-interpretability/references/tutorials.md)
- [skills/transformers/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformers/SKILL.md)
- [skills/transformers/references/generation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformers/references/generation.md)
- [skills/transformers/references/models.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformers/references/models.md)
- [skills/transformers/references/pipelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformers/references/pipelines.md)
- [skills/transformers/references/tokenizers.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformers/references/tokenizers.md)
- [skills/transformers/references/training.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/transformers/references/training.md)
- [skills/treatment-plans/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/SKILL.md)
- [skills/treatment-plans/references/README.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/references/README.md)
- [skills/treatment-plans/references/documentation_workflow.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/references/documentation_workflow.md)
- [skills/treatment-plans/references/privacy_governance.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/references/privacy_governance.md)
- [skills/treatment-plans/references/safety_scope.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/references/safety_scope.md)
- [skills/treatment-plans/references/security_validation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/references/security_validation.md)
- [skills/treatment-plans/references/shared_decision_handoff.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/references/shared_decision_handoff.md)
- [skills/treatment-plans/references/source_boundaries.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/references/source_boundaries.md)
- [skills/treatment-plans/references/source_ledger.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/treatment-plans/references/source_ledger.md)
- [skills/umap-learn/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/umap-learn/SKILL.md)
- [skills/umap-learn/references/advanced-features.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/umap-learn/references/advanced-features.md)
- [skills/umap-learn/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/umap-learn/references/api_reference.md)
- [skills/uncertainty-and-units/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/uncertainty-and-units/SKILL.md)
- [skills/uncertainty-and-units/references/domain-conversions.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/uncertainty-and-units/references/domain-conversions.md)
- [skills/uncertainty-and-units/references/gum-methodology.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/uncertainty-and-units/references/gum-methodology.md)
- [skills/uncertainty-and-units/references/pint-recipes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/uncertainty-and-units/references/pint-recipes.md)
- [skills/uncertainty-and-units/references/plausibility-scales.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/uncertainty-and-units/references/plausibility-scales.md)
- [skills/uncertainty-and-units/references/reporting-rules.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/uncertainty-and-units/references/reporting-rules.md)
- [skills/uncertainty-and-units/references/uncertainties-recipes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/uncertainty-and-units/references/uncertainties-recipes.md)
- [skills/unslop-academic-writing/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/unslop-academic-writing/SKILL.md)
- [skills/unslop-academic-writing/references/discipline-voice.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/unslop-academic-writing/references/discipline-voice.md)
- [skills/unslop-academic-writing/references/patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/unslop-academic-writing/references/patterns.md)
- [skills/unsloth/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/unsloth/SKILL.md)
- [skills/unsloth/references/index.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/unsloth/references/index.md)
- [skills/unsloth/references/llms-full.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/unsloth/references/llms-full.md)
- [skills/unsloth/references/llms-txt.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/unsloth/references/llms-txt.md)
- [skills/unsloth/references/llms.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/unsloth/references/llms.md)
- [skills/usfiscaldata/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/SKILL.md)
- [skills/usfiscaldata/references/api-basics.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/references/api-basics.md)
- [skills/usfiscaldata/references/datasets-debt.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/references/datasets-debt.md)
- [skills/usfiscaldata/references/datasets-fiscal.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/references/datasets-fiscal.md)
- [skills/usfiscaldata/references/datasets-interest-rates.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/references/datasets-interest-rates.md)
- [skills/usfiscaldata/references/datasets-securities.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/references/datasets-securities.md)
- [skills/usfiscaldata/references/examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/references/examples.md)
- [skills/usfiscaldata/references/parameters.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/references/parameters.md)
- [skills/usfiscaldata/references/response-format.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/usfiscaldata/references/response-format.md)
- [skills/vaex/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/vaex/SKILL.md)
- [skills/vaex/references/core_dataframes.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/vaex/references/core_dataframes.md)
- [skills/vaex/references/data_processing.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/vaex/references/data_processing.md)
- [skills/vaex/references/io_operations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/vaex/references/io_operations.md)
- [skills/vaex/references/machine_learning.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/vaex/references/machine_learning.md)
- [skills/vaex/references/performance.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/vaex/references/performance.md)
- [skills/vaex/references/visualization.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/vaex/references/visualization.md)
- [skills/venue-templates/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/SKILL.md)
- [skills/venue-templates/assets/examples/cell_summary_example.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/assets/examples/cell_summary_example.md)
- [skills/venue-templates/assets/examples/medical_structured_abstract.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/assets/examples/medical_structured_abstract.md)
- [skills/venue-templates/assets/examples/nature_abstract_examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/assets/examples/nature_abstract_examples.md)
- [skills/venue-templates/assets/examples/neurips_introduction_example.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/assets/examples/neurips_introduction_example.md)
- [skills/venue-templates/references/cell_press_style.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/cell_press_style.md)
- [skills/venue-templates/references/conferences_formatting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/conferences_formatting.md)
- [skills/venue-templates/references/cs_conference_style.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/cs_conference_style.md)
- [skills/venue-templates/references/grants_requirements.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/grants_requirements.md)
- [skills/venue-templates/references/journals_formatting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/journals_formatting.md)
- [skills/venue-templates/references/medical_journal_styles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/medical_journal_styles.md)
- [skills/venue-templates/references/ml_conference_style.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/ml_conference_style.md)
- [skills/venue-templates/references/nature_science_style.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/nature_science_style.md)
- [skills/venue-templates/references/posters_guidelines.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/posters_guidelines.md)
- [skills/venue-templates/references/reviewer_expectations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/reviewer_expectations.md)
- [skills/venue-templates/references/venue_writing_styles.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/venue-templates/references/venue_writing_styles.md)
- [skills/verl-rl-training/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/verl-rl-training/SKILL.md)
- [skills/verl-rl-training/references/api-reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/verl-rl-training/references/api-reference.md)
- [skills/verl-rl-training/references/troubleshooting.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/verl-rl-training/references/troubleshooting.md)
- [skills/waypoint-bio/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/waypoint-bio/SKILL.md)
- [skills/waypoint-bio/references/cli-reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/waypoint-bio/references/cli-reference.md)
- [skills/waypoint-bio/references/compass-benchmark.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/waypoint-bio/references/compass-benchmark.md)
- [skills/waypoint-bio/references/data-preparation.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/waypoint-bio/references/data-preparation.md)
- [skills/waypoint-bio/references/python-api.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/waypoint-bio/references/python-api.md)
- [skills/weights-and-biases/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/weights-and-biases/SKILL.md)
- [skills/weights-and-biases/references/artifacts.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/weights-and-biases/references/artifacts.md)
- [skills/weights-and-biases/references/hyperparameter-sweeps.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/weights-and-biases/references/hyperparameter-sweeps.md)
- [skills/weights-and-biases/references/integration-examples.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/weights-and-biases/references/integration-examples.md)
- [skills/weights-and-biases/references/integrations.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/weights-and-biases/references/integrations.md)
- [skills/weights-and-biases/references/sweeps.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/weights-and-biases/references/sweeps.md)
- [skills/whisper/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/whisper/SKILL.md)
- [skills/whisper/references/languages.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/whisper/references/languages.md)
- [skills/zarr-python/SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/zarr-python/SKILL.md)
- [skills/zarr-python/references/api_reference.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/zarr-python/references/api_reference.md)
- [skills/zarr-python/references/chunking_and_compression.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/zarr-python/references/chunking_and_compression.md)
- [skills/zarr-python/references/integration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/zarr-python/references/integration.md)
- [skills/zarr-python/references/performance_and_patterns.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/zarr-python/references/performance_and_patterns.md)
- [skills/zarr-python/references/storage_backends.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/zarr-python/references/storage_backends.md)
- [skills/zarr-python/references/v3_migration.md](https://github.com/KalarisLabs/research-agent-skills/blob/df088027ff233dc511fa74cb7f406b4e87fa438c/skills/zarr-python/references/v3_migration.md)

Standard: https://agent-plugins.org · Indexed commit: df088027ff233dc511fa74cb7f406b4e87fa438c