Skill attribution

Most of the bundled skills under this directory began life in other open collections. This file records where each one came from, under which license, and how far it has been changed here, so the people who wrote them are credited and the terms they chose are kept. Each skill's SKILL.md frontmatter carries the same facts under metadata.upstream*; when a skill is added or re-synced, update both. Skills not listed here were written for OpenScience by Synthetic Sciences.

Relationship values: derived (the upstream text, edited for OpenScience's tools and conventions), adapted and rewritten (the upstream skill is the origin; the text is new), references and scripts derived (the SKILL.md is OpenScience's; reference documents or scripts under the skill come from upstream), vendored (unchanged apart from paths).

K-Dense Scientific Agent Skills — 166 skills

• Repository: https://github.com/K-Dense-AI/scientific-agent-skills

• Copyright: K-Dense Inc.

• License: MIT

• Paper: Kassis, T., Agarwal, V., He, Y., Patel, D., & Brueckner, A. M. (2026). Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents. arXiv:2609.00065. https://arxiv.org/abs/2609.00065

• Skills whose upstream path begins with scientific-skills/, scientific-databases/ or scientific-packages/ were taken from the collection's 2025–2026 layout before it was flattened into skills/.

Skill	Upstream path	Relationship
biology/anndata	skills/anndata	derived
biology/benchling-integration	skills/benchling-integration	derived
biology/bids	skills/bids	derived
biology/biopython	skills/biopython	derived
biology/bioservices	skills/bioservices	derived
biology/bulk-rnaseq	skills/bulk-rnaseq	derived
biology/clinical-decision-support	scientific-skills/clinical-decision-support	derived
biology/clinical-reports	skills/clinical-reports	derived
biology/cobrapy	skills/cobrapy	derived
biology/deepspot-m	skills/deepspot-m	derived
biology/deeptools	skills/deeptools	derived
biology/dnanexus-integration	scientific-skills/dnanexus-integration	derived
biology/esm	skills/esm	derived
biology/etetoolkit	scientific-skills/etetoolkit	derived
biology/flowio	scientific-skills/flowio	derived
biology/folklore-variant-evidence	skills/folklore-variant-evidence	derived
biology/genomic-coordinates	skills/genomic-coordinates	derived
biology/genomic-intelligence	skills/genomic-intelligence	derived
biology/gget	scientific-skills/gget	derived
biology/ginkgo-cloud-lab	skills/ginkgo-cloud-lab	derived
biology/glycoengineering	skills/glycoengineering	derived
biology/histolab	skills/histolab	derived
biology/lamindb	skills/lamindb	derived
biology/latchbio-integration	scientific-skills/latchbio-integration	derived
biology/neurokit2	scientific-skills/neurokit2	derived
biology/neuropixels-analysis	scientific-skills/neuropixels-analysis	derived
biology/nextflow	skills/nextflow	derived
biology/omero-integration	scientific-skills/omero-integration	derived
biology/opentrons-integration	scientific-skills/opentrons-integration	derived
biology/pacsomatic	skills/pacsomatic	derived
biology/pathml	scientific-skills/pathml	derived
biology/pathogen-variant-surveillance	skills/pathogen-variant-surveillance	derived
biology/pathway-enrichment	skills/pathway-enrichment	derived
biology/phylogenetics	skills/phylogenetics	derived
biology/polars-bio	skills/polars-bio	derived
biology/protocolsio-integration	skills/protocolsio-integration	derived
biology/pydeseq2	skills/pydeseq2	derived
biology/pydicom	skills/pydicom	derived
biology/pyhealth	scientific-skills/pyhealth	derived
biology/pylabrobot	scientific-skills/pylabrobot	derived
biology/pysam	scientific-skills/pysam	derived
biology/relsa-severity-assessment	skills/relsa-severity-assessment	derived
biology/scanpy	skills/scanpy	derived
biology/scikit-bio	skills/scikit-bio	derived
biology/scikit-survival	scientific-skills/scikit-survival	derived
biology/scvelo	skills/scvelo	derived
biology/scvi-tools	skills/scvi-tools	derived
biology/tamarind	skills/tamarind	derived
biology/tiledbvcf	skills/tiledbvcf	derived
biology/treatment-plans	skills/treatment-plans	derived
biology/waypoint-bio	skills/waypoint-bio	derived
chemistry/analytical-method-validation	skills/analytical-method-validation	derived
chemistry/datamol	scientific-skills/datamol	derived
chemistry/deepchem	skills/deepchem	derived
chemistry/diffdock	skills/diffdock	derived
chemistry/hypogenic	scientific-skills/hypogenic	derived
chemistry/matchms	scientific-skills/matchms	derived
chemistry/medchem	scientific-skills/medchem	derived
chemistry/molecular-dynamics	skills/molecular-dynamics	derived
chemistry/molfeat	skills/molfeat	derived
chemistry/pkpd-modeling	skills/pkpd-modeling	derived
chemistry/pyopenms	scientific-skills/pyopenms	derived
chemistry/pytdc	skills/pytdc	derived
chemistry/rdkit	scientific-skills/rdkit	derived
chemistry/torchdrug	scientific-skills/torchdrug	derived
cloud-compute/modal	scientific-packages/modal	adapted and rewritten
coding/arboreto	skills/arboreto	derived
coding/denario	scientific-skills/denario	derived
coding/exploratory-data-analysis	scientific-skills/exploratory-data-analysis	derived
coding/gtars	scientific-skills/gtars	derived
coding/matlab	scientific-skills/matlab	derived
coding/networkx	skills/networkx	derived
coding/optimize-for-gpu	skills/optimize-for-gpu	derived
coding/pymc	skills/pymc	derived
coding/pymoo	skills/pymoo	derived
coding/rowan	scientific-skills/rowan	derived
coding/scikit-learn	skills/scikit-learn	derived
coding/shap	scientific-skills/shap	derived
coding/simpy	skills/simpy	derived
coding/statistical-analysis	scientific-skills/statistical-analysis	derived
coding/statsmodels	skills/statsmodels	derived
coding/sympy	skills/sympy	derived
coding/timesfm-forecasting	skills/timesfm-forecasting	derived
coding/torch_geometric	scientific-skills/torch_geometric	derived
coding/umap-learn	skills/umap-learn	derived
core/research-lookup	scientific-skills/research-lookup	adapted and rewritten
data-engineering/aeon	skills/aeon	derived
data-engineering/dask	skills/dask	derived
data-engineering/datalad	skills/datalad	derived
data-engineering/geomaster	skills/geomaster	derived
data-engineering/geopandas	scientific-skills/geopandas	derived
data-engineering/polars	skills/polars	derived
data-engineering/vaex	skills/vaex	derived
data-engineering/zarr-python	scientific-skills/zarr-python	derived
databases/alphafold-database	scientific-skills/alphafold-database	derived
databases/biorxiv-database	scientific-skills/biorxiv-database	derived
databases/brenda-database	scientific-skills/brenda-database	derived
databases/cellxgene-census	skills/cellxgene-census	derived
databases/chembl-database	scientific-skills/chembl-database	derived
databases/clinicaltrials-database	scientific-skills/clinicaltrials-database	derived
databases/clinpgx-database	scientific-skills/clinpgx-database	derived
databases/clinvar-database	scientific-skills/clinvar-database	derived
databases/cosmic-database	scientific-skills/cosmic-database	derived
databases/database-lookup	skills/database-lookup	derived
databases/datacommons-client	scientific-skills/datacommons-client	derived
databases/depmap	skills/depmap	derived
databases/drugbank-database	scientific-skills/drugbank-database	derived
databases/ena-database	scientific-skills/ena-database	derived
databases/ensembl-database	scientific-skills/ensembl-database	derived
databases/fda-database	scientific-skills/fda-database	derived
databases/fred-economic-data	scientific-skills/fred-economic-data	derived
databases/gene-database	scientific-skills/gene-database	derived
databases/geo-database	scientific-skills/geo-database	derived
databases/gwas-database	scientific-skills/gwas-database	derived
databases/hmdb-database	scientific-skills/hmdb-database	derived
databases/imaging-data-commons	scientific-skills/imaging-data-commons	derived
databases/kegg-database	scientific-skills/kegg-database	derived
databases/metabolomics-workbench-database	scientific-skills/metabolomics-workbench-database	derived
databases/ncats-arax	skills/ncats-arax	derived
databases/onekgpd	skills/onekgpd	derived
databases/ontology-term-resolution	skills/ontology-term-resolution	derived
databases/openalex-database	scientific-skills/openalex-database	derived
databases/opentargets-database	scientific-skills/opentargets-database	derived
databases/pdb-database	scientific-skills/pdb-database	derived
databases/primekg	skills/primekg	derived
databases/pubchem-database	scientific-skills/pubchem-database	derived
databases/pubmed-database	scientific-skills/pubmed-database	derived
databases/reactome-database	scientific-skills/reactome-database	derived
databases/string-database	scientific-skills/string-database	derived
databases/uniprot-database	scientific-skills/uniprot-database	derived
databases/usfiscaldata	skills/usfiscaldata	derived
databases/uspto-database	scientific-skills/uspto-database	derived
databases/zinc-database	scientific-skills/zinc-database	derived
document-parsing/liteparse	scientific-skills/liteparse	adapted and rewritten
core/generate-image	skills/generate-image	prompt guidance adapted; rewritten around the native tool
llm-tools/transformers	skills/transformers	derived
ml-training/adaptyv	scientific-skills/adaptyv	derived
ml-training/geniml	scientific-skills/geniml	derived
ml-training/pufferlib	skills/pufferlib	derived
ml-training/stable-baselines3	skills/stable-baselines3	derived
other/get-available-resources	skills/get-available-resources	derived
other/iso-13485-certification	scientific-skills/iso-13485-certification	derived
other/iso-standards-readiness	skills/iso-standards-readiness	derived
other/lab-hardware-cad	skills/lab-hardware-cad	derived
other/labarchive-integration	scientific-skills/labarchive-integration	derived
physics/astropy	skills/astropy	derived
physics/fluidsim	scientific-skills/fluidsim	derived
physics/openpiv	skills/openpiv	derived
physics/pymatgen	scientific-skills/pymatgen	derived
physics/uncertainty-and-units	skills/uncertainty-and-units	derived
quantum/cirq	skills/cirq	derived
quantum/pennylane	skills/pennylane	derived
quantum/qiskit	scientific-skills/qiskit	derived
quantum/qutip	skills/qutip	derived
research/experimental-design	skills/experimental-design	derived
research/market-research-reports	skills/market-research-reports	derived
research/paper-lookup	skills/paper-lookup	derived
research/statistical-power	skills/statistical-power	derived
scholar-evaluation	scientific-skills/scholar-evaluation	derived
visualization/matplotlib	skills/matplotlib	derived
visualization/plotly	scientific-skills/plotly	derived
core/scientific-visualization	skills/scientific-visualization (v1.2)	vendored, frontmatter adapted
core/schematics	skills/scientific-schematics (v1.7)	workflow, prompt standards, review rubric and references adapted; scripts derived
visualization/seaborn	skills/seaborn	derived
writing/markdown-mermaid-writing	skills/markdown-mermaid-writing	derived
writing/paper-2-web	scientific-skills/paper-2-web	derived
writing/pyzotero	skills/pyzotero	derived

K-Dense Claude Scientific Writer — 14 skills

• Repository: https://github.com/K-Dense-AI/claude-scientific-writer
• Copyright: K-Dense Inc.
• License: MIT

Skill	Upstream path	Relationship
core/brainstorming	skills/scientific-brainstorming	adapted and rewritten
core/citations	skills/citation-management	adapted and rewritten
core/hypotheses	—	references and scripts derived
core/literature-review	—	references and scripts derived
core/ml-paper-writing	—	references and scripts derived
core/paper-writing	—	references and scripts derived
core/peer-review	—	references and scripts derived
core/sources	skills/verify	adapted and rewritten
research/research-grants	skills/research-grants/references/core_components.md	derived
visualization/infographics	skills/infographics	derived
writing/latex-posters	skills/latex-posters/references/ai_graphics_for_posters.md	derived
writing/pptx-posters	—	references and scripts derived
writing/scientific-slides	skills/scientific-slides	derived

Orchestra Research AI Research Skills — 79 skills

• Repository: https://github.com/Orchestra-Research/AI-Research-SKILLs
• Copyright: Orchestra Research
• License: MIT

Skill	Upstream path	Relationship
cloud-compute/lambda-labs	lambda-labs	adapted and rewritten
cloud-compute/skypilot	09-infrastructure/skypilot	derived
coding/audiocraft	18-multimodal/audiocraft	derived
coding/slime	06-post-training/slime	derived
data-engineering/ray-data	05-data-processing/ray-data	derived
llm-tools/autogpt	14-agents/autogpt	derived
llm-tools/blip-2	18-multimodal/blip-2	derived
llm-tools/chroma	15-rag/chroma	derived
llm-tools/clip	18-multimodal/clip	derived
llm-tools/constitutional-ai	07-safety-alignment/constitutional-ai	derived
llm-tools/crewai	14-agents/crewai	derived
llm-tools/dspy	16-prompt-engineering/dspy	derived
llm-tools/faiss	15-rag/faiss	derived
llm-tools/guidance	16-prompt-engineering/guidance	derived
llm-tools/huggingface-tokenizers	02-tokenization/huggingface-tokenizers	derived
llm-tools/instructor	16-prompt-engineering/instructor	derived
llm-tools/langchain	14-agents/langchain	derived
llm-tools/langsmith	17-observability/langsmith	derived
llm-tools/llamaguard	07-safety-alignment/llamaguard	derived
llm-tools/llamaindex	14-agents/llamaindex	derived
llm-tools/llava	18-multimodal/llava	derived
llm-tools/long-context	19-emerging-techniques/long-context	derived
llm-tools/nemo-guardrails	07-safety-alignment/nemo-guardrails	derived
llm-tools/outlines	16-prompt-engineering/outlines	derived
llm-tools/pinecone	15-rag/pinecone	derived
llm-tools/qdrant	15-rag/qdrant	derived
llm-tools/segment-anything	18-multimodal/segment-anything	derived
llm-tools/sentence-transformers	15-rag/sentence-transformers	derived
llm-tools/sentencepiece	02-tokenization/sentencepiece	derived
llm-tools/stable-diffusion	18-multimodal/stable-diffusion	derived
llm-tools/whisper	18-multimodal/whisper	derived
ml-inference/gguf	10-optimization/gguf	derived
ml-inference/llama-cpp	12-inference-serving/llama-cpp	derived
ml-inference/miles	06-post-training/miles	derived
ml-inference/phoenix	17-observability/phoenix	derived
ml-inference/sglang	12-inference-serving/sglang	derived
ml-inference/speculative-decoding	19-emerging-techniques/speculative-decoding	derived
ml-inference/tensorrt-llm	12-inference-serving/tensorrt-llm	derived
ml-inference/vllm	12-inference-serving/vllm	derived
ml-training/accelerate	08-distributed-training/accelerate	derived
ml-training/awq	10-optimization/awq	derived
ml-training/axolotl	03-fine-tuning/axolotl	derived
ml-training/bigcode-evaluation-harness	11-evaluation/bigcode-evaluation-harness	derived
ml-training/bitsandbytes	10-optimization/bitsandbytes	derived
ml-training/deepspeed	08-distributed-training/deepspeed	derived
ml-training/flash-attention	10-optimization/flash-attention	derived
ml-training/gptq	10-optimization/gptq	derived
ml-training/grpo-rl-training	06-post-training/grpo-rl-training	derived
ml-training/hqq	10-optimization/hqq	derived
ml-training/knowledge-distillation	19-emerging-techniques/knowledge-distillation	derived
ml-training/litgpt	01-model-architecture/litgpt	derived
ml-training/llama-factory	03-fine-tuning/llama-factory	derived
ml-training/lm-evaluation-harness	11-evaluation/lm-evaluation-harness	derived
ml-training/mamba	01-model-architecture/mamba	derived
ml-training/megatron-core	08-distributed-training/megatron-core	derived
ml-training/mlflow	13-mlops/mlflow	derived
ml-training/model-merging	19-emerging-techniques/model-merging	derived
ml-training/model-pruning	19-emerging-techniques/model-pruning	derived
ml-training/moe-training	19-emerging-techniques/moe-training	derived
ml-training/nanogpt	01-model-architecture/nanogpt	derived
ml-training/nemo-curator	05-data-processing/nemo-curator	derived
ml-training/nemo-evaluator	11-evaluation/nemo-evaluator	derived
ml-training/nnsight	04-mechanistic-interpretability/nnsight	derived
ml-training/openrlhf	06-post-training/openrlhf	derived
ml-training/peft	03-fine-tuning/peft	derived
ml-training/pytorch-lightning	08-distributed-training/pytorch-lightning	derived
ml-training/pyvene	04-mechanistic-interpretability/pyvene	derived
ml-training/ray-train	08-distributed-training/ray-train	derived
ml-training/rwkv	01-model-architecture/rwkv	derived
ml-training/saelens	04-mechanistic-interpretability/saelens	derived
ml-training/simpo	06-post-training/simpo	derived
ml-training/tensorboard	13-mlops/tensorboard	derived
ml-training/torchforge	06-post-training/torchforge	derived
ml-training/torchtitan	01-model-architecture/torchtitan	derived
ml-training/transformer-lens	04-mechanistic-interpretability/transformer-lens	derived
ml-training/trl-fine-tuning	06-post-training/trl-fine-tuning	derived
ml-training/unsloth	unsloth	adapted and rewritten
ml-training/verl	06-post-training/verl	derived
ml-training/weights-and-biases	13-mlops/weights-and-biases	derived

Hugging Face skills — 8 skills

• Repository: https://github.com/huggingface/skills
• Copyright: Hugging Face
• License: Apache-2.0

Skill	Upstream path	Relationship
data-engineering/hugging-face-datasets	skills/huggingface-datasets	adapted and rewritten
llm-tools/hugging-face-cli	skills/hf-cli	adapted and rewritten
llm-tools/hugging-face-tool-builder	skills/huggingface-tool-builder	derived
ml-training/hugging-face-evaluation	skills/huggingface-community-evals	adapted and rewritten
ml-training/hugging-face-model-trainer	skills/huggingface-llm-trainer	derived
other/hugging-face-jobs	skills/hugging-face-jobs	adapted and rewritten
other/hugging-face-trackio	skills/huggingface-trackio	derived
writing/hugging-face-paper-publisher	skills/huggingface-paper-publisher	derived

Anthropic document skills — 4 skills

• Repository: https://github.com/anthropics/skills

• Copyright: Anthropic, PBC

• License: Anthropic terms (see each skill's LICENSE.txt)

• Vendored through K-Dense Scientific Agent Skills, which tracks the Anthropic originals. Each skill directory keeps Anthropic's LICENSE.txt.

Skill	Upstream path	Relationship
document-parsing/docx	skills/docx	vendored
document-parsing/pdf	skills/pdf	vendored
document-parsing/pptx	skills/pptx	vendored
document-parsing/xlsx	skills/xlsx	vendored

NVIDIA BioNeMo Agent Toolkit — 2 skills

• Repository: https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit

• Copyright: NVIDIA Corporation

• License: CC-BY-4.0 (skills) / Apache-2.0 (code)

• Pinned upstream commit 0e67a612e4045f007e38fa77adc8f3ebfc5616b6; skills and documentation are CC-BY-4.0, code Apache-2.0, and the models the workflow calls carry their own terms.

Skill	Upstream path	Relationship
biology/protein-binder-design	workflows/generative-protein-binder-design/protein-binder-design	adapted and rewritten
biology/bionemo-nims	the toolkit's NIM usage guidance	written for the hosted adapters; model names and terms from NVIDIA

Microsoft MarkItDown — 1 skill

• Repository: https://github.com/microsoft/markitdown
• Copyright: Microsoft Corporation
• License: MIT

Skill	Upstream path	Relationship
data-engineering/markitdown	—	vendored

273 of the bundled skills are covered above. biology/pacsomatic additionally carries its own MIT license from Beifang Niu, which K-Dense's collection preserves and this one keeps.