Support the Open Source Projects We Depend On

Scientific Agent Skills is built on the shoulders of giants. The 150 skills in this repository leverage dozens of incredible open source projects created and maintained by dedicated developers and research communities around the world.

If you find value in these skills, please consider supporting the underlying open source projects that make them possible.

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How to Support Open Source

1. Star repositories on GitHub - It's free and helps projects gain visibility
2. Sponsor maintainers directly through GitHub Sponsors, Open Collective, or project-specific donation pages
3. Contribute code, documentation, or bug reports
4. Cite projects in your publications
5. Share projects with colleagues

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Featured Projects by Domain

Bioinformatics & Genomics

Project	Description	Links
Biopython	Computational molecular biology toolkit	GitHub - Donate
Scanpy	Single-cell analysis in Python	GitHub - scverse
AnnData	Annotated data matrices for single-cell	GitHub
scvi-tools	Deep learning for single-cell omics	GitHub
Arboreto	Gene regulatory network inference	GitHub
pysam	SAM/BAM/VCF file interface	GitHub
scikit-bio	Bioinformatics library	GitHub
gget	Gene and transcript info retrieval	GitHub
deepTools	Tools for deep-sequencing data	GitHub
geniml	Machine learning for genomic interval sets	GitHub
Gtars	Rust/Python genomic interval toolkit	GitHub
ETE Toolkit	Phylogenetic tree analysis	GitHub

Cheminformatics & Drug Discovery

Project	Description	Links
RDKit	Cheminformatics toolkit	GitHub - Donate
Datamol	Molecular manipulation made easy	GitHub
DeepChem	Deep learning for chemistry	GitHub
TorchDrug	Drug discovery with PyTorch	GitHub
molfeat	Molecular featurization	GitHub
MedChem	Medicinal chemistry filters	GitHub
PyTDC	Therapeutics Data Commons	GitHub

Proteomics & Mass Spectrometry

Project	Description	Links
matchms	Mass spectrometry data processing	GitHub
pyOpenMS	Mass spectrometry toolkit	GitHub

Machine Learning & AI

Project	Description	Links
PyTorch Lightning	Deep learning framework	GitHub - Sponsor
Transformers	State-of-the-art NLP	GitHub
scikit-learn	Machine learning in Python	GitHub - Donate
PyTorch Geometric	Geometric deep learning	GitHub
PyMC	Probabilistic programming	GitHub - Donate
SHAP	Model interpretability	GitHub
Stable Baselines3	Reinforcement learning	GitHub
PufferLib	High-performance reinforcement learning environments and training	GitHub
scikit-survival	Survival analysis	GitHub
aeon	Time series ML toolkit	GitHub
PyMOO	Multi-objective optimization	GitHub
UMAP	Dimensionality reduction	GitHub
HypoGeniC	LLM-assisted candidate textual hypothesis generation from labeled data	GitHub

Data Science & Visualization

Project	Description	Links
Matplotlib	Plotting library	GitHub - Donate
Seaborn	Statistical visualization	GitHub
Plotly	Interactive visualizations	GitHub
NetworkX	Network analysis	GitHub - Donate
SymPy	Symbolic mathematics	GitHub - Donate
statsmodels	Statistical modeling	GitHub
GeoPandas	Geospatial data in Python	GitHub
Polars	Fast DataFrame library	GitHub
Dask	Parallel computing	GitHub - Donate
Vaex	Out-of-core DataFrames	GitHub

Medical Imaging & Digital Pathology

Project	Description	Links
pydicom	DICOM file handling	GitHub
histolab	Digital pathology preprocessing	GitHub
PathML	Pathology ML toolkit	GitHub
OMERO.py	Python client for the OMERO microscopy data platform	GitHub

Healthcare & Clinical

Project	Description	Links
PyHealth	Healthcare AI toolkit	GitHub
NeuroKit2	Neurophysiological signal processing	GitHub

Materials Science & Physics

Project	Description	Links
Pymatgen	Materials analysis	GitHub
COBRApy	Metabolic modeling	GitHub
Astropy	Astronomy library	GitHub - Donate

Quantum Computing

Project	Description	Links
Qiskit	IBM quantum computing SDK	GitHub
Cirq	Google quantum computing	GitHub
PennyLane	Quantum ML library	GitHub
QuTiP	Quantum toolbox in Python	GitHub

Simulation & Engineering

Project	Description	Links
SimPy	Discrete-event simulation	GitLab
FluidSim	CFD framework	GitHub
FluidFFT	FFT framework and plugins used by FluidSim	GitHub

Laboratory & Automation

Project	Description	Links
PyLabRobot	Lab automation control	GitHub

Protein Engineering

Project	Description	Links
ESM	Evolutionary scale modeling	GitHub

Data Formats & I/O

Project	Description	Links
Zarr	Chunked array storage	GitHub
FlowIO	Flow cytometry I/O	GitHub

Scientific Communication & Documents

Project	Description	Links
python-pptx	Create and inspect editable PowerPoint .pptx files	GitHub

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NumFOCUS-Sponsored Projects

Many of the projects above are sponsored by NumFOCUS, a nonprofit supporting open source scientific computing. Consider donating to NumFOCUS to support the broader ecosystem.

NumFOCUS-sponsored projects in this collection:

• Biopython
• scikit-learn
• Matplotlib
• NetworkX
• SymPy
• Dask
• Astropy
• PyMC

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scverse Ecosystem

The scverse consortium maintains foundational tools for single-cell omics:

• Scanpy
• AnnData
• scvi-tools
• And more

Consider supporting their mission to advance single-cell research.

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A Note from K-Dense

At K-Dense, we believe in giving back to the communities that make our work possible. We encourage all users of Scientific Agent Skills to:

1. Acknowledge these projects when you use them in research
2. Contribute back improvements when you can
3. Support maintainers financially if you derive commercial value

The open source scientific Python ecosystem is a shared resource. Let's keep it thriving together.

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This list is not exhaustive. Many other excellent open source projects power the skills in this repository. If you notice a project that should be listed here, please open a PR!