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Support the Open Source Projects We Depend On

Scientific Agent Skills is built on the shoulders of giants. The 135 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.

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

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
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
scikit-survival Survival analysis GitHub
aeon Time series ML toolkit GitHub
PyMOO Multi-objective optimization GitHub
UMAP Dimensionality reduction 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

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 GitHub
FluidSim CFD framework 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

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

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.

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.

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!