# 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.**

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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](https://github.com/biopython/biopython) - [Donate](https://numfocus.org/donate-to-biopython) |
| **Scanpy** | Single-cell analysis in Python | [GitHub](https://github.com/scverse/scanpy) - [scverse](https://scverse.org/) |
| **AnnData** | Annotated data matrices for single-cell | [GitHub](https://github.com/scverse/anndata) |
| **scvi-tools** | Deep learning for single-cell omics | [GitHub](https://github.com/scverse/scvi-tools) |
| **Arboreto** | Gene regulatory network inference | [GitHub](https://github.com/aertslab/arboreto) |
| **pysam** | SAM/BAM/VCF file interface | [GitHub](https://github.com/pysam-developers/pysam) |
| **scikit-bio** | Bioinformatics library | [GitHub](https://github.com/scikit-bio/scikit-bio) |
| **gget** | Gene and transcript info retrieval | [GitHub](https://github.com/pachterlab/gget) |
| **deepTools** | Tools for deep-sequencing data | [GitHub](https://github.com/deeptools/deepTools) |
| **ETE Toolkit** | Phylogenetic tree analysis | [GitHub](https://github.com/etetoolkit/ete) |

### Cheminformatics & Drug Discovery

| Project | Description | Links |
|---------|-------------|-------|
| **RDKit** | Cheminformatics toolkit | [GitHub](https://github.com/rdkit/rdkit) - [Donate](https://github.com/sponsors/rdkit) |
| **Datamol** | Molecular manipulation made easy | [GitHub](https://github.com/datamol-io/datamol) |
| **DeepChem** | Deep learning for chemistry | [GitHub](https://github.com/deepchem/deepchem) |
| **TorchDrug** | Drug discovery with PyTorch | [GitHub](https://github.com/DeepGraphLearning/torchdrug) |
| **molfeat** | Molecular featurization | [GitHub](https://github.com/datamol-io/molfeat) |
| **MedChem** | Medicinal chemistry filters | [GitHub](https://github.com/datamol-io/medchem) |
| **PyTDC** | Therapeutics Data Commons | [GitHub](https://github.com/mims-harvard/TDC) |

### Proteomics & Mass Spectrometry

| Project | Description | Links |
|---------|-------------|-------|
| **matchms** | Mass spectrometry data processing | [GitHub](https://github.com/matchms/matchms) |
| **pyOpenMS** | Mass spectrometry toolkit | [GitHub](https://github.com/OpenMS/OpenMS) |

### Machine Learning & AI

| Project | Description | Links |
|---------|-------------|-------|
| **PyTorch Lightning** | Deep learning framework | [GitHub](https://github.com/Lightning-AI/pytorch-lightning) - [Sponsor](https://github.com/sponsors/Lightning-AI) |
| **Transformers** | State-of-the-art NLP | [GitHub](https://github.com/huggingface/transformers) |
| **scikit-learn** | Machine learning in Python | [GitHub](https://github.com/scikit-learn/scikit-learn) - [Donate](https://numfocus.org/donate-to-scikit-learn) |
| **PyTorch Geometric** | Geometric deep learning | [GitHub](https://github.com/pyg-team/pytorch_geometric) |
| **PyMC** | Probabilistic programming | [GitHub](https://github.com/pymc-devs/pymc) - [Donate](https://numfocus.org/donate-to-pymc) |
| **SHAP** | Model interpretability | [GitHub](https://github.com/shap/shap) |
| **Stable Baselines3** | Reinforcement learning | [GitHub](https://github.com/DLR-RM/stable-baselines3) |
| **scikit-survival** | Survival analysis | [GitHub](https://github.com/sebp/scikit-survival) |
| **aeon** | Time series ML toolkit | [GitHub](https://github.com/aeon-toolkit/aeon) |
| **PyMOO** | Multi-objective optimization | [GitHub](https://github.com/anyoptimization/pymoo) |
| **UMAP** | Dimensionality reduction | [GitHub](https://github.com/lmcinnes/umap) |

### Data Science & Visualization

| Project | Description | Links |
|---------|-------------|-------|
| **Matplotlib** | Plotting library | [GitHub](https://github.com/matplotlib/matplotlib) - [Donate](https://numfocus.org/donate-to-matplotlib) |
| **Seaborn** | Statistical visualization | [GitHub](https://github.com/mwaskom/seaborn) |
| **Plotly** | Interactive visualizations | [GitHub](https://github.com/plotly/plotly.py) |
| **NetworkX** | Network analysis | [GitHub](https://github.com/networkx/networkx) - [Donate](https://numfocus.org/donate-to-networkx) |
| **SymPy** | Symbolic mathematics | [GitHub](https://github.com/sympy/sympy) - [Donate](https://numfocus.org/donate-to-sympy) |
| **statsmodels** | Statistical modeling | [GitHub](https://github.com/statsmodels/statsmodels) |
| **GeoPandas** | Geospatial data in Python | [GitHub](https://github.com/geopandas/geopandas) |
| **Polars** | Fast DataFrame library | [GitHub](https://github.com/pola-rs/polars) |
| **Dask** | Parallel computing | [GitHub](https://github.com/dask/dask) - [Donate](https://numfocus.org/donate-to-dask) |
| **Vaex** | Out-of-core DataFrames | [GitHub](https://github.com/vaexio/vaex) |

### Medical Imaging & Digital Pathology

| Project | Description | Links |
|---------|-------------|-------|
| **pydicom** | DICOM file handling | [GitHub](https://github.com/pydicom/pydicom) |
| **histolab** | Digital pathology preprocessing | [GitHub](https://github.com/histolab/histolab) |
| **PathML** | Pathology ML toolkit | [GitHub](https://github.com/Dana-Farber-AIOS/pathml) |

### Healthcare & Clinical

| Project | Description | Links |
|---------|-------------|-------|
| **PyHealth** | Healthcare AI toolkit | [GitHub](https://github.com/sunlabuiuc/PyHealth) |
| **NeuroKit2** | Neurophysiological signal processing | [GitHub](https://github.com/neuropsychology/NeuroKit) |

### Materials Science & Physics

| Project | Description | Links |
|---------|-------------|-------|
| **Pymatgen** | Materials analysis | [GitHub](https://github.com/materialsproject/pymatgen) |
| **COBRApy** | Metabolic modeling | [GitHub](https://github.com/opencobra/cobrapy) |
| **Astropy** | Astronomy library | [GitHub](https://github.com/astropy/astropy) - [Donate](https://numfocus.org/donate-to-astropy) |

### Quantum Computing

| Project | Description | Links |
|---------|-------------|-------|
| **Qiskit** | IBM quantum computing SDK | [GitHub](https://github.com/Qiskit/qiskit) |
| **Cirq** | Google quantum computing | [GitHub](https://github.com/quantumlib/Cirq) |
| **PennyLane** | Quantum ML library | [GitHub](https://github.com/PennyLaneAI/pennylane) |
| **QuTiP** | Quantum toolbox in Python | [GitHub](https://github.com/qutip/qutip) |

### Simulation & Engineering

| Project | Description | Links |
|---------|-------------|-------|
| **SimPy** | Discrete-event simulation | [GitHub](https://github.com/TeamSim/SimPy) |
| **FluidSim** | CFD framework | [GitHub](https://github.com/fluiddyn/fluidsim) |

### Laboratory & Automation

| Project | Description | Links |
|---------|-------------|-------|
| **PyLabRobot** | Lab automation control | [GitHub](https://github.com/PyLabRobot/pylabrobot) |

### Protein Engineering

| Project | Description | Links |
|---------|-------------|-------|
| **ESM** | Evolutionary scale modeling | [GitHub](https://github.com/facebookresearch/esm) |

### Data Formats & I/O

| Project | Description | Links |
|---------|-------------|-------|
| **Zarr** | Chunked array storage | [GitHub](https://github.com/zarr-developers/zarr-python) |
| **FlowIO** | Flow cytometry I/O | [GitHub](https://github.com/whitews/FlowIO) |

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## NumFOCUS-Sponsored Projects

Many of the projects above are sponsored by [NumFOCUS](https://numfocus.org/), a nonprofit supporting open source scientific computing. Consider [donating to NumFOCUS](https://numfocus.org/donate) 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](https://scverse.org/) 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!*
