From 20dc0a2303bcfbae833be9708e7ef1de4ac14b56 Mon Sep 17 00:00:00 2001 From: Timothy Kassis Date: Sun, 19 Oct 2025 15:32:52 -0700 Subject: [PATCH] Update readme --- README.md | 122 +++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 121 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 40743c5..b80d4bb 100644 --- a/README.md +++ b/README.md @@ -60,7 +60,14 @@ A comprehensive collection of ready-to-use scientific skills for Claude, curated - **Zarr** - Chunked, compressed N-dimensional array storage **Multi-omics & Integration:** -- **BioMNI** - Multi-omics data integration with LLM-powered analysis +- **BIOMNI** - Multi-omics data integration with LLM-powered analysis + +### Scientific Thinking & Analysis + +- **Hypothesis Generation** - Structured frameworks for generating and evaluating scientific hypotheses +- **Scientific Critical Thinking** - Tools and approaches for rigorous scientific reasoning and evaluation +- **Scientific Visualization** - Best practices and templates for creating publication-quality scientific figures +- **Statistical Analysis** - Comprehensive statistical testing, power analysis, and experimental design ## Try in Claude Code, Claude.ai, and the API @@ -88,3 +95,116 @@ To use any skill from this repository or upload custom skills, follow the instru ### Claude API You can use Anthropic's pre-built skills, and upload custom skills, via the Claude API. See the [Skills API Quickstart](https://docs.anthropic.com/claude/skills-api-quickstart) for more. + +## TODO: Future Scientific Capabilities (Availble currently in K-Dense) + +### Scientific Databases +- **UniProt** - Protein sequence and functional information database +- **KEGG** - Kyoto Encyclopedia of Genes and Genomes for pathways and metabolism +- **ChEMBL** - Bioactive molecules with drug-like properties database +- **NCBI Gene** - Gene-specific information from RefSeq, GenBank, and other sources +- **Protein Data Bank (PDB)** - 3D structural data of biological macromolecules +- **COSMIC** - Catalogue of Somatic Mutations in Cancer +- **ClinVar** - Clinical significance of genomic variants +- **AlphaFold DB** - Protein structure predictions from DeepMind +- **STRING** - Protein-protein interaction networks +- **GEO (Gene Expression Omnibus)** - Functional genomics data repository +- **European Nucleotide Archive (ENA)** - Comprehensive nucleotide sequence database +- **ZINC** - Free database of commercially available compounds for virtual screening + +### Bioinformatics & Genomics +- **pysam** - Interface to SAM/BAM/CRAM format files +- **pybedtools** - Wrapper for BEDTools genome arithmetic operations +- **mygene** - Python client for MyGene.Info gene query service +- **pyensembl** - Python interface to Ensembl reference genome metadata +- **nglview** - IPython/Jupyter widget for molecular visualization +- **pyvcf** - Variant Call Format (VCF) file parser +- **pyfaidx** - Efficient FASTA file indexing and retrieval +- **kipoiseq** - Genomic sequence data loading for ML models +- **genomepy** - Download and manage genome assemblies +- **MACS2/3** - Peak calling for ChIP-seq data + +### Cheminformatics & Drug Discovery +- **Open Babel** - Chemical file format conversion and molecular mechanics +- **ChemPy** - Chemistry and thermodynamics calculations +- **Psi4** - Quantum chemistry software for ab initio calculations +- **pmapper** - Pharmacophore modeling and fingerprinting +- **ODDT** - Open Drug Discovery Toolkit for structure-based drug design +- **ProLIF** - Protein-ligand interaction fingerprints +- **Mordred** - Molecular descriptor calculator (1800+ descriptors) +- **ProteinMPNN** - Deep learning for protein sequence design +- **ESM** - Evolutionary Scale Modeling for protein language models +- **OpenMM** - Molecular dynamics simulation toolkit + +### Proteomics & Mass Spectrometry +- **pyteomics** - Mass spectrometry data analysis +- **pyOpenMS** - OpenMS Python bindings for proteomics +- **matchms** - Processing and similarity matching of mass spectrometry data +- **MSstats** - Statistical analysis of quantitative proteomics + +### Systems Biology & Networks +- **NetworkX** - Complex network analysis and graph algorithms +- **igraph** - Fast network analysis library +- **PyBioNetFit** - Biological network modeling and fitting +- **PINT** - Pathway integration analysis +- **GEMEditor** - Graphical tool for genome-scale metabolic models + +### Structural Biology +- **MDAnalysis** - Molecular dynamics trajectory analysis +- **ProDy** - Protein dynamics and structure analysis +- **PyMOL** - Molecular visualization scripting +- **Chimera/ChimeraX** - UCSF molecular visualization +- **FreeSASA** - Solvent accessible surface area calculations +- **DSSP** - Secondary structure assignment + +### Machine Learning for Science +- **DGL-LifeSci** - Deep Graph Library for life sciences +- **ChemBERTa** - Transformer models for chemistry +- **TorchDrug** - PyTorch library for drug discovery +- **GraNNField** - Graph neural networks for force fields +- **SchNet/DimeNet** - Continuous-filter convolutional networks for molecules +- **MoleculeNet** - Benchmark datasets for molecular machine learning +- **TorchMD** - Molecular dynamics with PyTorch +- **jax-md** - Differentiable molecular dynamics in JAX + +### Imaging & Microscopy +- **scikit-image** - Image processing algorithms +- **CellProfiler** - Cell image analysis +- **Napari** - Multi-dimensional image viewer +- **Fiji/ImageJ** - Image processing scripting +- **StarDist** - Cell/nucleus detection with deep learning +- **Cellpose** - Generalist cell segmentation + +### Phylogenetics & Evolution +- **DendroPy** - Phylogenetic computing library +- **PyCogent** - Comparative genomics toolkit +- **TreeTime** - Phylodynamic analysis and molecular clock inference + +### Metabolomics +- **PyCytoData** - Cytometry data processing +- **MS-DIAL** - Data-independent MS/MS deconvolution +- **XCMS** - LC/MS and GC/MS data processing + +### Climate & Environmental Science +- **xarray** - N-dimensional labeled arrays and datasets +- **Iris** - Climate and weather data analysis +- **MetPy** - Meteorological data toolkit +- **climlab** - Climate modeling and analysis + +### Statistics & Experimental Design +- **statsmodels** - Statistical models and hypothesis testing +- **pingouin** - Statistical tests with clear output +- **PyDOE2** - Design of experiments +- **scipy.stats** - Statistical functions and distributions + +### Data Management & Processing +- **Dask** - Parallel computing for analytics +- **Parquet** - Columnar storage format for big data +- **DuckDB** - Analytical SQL database +- **SQLAlchemy** - SQL toolkit and ORM + +### Visualization +- **Plotly** - Interactive graphing library +- **Bokeh** - Interactive visualization for web browsers +- **Altair** - Declarative statistical visualization +- **PyVista** - 3D plotting and mesh analysis