#bioinformatics

MCP server exposing PlantCV as a measurement instrument — plant traits plus the segmentation overlay they were measured from

Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports

Making Protein folding accessible to all!

A Rust library for parsing PDB (Protein Data Bank) files

An open-source Python package to unify raw MS data accession and storage.

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

cython + htslib == fast VCF and BCF processing

Data visualisation web components for the life sciences.

GA4GH Variation Annotation Python Implementation

MCP server giving AI assistants verifiable access to PubMed, Europe PMC, US/UK drug labelling, and ClinicalTrials.gov. Built by PharmaTools.AI.

Sample level metadata system

The self-evolving agentic framework for bioinformatics

A Python library for simulating the evolution of species, genomes, sequences and traits

PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.

A fast multiple sequence alignment program.

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

High-performance graph database + vector search powered by InterSystems IRIS

Semantic prefix map registry

A companion for the Cromwell Server

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  

An agent that takes a dead research repo and turns it into a callable pipeline component.

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An agentic bioinformatics analyst: it runs the analysis on your own compute, self-heals failures, verifies the output, and returns a reproducible result.

HTSlib bindings for Ruby

Working with molecular structures in pandas DataFrames

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Real-time VSCode extension and standalone Python script for validating mmCIF/CIF files against the PDBx/mmCIF dictionary or any CIF dictionary.

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JAX-native differentiable protein folding framework integrating experimental NMR constraints (RDCs) and biophysical "self-correction." Several Jupyter Notebooks visualize the concepts.