computational-biology — open-source software health

PyPI

95Exceptionalhealth index

scverse/pertpy

Single-cell perturbation analysis

Python★ 337↓ 7,588/moAug 24, 2026

MITAug 24, 2026 · metrics 2.10.0

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91Excellenthealth index

opensim-org/opensim-core

SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

C++★ 1,098Aug 22, 2026

Apache-2.0Aug 22, 2026 · metrics 2.10.0

PyPI

86Excellenthealth index

K-Dense-AI/scientific-agent-skills

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 170,000+ scientists worldwide. 158 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.

Python★ 32.6KAug 5, 2026

MITAug 5, 2026 · metrics 2.10.0

PyPI · crates.io

86Excellenthealth index

biotite-dev/biotite

A comprehensive library for computational molecular biology

Python · Rust★ 968↓ 3.7M/moAug 27, 2026

BSD-3-ClauseAug 27, 2026 · metrics 2.10.0

PyPI

80Excellenthealth index

cafferychen777/mLLMCelltype

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

Python · R★ 655↓ 285/moAug 2, 2026

MITAug 2, 2026 · metrics 2.10.0

crates.io

62Moderatehealth index

haddocking/haddock-restraints

Generate restraints to be used in HADDOCK

Rust★ 6↓ 54/moJul 17, 2026

MITJul 17, 2026 · metrics 2.10.0

60Moderatehealth index

TimOthYStIles/poly

A Go package for engineering organisms.

Go★ 731Jul 17, 2026

MITJul 17, 2026 · metrics 2.10.0

PyPI

57Moderatehealth index

BioPandas/biopandas

Working with molecular structures in pandas DataFrames

Python★ 756Jul 21, 2026

BSD-3-ClauseJul 21, 2026 · metrics 2.10.0

PyPI

56Moderatehealth index

DoctorDean/lazarus

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

Python★ 13↓ 375/moJul 17, 2026

MITJul 17, 2026 · metrics 2.10.0

crates.io

56Moderatehealth index

bio-rs/bio-rs

AI-ready biological data I/O, validation, and tokenization engine

Rust · Python★ 3Jul 15, 2026

Custom licenseJul 15, 2026 · metrics 2.10.0

PyPI

53Moderatehealth index

mooreneural/proteintensor

AI-native tensor format (.ptt) for protein-structure ML. Convert a structure or sequence once; load backbone, MSA, ESM embeddings, sparse pair features, and ligands with zero parsing. Feeds AlphaFold/Boltz (Boltz-2 verified). Zarr-backed, lossless, PyTorch/JAX-ready, streams from S3/GCS.

Python★ 1Jul 15, 2026

MITJul 15, 2026 · metrics 2.10.0

PyPI · npm

36Weakhealth index

smartsbio/smarts-bio-jupyterlab

No repository description published.

TypeScript★ 1Jul 17, 2026

MITJul 17, 2026 · metrics 2.10.0

PyPI

25At Riskhealth index

chiffa/bioflow

Information Flow Analysis toolkit for biological networks