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biotite-dev
biotite

A comprehensive library for computational molecular biology

4.7M 944 136
scikit-bio
scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

106K 1K 328
opencobra
cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

62K 560 234
rasbt
biopandas

Working with molecular structures in pandas DataFrames

35K 751 117
biosimulators
biosimulators-utils

Utilities for building standardized command-line interfaces for biosimulation software packages

9K 4 6
gyorilab
indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

8K 209 77
myokit
myokit

A modeling and simulation tool for cardiac cellular electrophysiology

7K 45 9
albertyw
itolapi

Python API for the Interactive Tree of Life (iTOL)

5K 37 11
BojarLab
glycowork

Package for processing and analyzing glycans and their role in biology.

5K 91 18
a-r-j
graphein

Protein Graph Library

5K 1K 140
adibvafa
codontransformer

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

4K 206 31
biosimulators
biosimulators-test-suite

Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators

3K 7 2
epifluidlab
finaletoolkit

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

3K 37 17
SED-ML
kisao

Ontology of algorithms for analyzing biological models, their parameters, and their outputs

3K 12 0
jyzhu-pointless
natal-core

Numba-Accelerated Toolkit for Analysis of Lifecycles

3K 3 1
theochem
qc-iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

3K 162 55
broadinstitute
tangram-sc

Spatial alignment of single cell transcriptomic data.

3K 362 64
PDBeurope
pdbe-arpeggio

Arpeggio calculates interatomic contacts based on the rules defined in CREDO.

2K 126 23
faridrashidi
scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

2K 7 1
akensert
molgraph

Graph neural networks for molecular machine learning: Implemented and compatible with TensorFlow and Keras.

2K 64 5
trytoolchest
toolchest-client

Python client for Toolchest

2K 15 0
alondmnt
codon-bias

Python package of codon usage bias analysis tools

2K 21 9
cafferychen777
chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

2K 34 8
biosimulators
biosimulators-copasi

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

2K 2 3
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