An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium

Semantic Capture of Relationships In Biological Literature (scribl)

A comprehensive library for computational molecular biology

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

MuRaL is a deep learning framework for estimating single-nucleotide mutation rates across the genome.

A supertree method for rooted source trees

Comprehensive lifecycle tracking algorithms for yeast cells

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

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.

A complete python interface to Racmacs via rpy2

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

An interoperable Python framework for biomolecular simulation.

A new implementation of a well-known stochastic model for carcinogenesis, augmented with competition dynamics and spatial structuring.

📐 Symmetry-corrected RMSD in Python

R code for the PBS users for generating and working on the PBS clusters

DANCE: a deep learning library and benchmark platform for single-cell analysis

Myokit: A simple interface to cardiac cellular electrophysiology

A modular inverse QSAR pipeline

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking