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

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

Curated (meta)list of resources for Biology.

python Parameter EStimation TOolbox

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Python framework for Systems Biology modeling

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.

PANDORA - Predictive Analytics aNd Data Oriented Research Applications 💻

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

A Python framework for structural systems biology

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

The consensus GEM for Saccharomyces cerevisiae

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

Python package to study microbial communities using metabolic modeling.

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.

An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena

Toolbox for including enzyme constraints on a genome-scale model.