Top 26 systems-biology open source projects

Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

Fast Inference of Networks from Directed Regulations

python Parameter EStimation TOolbox

An interactive web portal for exploring immuno-oncology data

Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

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

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

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

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Workshop in omics integration and systems biology

A web application to visualize and edit pathway models

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

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

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

💹 SIMON is powerful, flexible, open-source and easy to use machine learning knowledge discovery platform 💻

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.

A python library for metabolic networks sampling and analysis

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

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!

The consensus GEM for Saccharomyces cerevisiae