A Python framework for structural systems biology
Python package to study microbial communities using metabolic modeling.
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Reaction Inclusion by Parsimony and Transcript Distribution
Multivariate thermodynamics-based metabolic flux analysis in Python.
Python package and workflow for EFM calculation via (mp)lrs and efmtool
Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression
Multi-scale model of Metabolism In Cellular Systems
findCP CLI package - find ChokePoint reactions in genome-scale metabolic models
Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis
ECMproject is a standalone python program, which enumerates Elementary Conversion Modes (ECMs) of metabolic models.
findCP core package - find ChokePoint reactions in genome-scale metabolic models
Master on Integrative Synthetic Biology (MISB) training sessions
Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
Shiny app for visualization of the toy GENREs
diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library
iGEM 2025. McMasterU. Flux-balance analysis
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