A Python framework for structural systems biology
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Updated
Dec 7, 2020 - Python
A Python framework for structural systems biology
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Python package to study microbial communities using metabolic modeling.
Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
Reaction Inclusion by Parsimony and Transcript Distribution
Constraint-based modeling of metabolism using Mixed Integer Optimization
Multivariate thermodynamics-based metabolic flux analysis in Python.
Python package and workflow for EFM calculation via (mp)lrs and efmtool
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
Bioinformatics project analyzing cancer metabolism using computational modeling and analysis. The project was awarded the GIDI-UP: Summer Research Award and includes data, models, and scripts.
Docker image for a full ME model stack.
FBAhv: FBA analysis of host-virus metabolic model (read related publication at: https://www.life-science-alliance.org/content/4/1/e202000869)
findCP core package - find ChokePoint reactions in genome-scale metabolic models
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