Python package to study microbial communities using metabolic modeling.

A Python framework for structural systems biology

StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy

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

Python package for building and analyzing models using ModelSEED

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

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

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

Constraint-based model vulnerabilities analysis - Python analysis tool http://contrabass.unizar.es

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.

COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Flux Balance Analysis of E. coli Core Model using COBRApy | Systems Biology & Data Science

findCP core package - find ChokePoint reactions in genome-scale metabolic models

Master on Integrative Synthetic Biology (MISB) training sessions

FBAhv: FBA analysis of host-virus metabolic model (read related publication at: https://www.life-science-alliance.org/content/4/1/e202000869)

A class based on COBRApy to handle quantitative mutations on metabolic models.

Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.

Pathways That Harvest Chemical Reactions

Shiny app for visualization of the toy GENREs

diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library

Docker image for a full ME model stack.

A metabolic engineering strategy which determines the optimal reaction modifications (knock-out, up-regulation, down-regulation) to increase the flux through a target reaction, while retaining a certain percentage of optimal biomass flux.

Repositório para apresentação de código e posterior análise, desenvolvido pelo grupo 1 para a UC Biologia de Sistemas, do Mestraddo em Bioinformática, ano lectivo 23-24.

Metabolic simulation of lipid and energy pathways in mouse Genome-scale model and investigation of PFAS congeners' toxicity