COBRApy is a package for constraint-based modeling of metabolic networks.
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Updated
Sep 19, 2024 - Python
COBRApy is a package for constraint-based modeling of metabolic networks.
A python library for metabolic networks sampling and analysis
Curation and analysis of metabolic models
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Pathway Tools multiprocessing wrapper (for PathoLogic).
MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.
Python package and workflow for EFM calculation via (mp)lrs and efmtool
Enzymatic Link Prediction
Create stoichiometric metabolic network models of single-species or multi-species communities
findCP CLI package - find ChokePoint reactions in genome-scale metabolic models
Chemical reaction balancing web service
Trim, extract, and convert GEMs
Compute minimal metabolic precursors sets that enable the production of target metabolites
Enumeration of biosynthetic pathways from metabolic networks
Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002
The systematic identification of functional metabolic control mechanisms relies mostly on the integration of data but barely considers the connectivity of the metabolic network. However, recent geometric deep learning approaches show promising performances in the prediction of links in network or graph structures. By using a dream-case in silico…
[Not maintained and not updated] Draft metabolic network reconstruction using Rhea database, Uniprot and SPARQL queries.
Detection of deadends in metabolic networks
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