Metabolism Python Packages

cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

59K 560 234

riptide

Reaction Inclusion by Parsimony and Transcript Distribution

8K 13 7

carveme

CarveMe: genome-scale metabolic model reconstruction

2K 203 63

reframed

ReFramed: metabolic modeling package

2K 63 15

sccellfie

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

1K 57 3

framed

framed: a metabolic modeling package for python

949 26 10

scmeta

A python library for single-cell metabolism data analysis.

673 20 5

miom

Constraint-based modeling of metabolism using Mixed Integer Optimization

579 12 2

efmlrs

Extracts EFMs from result file of mplrs and decompresses EFMs from efmtool and mplrs results that have been compressed with EFMlrs

558 6 1

brendapyrser

A Python parser for the BRENDA database

541 33 10

biosimulators-masspy

MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container

541 1 0

corda

Genome-scale model construction with CORDA

527 25 8

findcpcli

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

324 3 0

biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

279 1 0

pygenprop

A python library for programmatic usage of EBI InterPro Genome Properties.

245 9 5

gmcspy

gMCSpy is a python package for the calculation of Genetic Minimal Cut sets (GMCS). In simple terms, the idea is to take a metabolic model and calculate the genetic vulnerabilities that will render the biomass production impossible. This is done through a Mixed-Integer Linear problem (MILP) formulation and the use of a linear solver.

210 6 1