Metabolism Python Packages

cobra

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

riptide

Reaction Inclusion by Parsimony and Transcript Distribution

reframed

ReFramed: metabolic modeling package

sccellfie

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

carveme

CarveMe: genome-scale metabolic model reconstruction

scmeta

A python library for single-cell metabolism data analysis.

biosimulators-masspy

BioSimulators-compliant command-line interface to the MassPY simulation program <https://masspy.readthedocs.io/>.

corda

Genome-scale model construction with CORDA

framed

framed: a metabolic modeling package for python

efmlrs

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

brendapyrser

Tools to parse the BRENDA database

miom

Mixed Integer Optimization for Metabolism

biosimulations-bigg

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

findcpcli

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

contrabass

Constraint-based model vulnerabilities analysis

cellmetpro

Analyse cellular metabolic states of cells from scRNA-seq data using FBA and Genome-scale Metabolic Models

pygenprop

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

biocatalyzer

BioCatalyzer: a rule-based tool to predict compound metabolism

gmcspy

Efficient calculation of gMCS in python.

multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

fasting

A Python package to interact with fasting logs from apps like Zero.

ggshu

Grammar of Graphics for shu.

designmc

Designing microbial communities