Metabolism Python Packages

cobra

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

riptide

Reaction Inclusion by Parsimony and Transcript Distribution (RIPTiDe)

reframed

ReFramed: metabolic modeling package

nutramilo-nis

Open-source algorithm for estimating the relative insulinogenic potential of meals from nutritional composition.

carveme

CarveMe: genome-scale metabolic model reconstruction

sccellfie

A tool for inferring metabolic activities from single-cell and spatial transcriptomics

cellmetpro

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

efmlrs

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

framed

framed: a metabolic modeling package for python

biosimulators-masspy

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

scmeta

A python package for single-cell metabolism analysis.

corda

Genome-scale model construction with CORDA

miom

Mixed Integer Optimization for Metabolism

findcpcli

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

biosimulations-bigg

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

biocatalyzer

BioCatalyzer: a rule-based tool to predict compound metabolism

brendapyrser

A Python parser for the BRENDA database

gmcspy

Efficient calculation of gMCS in python.

contrabass

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

ggshu

Grammar of Graphics for shu.

multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

pygenprop

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

fasting

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

designmc

Designing microbial communities