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carbofix

A algorithm for automatic design of carbon fixation cycles

component-contribution

Standard reaction Gibbs energy estimation for biochemical reactions

dynamic-labeling-cascade

enzyme-cost

Kinetic modeling of pathway fluxes for estimating the specific cost in enzymes for sustaining a given flux

enzyme-cost-minimization

Code for flux-specific enzyme cost calculations

equilibrator

equilibrator-api

A command-line version of eQuilibrator with minimal dependencies

equilibrator-kbase

A KBase module for the Component Contribution method (AKA eQuilibrator)

equilibrator3

examples

flux-enzyme-cost-minimization

Explore optimal metabolic states by screening of metabolic flux distributions and computing their enzyme cost via kinetic models

flux-html-report

A python script that creates an HTML output file for FBA results

kinetic-params

kvivo_max

metabolic_modelling

milo-lab

Automatically exported from code.google.com/p/milo-lab

ms-tools

A collection of scripts for analyzing MS data

optlang

optlang - sympy based mathematical programming language

optslope

A toolbox for running OptSlope, an algorithm for metabolic engineering

pkasolver

toolkit for prediction pKa values of small molecules via graph convolutional networks

pmfa

Principal Metabolic Flux Mode Analysis

proteomaps

Scripts and data for generating proteome treemaps (AKA proteomaps)

pulsefeeding-analysis

MATLAB and Python code used for analysis and figure generation of E. coli pulsing/starvation project

replace-animals

A collaborative effort to investigate the advantage of replacing an animal-based diet with a plant-based one

sbtab

SBtab - Table format for Systems Biology:

sbtab-matlab

Matlab functions for SBtab format

sloppy

A cobrapy-based library that finds knockout and carbon-source combinations that enforce flux-biomass coupling

small-molecule-regulation

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

stfba

Implementation of the st-FBA algorithm, dependent on COBRApy