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beng_213

cobrame

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

cobrame_supplement

Scripts needed to reproduce the figures in https://doi.org/10.1371/journal.pcbi.1006302

cobrapy

COBRApy is a package for constraints-based modeling of biological networks

ecolime

Data and tools necessary to construct iLE1678-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

fba4l_course_material

keff_mapping

Scripts to reproduce ME-model simulations from "Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers"

me_biomass

Reproduce the figures in "Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth"

minspan

optaux

Reproduce the figures in "The genetic basis for adaptation of model-designed syntrophic co-cultures"

patroon

Workflow solutions for mass-spectrometry based non-target analysis.

qbio

Material for qbio18 mx

solvemepy

solveME public repository