joyvgeerestein

joyvgeerestein's Stars

• gibbslab/exp2flux

  An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.

  Language:R3

• CABSEL/DeltaFBA

  DeltaFBA is a set of MATLAB functions that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the intracellular flux distribution between two conditions.

  Language:MATLAB52

• cnapy-org/CNApy-projects

  :world_map: A repository of CNApy projects

  Language:Tcl61

• MetaSys-LISBP/PhysioFit

  Estimation of extracellular fluxes and growth rate

  Language:Python85

• SysBioChalmers/ecFactory

  A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism

  Language:MATLAB73

• modsim/FluxML

  A Universal Modeling Language for Metabolic Flux Analysis

  Language:C++96

• mauriceling/advancesyntoolkit

  Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

  Language:Python1240

• SBRG/cobrame

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

  Language:Python3317

• cnapy-org/CNApy

  An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

  Language:Python447

• cdanielmachado/smetana

  SMETANA: a tool to analyse interactions in microbial communities

  Language:Python5711

• jotech/gapseq

  Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

  Language:R15332

• micom-dev/micom

  Python package to study microbial communities using metabolic modeling.

  Language:Python8918