Models and main dataset - Constraint-based metabolic control analysis for rational strain engineering

Models and dataset needed to reproduce the case studies for the manuscript Constraint-based metabolic control analysis for rational strain engineering by S. Tsouka et al.

The code and software requirements to run simulations explained and available at: https://github.com/EPFL-LCSB/NRA and https://gitlab.com/realLCSB/nra

Models:

• Consistently reduced stoichiometric model of E. coli metabolism in the SBML format (from Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations by Hameri et al. - https://doi.org/10.1016/j.ymben.2018.10.005): reducedD1Model_FBA.xml
• Thermodynamically curated model of E.coli metabolism in MATLAB's mat format (from Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations by Hameri et al. - https://doi.org/10.1016/j.ymben.2018.10.005): D1_FDP1.mat

Datasets:

• Files containing various data and options used in the generation of control coefficients (dataInfo.mat, metSampDataD1_FDP1.mat)
• Files containing statistics for the previously generated population of 50'000 sets of flux and concentration control coefficients (raw data provided below as Supplementary datasets): CpaggDATA.mat (flux CCs), and CxaggDATA.mat (concentration CCs)
• Files containing the reference and 18 extreme sets of flux and concentration CCs used in the present study: CCforNRA_RXN_GLCptspp.mat (chosen through Principal Component Analysis (PCA) based on the GLCptspp parameter) and CCforNRA_RXN_PYRtex.mat (chosen through PCA based on the PYRtex parameter)
• Supplementary datasets 1-5, 50 files each containing 1000 sets of flux and concentration CCs, named as DataD1_FDP1xx.mat where xx ranges from 1-50. The files are available as:
  • Supplementary dataset 1: http://doi.org/10.5281/zenodo.4500807
  • Supplementary dataset 2: http://doi.org/10.5281/zenodo.4500874
  • Supplementary dataset 3: http://doi.org/10.5281/zenodo.4500971
  • Supplementary dataset 4: http://doi.org/10.5281/zenodo.4501050
  • Supplementary dataset 5: http://doi.org/10.5281/zenodo.4501147