Data/Software repository of LCSB (EPFL)
Published March 7, 2021 | Version v1
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Models and datasets - The effects of model complexity and size on metabolic flux distribution and control. Case study in Escherichia coli.

Authors/Creators

  • 1. EPFL

Description

Models and raw datasets required for reproducing the results of the manuscript The effects of model complexity and size on metabolic flux distribution and control. Case study in Escherichia coli. by Hameri et al. 

Models:

Three thermodynamically curated models of E.coli metabolism of increasing size - namely D1, D2 and D3 - are provided in MATLAB format .mat files:

  • D1: D1_FDP1.mat
  • D2: D2_FDP1.mat
  • D3: D3_FDP1.mat

Datasets:

Configuration MATLAB .mat files that were used to generate the control coefficient (Metabolic Control Analysis) for D1, D2 and D3. Also, the steady-state metabolic flux and concentration vectors are provided.

  • D1: metSampDataD1_FDP1.mat
  • D2: metSampDataD2_FDP1.mat
  • D3: metSampDataD3_FDP1.mat

The populations of 50’000 control coefficients for D1, D2 and D3 are provided for each model in five separate subsets/batches of 10’000 control coefficients. Each model X has 50 files YY of 1’000 control coefficients DataDX_FDP1YY, where X is the model ranging from 1-3 and YY is the file number ranging 1-50.

D1:

  • Supplementary dataset 1: https://doi.org/10.5281/zenodo.4585663
  • Supplementary dataset 2: https://doi.org/10.5281/zenodo.4585702
  • Supplementary dataset 3: https://doi.org/10.5281/zenodo.4585719
  • Supplementary dataset 4: https://doi.org/10.5281/zenodo.4585739
  • Supplementary dataset 5: https://doi.org/10.5281/zenodo.4585865

D2:

  • Supplementary dataset 6: https://doi.org/10.5281/zenodo.4585932
  • Supplementary dataset 7: https://doi.org/10.5281/zenodo.4585995
  • Supplementary dataset 8: https://doi.org/10.5281/zenodo.4586074
  • Supplementary dataset 9: https://doi.org/10.5281/zenodo.4586286
  • Supplementary dataset 10: https://doi.org/10.5281/zenodo.4586380

D3:

  • Supplementary dataset 11: https://doi.org/10.5281/zenodo.4586482
  • Supplementary dataset 12: https://doi.org/10.5281/zenodo.4586597
  • Supplementary dataset 13: https://doi.org/10.5281/zenodo.4586660
  • Supplementary dataset 14: https://doi.org/10.5281/zenodo.4586732
  • Supplementary dataset 15: https://doi.org/10.5281/zenodo.4586767

Notes

This work was supported by funding from the Ecole Polytechnique Fédérale de Lausanne (EPFL), the 2015/313 ERASysAPP RobustYeast Project funded through SystemsX.ch, the Swiss Initiative for Systems Biology evaluated by the Swiss National Science Foundation, and the Swiss National Science Foundation grant 315230_163423. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Additional details

Funding

Swiss National Science Foundation
Computational Methods for modeling and analysis of large-scale metabolic networks 315230_163423