Models and main dataset - Constraint-based metabolic control analysis for rational strain engineering
Models and main dataset - Constraint-based metabolic control analysis for rational strain engineering
DOI10.5281/zenodo.4501189Zenodo4501189MaRDI QIDQ6702643FDOQ6702643
Dataset published at Zenodo repository.
Ljubiša Mišković, Meric Ataman, Vassily Hatzimanikatis, Hameri Tuure, Tsouka Sophia
Publication date: 4 February 2021
Copyright license: Creative Commons Attribution 4.0 International
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 MATLABs 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 50000 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
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