Data/Software repository of LCSB (EPFL)
Published May 21, 2021 | Version v2
Dataset Open

Dataset - A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Authors/Creators

  • 1. EPFL

Description

Models and dataset needed to reproduce the results for the manuscript "A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics" by O. Oftadeh et all

The code to generate yETFL models and reproduce the results of this manuscript is available at https://github.com/EPFL-LCSB/yetfl/ and https://gitlab.com/EPFL-LCSB/yetfl/. The execution of this code is dependent on the ETFL repository available at https://github.com/EPFL-LCSB/etf and https://gitlab.com/EPFL-LCSB/etfl.

Models:

  • File input_models.zip contains a structure with thermodynamically and stoichiometrically curated genome-scale model of S. cerevisiae in MATLAB's mat format (based on Yeast8.3.4)

Datasets:

  • File thermo_data_yeast8.mat contains a thermodynamic database for the standard formation free Gibbs energy of formation of different metabolites in Yeast8.
  • File info_yeast.zip contains data needed to run the code stored on the  GitHub and Gitlab repositories.

Notes

This work has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 814408 (OO), the Swiss National Science Foundation under grant agreement 200021_188623 (OO), the European Union's Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 722287 (PS), the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska Curie grant agreement No 675585 (MM), and the École Polytechnique Fédérale de Lausanne.

Files

info_yeast.zip

Files (2.7 MB)

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md5:4cb841f7d263a263769367b4395b5ed7
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md5:c93eb4d54fdd8bba4f2e25c703a3d9b5
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Additional details

Funding

European Commission
SyMBioSys - Systematic Models for Biological Systems Engineering Training Network 675585
European Commission
SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway 814408
European Commission
PAcMEN - Predictive and Accelerated Metabolic Engineering Network 722287
Swiss National Science Foundation
Models, Algorithms, Software and Repositories for Synthetic Biology and Biotechnology 200021_188623