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.

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.