This repository provides resources and model files for the genome-scale model iSace1144 that accompanies the following manuscripts:
Proteome capacity constraints favor respiratory ATP generation
Yihui Shen, Hoang V. Dinh, Edward Cruz, Catherine M. Call, Heide Baron, Rolf-Peter Ryseck, Jimmy Pratas, Arjuna Subramanian, Zia Fatma, Daniel Weilandt, Sudharsan Dwaraknath, Tianxia Xiao, John I. Hendry, Vinh Tran, Lifeng Yang, Yasuo Yoshikuni, Huimin Zhao, Costas D. Maranas, Martin Wuhr, and Joshua D. Rabinowitz
bioRxiv 2022.08.10.503479; doi: https://doi.org/10.1101/2022.08.10.503479
(Original reconstruction. The model is sourced from yeast 8.3.4 (at https://github.com/SysBioChalmers/yeast-GEM) and then is reformatted to the format in another yeast model (at https://github.com/maranasgroup/iRhto_memote) plus additional curations and fixes.)
Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis
Hoang V. Dinh and Costas D. Maranas
bioRxiv 2022.09.20.508694; doi: https://doi.org/10.1101/2022.09.20.508694
(Further important updates to the model's growth and non-growth associated ATP maintenance (i.e., GAM and NGAM) parameters have been added.)
- Reactions and metabolites' IDs are in BiGG format
- Simplified lipid metabolism: modeling lipid species with average acyl-group representation rather than listing all specific lipid species containing combinations of acyl groups of different chain lengths.
- Updated and reformatted biomass reaction (see ./resources/)
- Content curations and fixes (see ./change_log/*)
- Condition-specific GAM and NGAM values derived from experimental data for: (i) Batch, anaerobic, (ii) C-lim, anaerobic, (iii) Batch and C-lim, aerobic, (iv) N-lim and aerobic