Abstract
Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae––an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8DB), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits.
Highlights
S. cerevisiae is a widely used cell factory[11,12] and is extensively used as a model organism in basic biological and medical research[13,14]
With Git and GitHub, each version of the yeast genome scale metabolic models (GEMs) can be released periodically, which helps to promote the simultaneous development of a model ecosystem around yeast GEM (Fig. 1b)
As part of this study, we have developed Yeast[8] aided by version control and open collaboration, which has provided a platform for a continued community-driven expansion of the model
Summary
S. cerevisiae is a widely used cell factory[11,12] and is extensively used as a model organism in basic biological and medical research[13,14]. We introduce a model ecosystem around this GEM, including ecYeast[8], a model incorporating enzyme constraints; panYeast[8] and coreYeast[8], representing the pan and core metabolic networks of 1011 S. cerevisiae strains; and proYeast8DB, a database containing 3D structures of metabolic proteins. This model ecosystem has the ability to meet wide application demands from the large scientific yeast community in systems and synthetic biology of yeast. With Yeast[8] and its model ecosystem, we demonstrate that the metabolism of yeast can be characterised and explored in a systematic way
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
