Yeast-GEM: Reviving the Consensus Genome-Scale Model of S. Cerevisiae As a Standard in the Community

Genome-scale models (GEMs) are essential tools for understanding and computing metabolism. However, as they are so large (thousands of metabolites and reactions), it becomes challenging to keep track of changes between two versions of the same model. Furthermore, a framework is needed for researchers to work on a single model at the same time, without creating conflicts.

Here, we have brought back to life the GEM for Saccharomyces cerevisiae as yeast-GEM: a version controlled model publicly available for open collaboration. Changes are tracked with Git, can be easily visualized on Github, and are linked to complementary data and scripts, so anyone can know what was changed, who did it and why. By hosting the model in Github we also allow model developers to work on parallel, we periodically release new versions of the model, and we publicly display current and future work, organized in different projects. Additionally, we take advantage of memote, the metabolic model test suite, to display the quality of our model as we work on it.

We will present numerous model improvements that we have performed using this framework, such as an extensive curation to metabolites, reactions and genes based on new genome annotation; the introduction of SLIME reactions, which Split Lipids Into Measurable Entities for properly representing limitations on both the lipid classes and at the same time the acyl chains; and a growth validation study under different carbon/nitrogen/sulphur/phosphate sources.

Finally, we will show how we connect this model to GECKO, a toolbox for adding enzyme constraints to a GEM, and achieve a continuous synchrony of the metabolic model (yeast-GEM) and the enzyme-constrained model (ecYeast-GEM), to offer to the community a set of ready to use constrained-based models of yeast. See more of yeast-GEM, and contribute if you wish, at https://github.com/SysBioChalmers/yeast-GEM