Our take on the practical aspects of genome-scale modeling

Some time ago, we started an initiative in the lab to collect all the best (and worst) practices on how to reconstruct, curate, and simulate genome-scale metabolic models (GEMs). A total of 7 colleagues, including a visiting PhD student Gioele Lazzari from the University of Verona, and a MSc rotation student Steven Wijnen, have put their forces together with Pranas to reflect on their experience, share tips, tricks, and caveats on the art of genome-scale modeling. After months of discussions, writing, and polishing, we would like to share the first public version of the handbook as an early Valentine’s present to the community :).

We cover topics from the very basics on data collection to make GEMs to rather advanced material, such as creating context-specific or community metabolic models. The handbook is accompanied by two Jupyter notebooks that can be used for training colleagues new to GEMs, or in your teaching. All materials are licensed under CC-BY-NC, which permits unrestricted non-commercial use of the materials as long as attribution is given.

It has been a great experience, and the initiative has been received very well by the lab members outside of this writing group. We invite fellow colleagues to contribute with ideas, thinking, and writing, if they see value in a community effort to share their best practices. You are always welcome to drop a line to Pranas on these matters.

Happy modeling!