After the successful Whole Cell Modeling Summer School in Rostock in March 2015, we ran a second meeting in Salt Lake City in 2015, co-located with COMBINE 2015. Both were practical meetings for young scientists aiming at recoding a Whole Cell model in standard formats and using open tools.
We provide all code on github. The outcomes of the meetings, a discussion on the suitability of standards for whole cell modells, and our experiences with organising hands-on educational events are described in our new paper entitled: “Toward community standards and software for whole-cell modeling” in the journal IEEE Transactions on Biomedical Engineering.
“Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells.
Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML.
Results: Our analysis revealed several challenges to representing WC models using the current standards.
Conclusion: We, therefore, propose several new WC modeling standards, software, and databases.
Significance: We anticipate that these new standards and software will enable more comprehensive models.”