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Toward Community Standards and Software for Whole-Cell Modeling
Objective:
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 the Systems Biology Markup Language.
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.
