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. ; The Rostock and Utah meetings were supported by the Volkswagen Foundation (Grant 88495 to D. Waltemath and F. Schreiber). The work of J. R. Karr was supported by the James S. McDonnell Foundation Postdoctoral Fellowship Award in Studying Complex Systems and the National Science Foundation under Grant 1548123. The work of J. Cursons was supported by the Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology through Project CE140100036. Asterisk indicates corresponding authors. ; computational biology; education; simulation; standards; systems biology; whole-cell (WC) modeling