Toward community standards and software for whole-cell modeling

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias CzaudernaArthur P. Goldberg, Harold F. Gomez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knupfer, Matthias Konig, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Toure, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber

Research output: Contribution to journalArticleResearchpeer-review

40 Citations (Scopus)


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.

Original languageEnglish
Article number7489010
Pages (from-to)2007-2014
Number of pages8
JournalIEEE Transactions on Biomedical Engineering
Issue number10
Publication statusPublished - 1 Oct 2016


  • Computational biology
  • Education
  • Simulation
  • Standards
  • Systems biology
  • Whole-cell (WC) modeling

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