Toward community standards and software for whole-cell modeling

Waltemath, Dagmar and Karr, Jonathan and Bergmann, Frank and Chelliah, Vijayalakshmi and Hucka, Michael and Krantz, Marcus and Liebermeister, Wolfram and Mendes, Pedro and Myers, Chris and Pir, Pinar and Alaybeyoglu, Begum and Aranganathan, Naveen and Baghalian, Kambiz and Bittig, Arne T. and Burke, Paulo and Cantarelli, Matteo and Chew, Yin and Costa, Rafael and Cursons, Joseph and Czauderna, Tobias and Goldberg, Arthur and Gomez, Harold and Hahn, Jens and Hameri, Tuure and Gardiol, Daniel and Kazakiewicz, Denis and Kiselev, Ilya and Knight-Schrijver, Vincent and Knupfer, Christian and Konig, Matthias and Lee, Daewon and Lloret-Villas, Audald and Mandrik, Nikita and Medley, J and Moreau, Bertrand and Naderi-Meshkin, Hojjat and Palaniappan, Sucheendra and Priego-Espinosa, Daniel and Scharm, Martin and Sharma, Mahesh and Smallbone, Kieran and Stanford, Natalie and Song, Je-Hoon and Theile, Tom and Tokic, Milenko and Tomar, Namrata and Toure, Vasundra and Uhlendorf, Jannis and Varusai, Thawfeek and Watanabe, Leandro and Wendland, Florian and Wolfien, Markus and Yurkovich, James and Zhu, Yan and Zardilis, Argyris and Zhukova, Anna and Schreiber, Falk (2016) Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering, 63 (10), pp. 2007-2014. ISSN 0018-9294.

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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.

Item Type: Article