Toward community standards and software for whole-cell modeling


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.


PubMed ID: 27305665

Projects: Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Publication type: Not specified

Journal: IEEE Trans Biomed Eng

Citation: IEEE Trans Biomed Eng. 2016 Jun 10.

Date Published: 16th Jun 2016

Registered Mode: Not specified

Authors: D. Waltemath, J. Karr, F. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C. Myers, P. Pir, B. Alaybeyoglu, N. Aranganathan, K. Baghalian, A. Bittig, P. Burke, M. Cantarelli, Y. Chew, R. Costa, J. Cursons, T. Czauderna, A. Goldberg, H. Gomez, J. Hahn, T. Hameri, D. Gardiol, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knupfer, M. Konig, D. Lee, A. Lloret-Villas, N. Mandrik, J. Medley, B. Moreau, H. Naderi-Meshkin, S. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N. Stanford, J. H. Song, T. Theile, M. Tokic, N. Tomar, V. Toure, J. Uhlendorf, T. Varusai, L. Watanabe, F. Wendland, M. Wolfien, J. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova, F. Schreiber

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Created: 25th Jul 2016 at 08:43

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