학술논문
Toward Community Standards and Software for Whole-Cell Modeling
Document Type
Periodical
Author
Waltemath, D.; Karr, J.R.; Bergmann, F.T.; Chelliah, V.; Hucka, M.; Krantz, M.; Liebermeister, W.; Mendes, P.; Myers, C.J.; Pir, P.; Alaybeyoglu, B.; Aranganathan, N.K.; Baghalian, K.; Bittig, A.T.; Burke, P.E.P.; Cantarelli, M.; Chew, Y.H.; Costa, R.S.; Cursons, J.; Czauderna, T.; Goldberg, A.P.; Gomez, H.F.; Hahn, J.; Hameri, T.; Gardiol, D.F.H.; Kazakiewicz, D.; Kiselev, I.; Knight-Schrijver, V.; Knupfer, C.; Konig, M.; Lee, D.; Lloret-Villas, A.; Mandrik, N.; Medley, J.K.; Moreau, B.; Naderi-Meshkin, H.; Palaniappan, S.K.; Priego-Espinosa, D.; Scharm, M.; Sharma, M.; Smallbone, K.; Stanford, N.J.; Song, J.; Theile, T.; Tokic, M.; Tomar, N.; Toure, V.; Uhlendorf, J.; Varusai, T.M.; Watanabe, L.H.; Wendland, F.; Wolfien, M.; Yurkovich, J.T.; Zhu, Y.; Zardilis, A.; Zhukova, A.; Schreiber, F.
Source
IEEE Transactions on Biomedical Engineering IEEE Trans. Biomed. Eng. Biomedical Engineering, IEEE Transactions on. 63(10):2007-2014 Oct, 2016
Subject
Language
ISSN
0018-9294
1558-2531
1558-2531
Abstract
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.