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Toward Community Standards and Software for Whole-Cell Modeling.

Authors :: Waltemath D
Karr JR
Bergmann FT
Chelliah V
Hucka M
Krantz M
Liebermeister W
Mendes P
Myers CJ
Pir P
Alaybeyoglu B
Aranganathan NK
Baghalian K
Bittig AT
Burke PE
Cantarelli M
Chew YH
Costa RS
Cursons J
Czauderna T
Goldberg AP
Gomez HF
Hahn J
Hameri T
Gardiol DF
Kazakiewicz D
Kiselev I
Knight-Schrijver V
Knupfer C
Konig M
Lee D
Lloret-Villas A
Mandrik N
Medley JK
Moreau B
Naderi-Meshkin H
Palaniappan SK
Priego-Espinosa D
Scharm M
Sharma M
Smallbone K
Stanford NJ
Song JH
Theile T
Tokic M
Tomar N
Toure V
Uhlendorf J
Varusai TM
Watanabe LH
Wendland F
Wolfien M
Yurkovich JT
Zhu Y
Zardilis A
Zhukova A
Schreiber F
Source :: IEEE transactions on bio-medical engineering [IEEE Trans Biomed Eng] 2016 Oct; Vol. 63 (10), pp. 2007-14. Date of Electronic Publication: 2016 Jun 10.
Publication Year :: 2016
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.<br />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.<br />Results: Our analysis revealed several challenges to representing WC models using the current standards.<br />Conclusion: We, therefore, propose several new WC modeling standards, software, and databases.<br />Significance: We anticipate that these new standards and software will enable more comprehensive models.