Toward Community Standards and Software for Whole-Cell Modeling

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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.
Publisher
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
Issue Date
2016-10
Language
English
Article Type
Article
Keywords

MARKUP LANGUAGE SBML; LEVEL 3; SYSTEMS; RECONSTRUCTION; CONSTRAINTS; SIMULATION; MAPS

Citation

IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, v.63, no.10, pp.2007 - 2014

ISSN
0018-9294
DOI
10.1109/TBME.2016.2560762
URI
http://hdl.handle.net/10203/213932
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