Journal
IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING
Volume 63, Issue 10, Pages 2007-2014Publisher
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
DOI: 10.1109/TBME.2016.2560762
Keywords
Computational biology; education; simulation; standards; systems biology; whole-cell (WC) modeling
Categories
Funding
- Volkswagen Foundation [88495]
- James S. McDonnell Foundation
- National Science Foundation [1548123]
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology [CE140100036]
- Biotechnology and Biological Sciences Research Council [1443802] Funding Source: researchfish
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [1548123] Funding Source: National Science Foundation
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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.
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