Toward Community Standards and Software for Whole-Cell Modeling

• Published in: IEEE transactions on biomedical engineering Vol. 63; no. 10; pp. 2007 - 2014
• Main Authors: Waltemath, Dagmar, Pir, Pinar, Alaybeyoglu, Begum, Aranganathan, Naveen K, Baghalian, Kambiz, Bittig, Arne T., Burke, Paulo E. Pinto, Cantarelli, Matteo, Chew, Yin Hoon, Costa, Rafael S., Cursons, Joseph, Karr, Jonathan R., Czauderna, Tobias, Goldberg, Arthur P., Gomez, Harold F., Hahn, Jens, Hameri, Tuure, Gardiol, Daniel F. Hernandez, Kazakiewicz, Denis, Kiselev, Ilya, Knight-Schrijver, Vincent, Knupfer, Christian, Bergmann, Frank T., Konig, Matthias, Lee, Daewon, Lloret-Villas, Audald, Mandrik, Nikita, Medley, J. Kyle, Moreau, Bertrand, Naderi-Meshkin, Hojjat, Palaniappan, Sucheendra K., Priego-Espinosa, Daniel, Scharm, Martin, Chelliah, Vijayalakshmi, Sharma, Mahesh, Smallbone, Kieran, Stanford, Natalie J., Song, Je-Hoon, Theile, Tom, Tokic, Milenko, Tomar, Namrata, Toure, Vasundra, Uhlendorf, Jannis, Varusai, Thawfeek M, Hucka, Michael, Watanabe, Leandro H., Wendland, Florian, Wolfien, Markus, Yurkovich, James T., Zhu, Yan, Zardilis, Argyris, Zhukova, Anna, Schreiber, Falk, Krantz, Marcus, Liebermeister, Wolfram, Mendes, Pedro, Myers, Chris J.
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.10.2016; Institute of Electrical and Electronics Engineers
• Subjects: Bioinformatics; Biological system modeling; Computational Biology; Computational modeling; Computer Science; Computer Simulation; Cytological Techniques; education; Female; Humans; Male; Mathematical model; Models, Biological; Optical wavelength conversion; simulation; Software; Systems biology; Systems Biology - education; Systems Biology - organization & administration; Systems Biology - standards; whole-cell (WC) modeling; standards; systems biology; education; whole-cell (WC) modeling; simulation; Computational biology
• ISSN: 0018-9294; 1558-2531; 1558-2531
• DOI: 10.1109/TBME.2016.2560762

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.