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

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 evaluat...