Toward community standards and software for whole-cell modeling

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 evalua...

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Detalles Bibliográficos
Autores principales: Waltemath, Dagmar, Karr, Jonathan R., Bergmann, Frank T., Chelliah, Vijayalakshmi, Hucka, Michael, Krantz, Marcus, Liebermeister, Wolfram, Mendes, Pedro, Myers, Chris J., Pir, Pinar, Alaybeyoglu, Begum, Aranganathan, Naveen K, Baghalian, Kambiz, Bittig, Arne T., Pinto Burke, Paulo E., Cantarelli, Matteo, Chew, Yin Hoon, Costa, Rafael S., Cursons, Joseph, Czauderna, Tobias, Goldberg, Arthur P., Gómez, Harold F., Hahn, Jens, Hameri, Tuure, Hernandez Gardiol, Daniel F., Kazakiewicz, Denis, Kiselev, Ilya, Knight-Schrijver, Vincent, Knüpfer, Christian, König, Matthias, Lee, Daewon, Lloret-Villas, Audald, Mandrik, Nikita, Medley, J. Kyle, Moreau, Bertrand, Naderi-Meshkin, Hojjat, Palaniappan, Sucheendra K., Priego-Espinosa, Daniel, Scharm, Martin, Sharma, Mahesh, Smallbone, Kieran, Stanford, Natalie J., Song, Je-Hoon, Theile, Tom, Tokic, Milenko, Tomar, Namrata, Touré, Vasundra, Uhlendorf, Jannis, Varusai, Thawfeek M, Watanabe, Leandro H., Wendland, Florian, Wolfien, Markus, Yurkovich, James T., Zhu, Yan, Zardilis, Argyris, Zhukova, Anna, Schreiber, Falk
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2016
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451320/
https://www.ncbi.nlm.nih.gov/pubmed/27305665
http://dx.doi.org/10.1109/TBME.2016.2560762
Descripción
Sumario: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 SBML. 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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