| Автор(ы): | Waltemath D., Karr J.R., Bergmann F.T., Chelliah V., Hucka M., Krantz M., Liebermeister W., Mendes P., Myers C.J., Pir P., Alaybeyoglu B., Aranganathan N.K., Baghalian K., Bittig A.T., Burke P.E.P., Cantarelli M., Chew Y.H., Costa R.S., Cursons J., Czauderna T., Goldberg A.P., Gomez H.F., Hahn J., Hameri T., Gardiol D.F.H., Kazakiewicz D., Kiselev I., Knight-Schrijver V., Knupfer C., Konig M., Lee D., Lloret-Villas A., Mandrik N., Medley J.K., Moreau B., Naderi-Meshkin H., Palaniappan S.K., Priego-Espinosa D., Scharm M., Sharma M., Smallbone K., Stanford N.J., Song J.H., Theile T., Tokic M., Tomar N., Toure V., Uhlendorf J., Varusai T.M., Watanabe L.H., Wendland F., Wolfien M., Yurkovich J.T., Zhu Y., Zardilis A., Zhukova A., Schreiber F. |
| Заглавие: | Toward Community Standards and Software for Whole-Cell Modeling |
| Библ. ссылка: | Waltemath D. et al. Toward Community Standards and Software for Whole-Cell Modeling // IEEE Transactions on Biomedical Engineering. - 2016. - Vol.63. - Iss. 10. - Art.7489010. - ISSN 0018-9294. - EISSN 1558-2531. |
| Внешние системы: | PubMed: 27305665; DOI: 10.1109/TBME.2016.2560762; WoS: 000384570200004; SCOPUS: 2-s2.0-84993897548; |
| Доп. информация: | eng: 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. |
| Ключевые слова: | MARKUP LANGUAGE SBML; LEVEL 3; MAPS; SIMULATION; CONSTRAINTS; systems biology; education; simulation; standards; RECONSTRUCTION; SYSTEMS; Computational biology; whole-cell (WC) modeling; |
| Год издания: | 2016 |
| Страницы или номер статьи: | 7489010, с.2007-2014 |
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