Toward Community Standards and Software for Whole-Cell Modeling

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.

doi:10.1109/TBME.2016.2560762

Инд. авторы:	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:	DOI: 10.1109/TBME.2016.2560762; PubMed: 27305665; SCOPUS: 2-s2.0-84993897548; WoS: 000384570200004;
Реферат:	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:	SYSTEMS; Computational biology; education; simulation; standards; systems biology; whole-cell (WC) modeling; MARKUP LANGUAGE SBML; LEVEL 3; MAPS; SIMULATION; CONSTRAINTS; RECONSTRUCTION;
Издано:	2016
Физ. характеристика:	7489010, с.2007-2014