SBML Level 3: an extensible format for the exchange and reuse of biological models

Keating, S. M.; Waltemath, D.; Koenig, M.; Zhang, F.; Draeger, A.; Chaouiya, C.; Bergmann, F.; Finney, A.; Gillespie, C. S.; Helikar, T.; Hoops, S.; Malik-Sheriff, R. S.; Moodie, S. L.; Moraru, I. I.; Myers, C.; Naldi, A.; Olivier, B. G.; Sahle, S.; Schaff, J. C.; Smith, L. P.; Swat, M. J.; Thieffry, D.; Watanabe, L.; Wilkinson, D. J.; Blinov, M. L.; Begley, K.; Faeder, J. R.; Gomez, H. F.; Hamm, T. M.; Inagaki, Y.; Liebermeister, W.; Lister, A. L.; Lucio, D.; Mjolsness, E.; Proctor, C.; Červený, Jan

doi:https://dx.doi.org/10.15252/msb.20199110

Počet záznamů: 1

SBML Level 3: an extensible format for the exchange and reuse of biological models

1.

SYSNO ASEP	0534211
Druh ASEP	J - Článek v odborném periodiku
Zařazení RIV	J - Článek v odborném periodiku
Poddruh J	Článek ve WOS
Název	SBML Level 3: an extensible format for the exchange and reuse of biological models
Tvůrce(i)	Keating, S. M. (US) Waltemath, D. (DE) Koenig, M. (DE) Zhang, F. (US) Draeger, A. (DE) Chaouiya, C. (FR) Bergmann, F. (DE) Finney, A. (GB) Gillespie, C. S. (GB) Helikar, T. (US) Hoops, S. (US) Malik-Sheriff, R. S. (GB) Moodie, S. L. (GB) Moraru, I. I. (US) Myers, C. (US) Naldi, A. (FR) Olivier, B. G. (NL) Sahle, S. (DE) Schaff, J. C. (US) Smith, L. P. (US) Swat, M. J. (GB) Thieffry, D. (FR) Watanabe, L. (US) Wilkinson, D. J. (GB) Blinov, M. L. (US) Begley, K. (US) Faeder, J. R. (US) Gomez, H. F. (CH) Hamm, T. M. (DE) Inagaki, Y. (JP) Liebermeister, W. (DE) Lister, A. L. (GB) Lucio, D. (US) Mjolsness, E. (US) Proctor, C. (GB) Červený, Jan (UEK-B)_{RID, ORCID, SAI}
Celkový počet autorů	53
Číslo článku	e9110
Zdroj.dok.	Molecular Systems Biology. - : Wiley - ISSN 1744-4292 Roč. 16, č. 8 (2020)
Poč.str.	21 s.
Jazyk dok.	eng - angličtina
Země vyd.	GB - Velká Británie
Klíč. slova	systems biology ; markup language ; simulation ; standards ; software ; information ; environment ; annotation ; repository ; ontology ; computational modeling ; file format ; interoperability ; reproducibility ; systems biology
Vědní obor RIV	IN - Informatika
Obor OECD	Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
CEP	LM2015055 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy
	GA18-24397S GA ČR - Grantová agentura ČR
	EF16_026/0008413 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy
Způsob publikování	Open access
Institucionální podpora	UEK-B - RVO:86652079
UT WOS	000567939700007
EID SCOPUS	85089933733
DOI	10.15252/msb.20199110
Anotace	Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developedSBMLLevel 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades ofSBMLand a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and howSBMLLevel 3 provides the foundation needed to support this evolution.
Pracoviště	Ústav výzkumu globální změny
Kontakt	Nikola Šviková, svikova.n@czechglobe.cz, Tel.: 511 192 268
Rok sběru	2021
Elektronická adresa	https://www.embopress.org/doi/full/10.15252/msb.20199110

Počet záznamů: 1