Comparing simulation results of SBML capable simulators

被引：20

作者：

Bergmann, Frank T. ^{[1
,2
]}

Sauro, Herbert M. ^{[1
]}

机构：

[1] Univ Washington, Dept Bioengn, Seattle, WA 98195 USA

[2] Keck Grad Inst, Claremont, CA 91711 USA

来源：

BIOINFORMATICS | 2008年 / 24卷 / 17期

关键词：

D O I：

10.1093/bioinformatics/btn319

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Simulations are an essential tool when analyzing biochemical networks. Researchers and developers seeking to refine simulation tools or develop new ones would benefit greatly from being able to compare their simulation results. Summary: We present an approach to compare simulation results between several SBML capable simulators and provide a website for the community to share simulation results.

引用

页码：1963 / 1965

页数：3

共 17 条

[1] SBW - A modular framework for systems biology [J].

Bergmann, Frank T. ;

Sauro, Herbert M. .

PROCEEDINGS OF THE 2006 WINTER SIMULATION CONFERENCE, VOLS 1-5, 2006, :1637-+

[2]

*CELLML ORG, 2008, CELLML SIM MET SPEC

[3]

CONRAD E, 2006, OSCILL8

[4]

Dorf R. C., 2006, MODERN CONTROL SYSTE, V9th

[5] The SBML discrete stochastic models test suite [J].

Evans, Thomas W. ;

Gillespie, Colin S. ;

Wilkinson, Darren J. .

BIOINFORMATICS, 2008, 24 (02) :285-286

[6]

Gear C. W., 1971, NUMERICAL INITIAL VA

[7] COPASI- A COmplex PAthway SImulator [J].

Hoops, Stefan ;

Sahle, Sven ;

Gauges, Ralph ;

Lee, Christine ;

Pahle, Juergen ;

Simus, Natalia ;

Singhal, Mudita ;

Xu, Liang ;

Mendes, Pedro ;

Kummer, Ursula .

BIOINFORMATICS, 2006, 22 (24) :3067-3074

[8] The systems biology markup language (SBML):: a medium for representation and exchange of biochemical network models [J].

Hucka, M ;

Finney, A ;

Sauro, HM ;

Bolouri, H ;

Doyle, JC ;

Kitano, H ;

Arkin, AP ;

Bornstein, BJ ;

Bray, D ;

Cornish-Bowden, A ;

Cuellar, AA ;

Dronov, S ;

Gilles, ED ;

Ginkel, M ;

Gor, V ;

Goryanin, II ;

Hedley, WJ ;

Hodgman, TC ;

Hofmeyr, JH ;

Hunter, PJ ;

Juty, NS ;

Kasberger, JL ;

Kremling, A ;

Kummer, U ;

Le Novère, N ;

Loew, LM ;

Lucio, D ;

Mendes, P ;

Minch, E ;

Mjolsness, ED ;

Nakayama, Y ;

Nelson, MR ;

Nielsen, PF ;

Sakurada, T ;

Schaff, JC ;

Shapiro, BE ;

Shimizu, TS ;

Spence, HD ;

Stelling, J ;

Takahashi, K ;

Tomita, M ;

Wagner, J ;

Wang, J .

BIOINFORMATICS, 2003, 19 (04) :524-531

[9]

KOHN D, 2007, MIASE MINIMUM INFORM

[10] BioModels Database:: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems [J].

Le Novere, Nicolas ;

Bornstein, Benjamin ;

Broicher, Alexander ;

Courtot, Melanie ;

Donizelli, Marco ;

Dharuri, Harish ;

Li, Lu ;

Sauro, Herbert ;

Schilstra, Maria ;

Shapiro, Bruce ;

Snoep, Jacky L. ;

Hucka, Michael .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D689-D691

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