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Results: 1 to 20 of 101

1.

A C library for retrieving specific reactions from the BioModels database.

Neal ML, Galdzicki M, Gallimore JT, Sauro HM.

Bioinformatics. 2014 Jan 1;30(1):129-30. doi: 10.1093/bioinformatics/btt567. Epub 2013 Sep 29.

PMID:
24078714
[PubMed - indexed for MEDLINE]
2.

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.

Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C.

BMC Syst Biol. 2010 Jun 29;4:92. doi: 10.1186/1752-0509-4-92.

PMID:
20587024
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Qualitative translation of relations from BioPAX to SBML qual.

Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, Zell A.

Bioinformatics. 2012 Oct 15;28(20):2648-53. doi: 10.1093/bioinformatics/bts508. Epub 2012 Aug 24.

PMID:
22923304
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

libAnnotationSBML: a library for exploiting SBML annotations.

Swainston N, Mendes P.

Bioinformatics. 2009 Sep 1;25(17):2292-3. doi: 10.1093/bioinformatics/btp392. Epub 2009 Jun 26.

PMID:
19561017
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

LibSBMLSim: a reference implementation of fully functional SBML simulator.

Takizawa H, Nakamura K, Tabira A, Chikahara Y, Matsui T, Hiroi N, Funahashi A.

Bioinformatics. 2013 Jun 1;29(11):1474-6. doi: 10.1093/bioinformatics/btt157. Epub 2013 Apr 5.

PMID:
23564843
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

SBMLToolbox: an SBML toolbox for MATLAB users.

Keating SM, Bornstein BJ, Finney A, Hucka M.

Bioinformatics. 2006 May 15;22(10):1275-7. Epub 2006 Mar 30.

PMID:
16574696
[PubMed - indexed for MEDLINE]
Free Article
7.

LibSBML: an API library for SBML.

Bornstein BJ, Keating SM, Jouraku A, Hucka M.

Bioinformatics. 2008 Mar 15;24(6):880-1. doi: 10.1093/bioinformatics/btn051. Epub 2008 Feb 5.

PMID:
18252737
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

SBML export interface for the systems biology toolbox for MATLAB.

Schmidt H, Drews G, Vera J, Wolkenhauer O.

Bioinformatics. 2007 May 15;23(10):1297-8. Epub 2007 Mar 23.

PMID:
17384017
[PubMed - indexed for MEDLINE]
Free Article
9.

JSBML: a flexible Java library for working with SBML.

Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M.

Bioinformatics. 2011 Aug 1;27(15):2167-8. doi: 10.1093/bioinformatics/btr361. Epub 2011 Jun 22.

PMID:
21697129
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

Li C, Courtot M, Le Novère N, Laibe C.

Brief Bioinform. 2010 May;11(3):270-7. doi: 10.1093/bib/bbp056. Epub 2009 Nov 25.

PMID:
19939940
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

BioModels Database: a repository of mathematical models of biological processes.

Chelliah V, Laibe C, Le Novère N.

Methods Mol Biol. 2013;1021:189-99. doi: 10.1007/978-1-62703-450-0_10.

PMID:
23715986
[PubMed - indexed for MEDLINE]
12.

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

Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D689-91.

PMID:
16381960
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

MyMolDB: a micromolecular database solution with open source and free components.

Xia B, Tai ZF, Gu YC, Li BJ, Ding LS, Zhou Y.

J Comput Chem. 2011 Oct;32(13):2942-8. doi: 10.1002/jcc.21874. Epub 2011 Jul 5.

PMID:
21728180
[PubMed - indexed for MEDLINE]
14.

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

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; SBML Forum.

Bioinformatics. 2003 Mar 1;19(4):524-31.

PMID:
12611808
[PubMed - indexed for MEDLINE]
Free Article
15.

Pattern search in BioPAX models.

Babur Ö, Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E.

Bioinformatics. 2014 Jan 1;30(1):139-40. doi: 10.1093/bioinformatics/btt539. Epub 2013 Sep 16.

PMID:
24045775
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.

Zi Z.

Bioinformatics. 2011 Apr 1;27(7):1028-9. doi: 10.1093/bioinformatics/btr038. Epub 2011 Feb 8.

PMID:
21303862
[PubMed - indexed for MEDLINE]
Free Article
17.

Annotation and merging of SBML models with semanticSBML.

Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W.

Bioinformatics. 2010 Feb 1;26(3):421-2. doi: 10.1093/bioinformatics/btp642. Epub 2009 Nov 17.

PMID:
19933161
[PubMed - indexed for MEDLINE]
Free Article
18.

Tools for the SBML Community.

Gillespie CS, Wilkinson DJ, Proctor CJ, Shanley DP, Boys RJ, Kirkwood TB.

Bioinformatics. 2006 Mar 1;22(5):628-9. Epub 2006 Jan 12.

PMID:
16410323
[PubMed - indexed for MEDLINE]
Free Article
19.

The markup is the model: reasoning about systems biology models in the Semantic Web era.

Kell DB, Mendes P.

J Theor Biol. 2008 Jun 7;252(3):538-43. Epub 2007 Dec 3. Review.

PMID:
18054049
[PubMed - indexed for MEDLINE]
20.

SBML2TikZ: supporting the SBML render extension in LaTeX.

Shen SY, Bergmann F, Sauro HM.

Bioinformatics. 2010 Nov 1;26(21):2794-5. doi: 10.1093/bioinformatics/btq512. Epub 2010 Sep 9.

PMID:
20829443
[PubMed - indexed for MEDLINE]
Free PMC Article

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