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Results: 1 to 20 of 102

1.

Standard virtual biological parts: a repository of modular modeling components for synthetic biology.

Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A.

Bioinformatics. 2010 Apr 1;26(7):925-31. doi: 10.1093/bioinformatics/btq063. Epub 2010 Feb 16.

PMID:
20160009
[PubMed - indexed for MEDLINE]
Free Article
2.

The CellML Model Repository.

Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF.

Bioinformatics. 2008 Sep 15;24(18):2122-3. doi: 10.1093/bioinformatics/btn390. Epub 2008 Jul 25.

PMID:
18658182
[PubMed - indexed for MEDLINE]
Free Article
3.

The Physiome Model Repository 2.

Yu T, Lloyd CM, Nickerson DP, Cooling MT, Miller AK, Garny A, Terkildsen JR, Lawson J, Britten RD, Hunter PJ, Nielsen PM.

Bioinformatics. 2011 Mar 1;27(5):743-4. doi: 10.1093/bioinformatics/btq723. Epub 2011 Jan 6.

PMID:
21216774
[PubMed - indexed for MEDLINE]
Free Article
4.

A method for visualizing CellML models.

Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.

Bioinformatics. 2009 Nov 15;25(22):3012-9. doi: 10.1093/bioinformatics/btp495. Epub 2009 Aug 24.

PMID:
19703920
[PubMed - indexed for MEDLINE]
Free Article
5.

Revision history aware repositories of computational models of biological systems.

Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead MD, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, Nielsen PM.

BMC Bioinformatics. 2011 Jan 14;12:22. doi: 10.1186/1471-2105-12-22.

PMID:
21235804
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

An overview of the CellML API and its implementation.

Miller AK, Marsh J, Reeve A, Garny A, Britten R, Halstead M, Cooper J, Nickerson DP, Nielsen PF.

BMC Bioinformatics. 2010 Apr 8;11:178. doi: 10.1186/1471-2105-11-178.

PMID:
20377909
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Standard biological parts knowledgebase.

Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH.

PLoS One. 2011 Feb 24;6(2):e17005. doi: 10.1371/journal.pone.0017005.

PMID:
21390321
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ 3rd, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD.

Bioinformatics. 2006 Apr 1;22(7):874-82. Epub 2006 Jan 12.

PMID:
16410321
[PubMed - indexed for MEDLINE]
Free Article
9.

Ranked retrieval of Computational Biology models.

Henkel R, Endler L, Peters A, Le Novère N, Waltemath D.

BMC Bioinformatics. 2010 Aug 11;11:423. doi: 10.1186/1471-2105-11-423.

PMID:
20701772
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.

Rialle S, Felicori L, Dias-Lopes C, Pérès S, El Atia S, Thierry AR, Amar P, Molina F.

Bioinformatics. 2010 Sep 15;26(18):2298-304. doi: 10.1093/bioinformatics/btq409. Epub 2010 Jul 13.

PMID:
20628073
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

CellML2SBML: conversion of CellML into SBML.

Schilstra MJ, Li L, Matthews J, Finney A, Hucka M, Le Novère N.

Bioinformatics. 2006 Apr 15;22(8):1018-20. Epub 2006 Feb 10.

PMID:
16473867
[PubMed - indexed for MEDLINE]
Free Article
12.

PROMOT: modular modeling for systems biology.

Mirschel S, Steinmetz K, Rempel M, Ginkel M, Gilles ED.

Bioinformatics. 2009 Mar 1;25(5):687-9. doi: 10.1093/bioinformatics/btp029. Epub 2009 Jan 15.

PMID:
19147665
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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]
14.

Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model.

Nickerson D, Buist M.

Prog Biophys Mol Biol. 2008 Sep;98(1):38-51. doi: 10.1016/j.pbiomolbio.2008.05.006. Epub 2008 Jun 23. Review.

PMID:
18606438
[PubMed - indexed for MEDLINE]
15.

Biophysical annotation and representation of CellML models.

Wimalaratne SM, Halstead MD, Lloyd CM, Crampin EJ, Nielsen PF.

Bioinformatics. 2009 Sep 1;25(17):2263-70. doi: 10.1093/bioinformatics/btp391. Epub 2009 Jun 29.

PMID:
19564239
[PubMed - indexed for MEDLINE]
Free Article
16.

Payao: a community platform for SBML pathway model curation.

Matsuoka Y, Ghosh S, Kikuchi N, Kitano H.

Bioinformatics. 2010 May 15;26(10):1381-3. doi: 10.1093/bioinformatics/btq143. Epub 2010 Apr 5.

PMID:
20371497
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Facilitating modularity and reuse: guidelines for structuring CellML 1.1 models by isolating common biophysical concepts.

Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.

Exp Physiol. 2009 May;94(5):472-85. doi: 10.1113/expphysiol.2008.045161. Epub 2009 Jan 16.

PMID:
19151076
[PubMed - indexed for MEDLINE]
Free Article
18.

An architecture for integrating cancer model repositories.

Sfakianakis S, Sakkalis V, Marias K, Stamatakos G, McKeever S, Deisboeck TS, Graf N.

Conf Proc IEEE Eng Med Biol Soc. 2012;2012:6628-31. doi: 10.1109/EMBC.2012.6347514.

PMID:
23367449
[PubMed - indexed for MEDLINE]
19.

TinkerCell: modular CAD tool for synthetic biology.

Chandran D, Bergmann FT, Sauro HM.

J Biol Eng. 2009 Oct 29;3:19. doi: 10.1186/1754-1611-3-19.

PMID:
19874625
[PubMed]
Free PMC Article
20.

A BioBrick compatible strategy for genetic modification of plants.

Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, Silver PA.

J Biol Eng. 2012 Jun 20;6(1):8. doi: 10.1186/1754-1611-6-8.

PMID:
22716313
[PubMed]
Free PMC Article

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