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Items: 18

1.

Controlled vocabularies and semantics in systems biology.

Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N.

Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77.

2.

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.

3.

Opal web services for biomedical applications.

Ren J, Williams N, Clementi L, Krishnan S, Li WW.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W724-31. doi: 10.1093/nar/gkq503. Epub 2010 Jun 6.

4.

myExperiment: a repository and social network for the sharing of bioinformatics workflows.

Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W677-82. doi: 10.1093/nar/gkq429. Epub 2010 May 25.

5.

BioCatalogue: a universal catalogue of web services for the life sciences.

Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W689-94. doi: 10.1093/nar/gkq394. Epub 2010 May 19.

6.

Web-based applications for building, managing and analysing kinetic models of biological systems.

Lee DY, Saha R, Yusufi FN, Park W, Karimi IA.

Brief Bioinform. 2009 Jan;10(1):65-74. doi: 10.1093/bib/bbn039. Epub 2008 Sep 19.

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.

8.

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

BioMoby Consortium, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano M, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A.

Brief Bioinform. 2008 May;9(3):220-31. doi: 10.1093/bib/bbn003. Epub 2008 Jan 31. Review.

PMID:
18238804
9.

Sensitivity analysis of intracellular signaling pathway kinetics predicts targets for stem cell fate control.

Mahdavi A, Davey RE, Bhola P, Yin T, Zandstra PW.

PLoS Comput Biol. 2007 Jul;3(7):e130.

10.

Physicochemical modelling of cell signalling pathways.

Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK.

Nat Cell Biol. 2006 Nov;8(11):1195-203. Review.

PMID:
17060902
11.

Taverna: a tool for building and running workflows of services.

Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32.

12.

Modeling the effects of HER/ErbB1-3 coexpression on receptor dimerization and biological response.

Shankaran H, Wiley HS, Resat H.

Biophys J. 2006 Jun 1;90(11):3993-4009. Epub 2006 Mar 13.

13.

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.

Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C.

Bioinformatics. 2006 Jun 1;22(11):1406-7. Epub 2006 Mar 9.

PMID:
16527832
14.

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.

15.

Sensitivity analysis for chemical models.

Saltelli A, Ratto M, Tarantola S, Campolongo F.

Chem Rev. 2005 Jul;105(7):2811-28. No abstract available.

PMID:
16011325
16.

In silico identification of the key components and steps in IFN-gamma induced JAK-STAT signaling pathway.

Zi Z, Cho KH, Sung MH, Xia X, Zheng J, Sun Z.

FEBS Lett. 2005 Feb 14;579(5):1101-8.

17.

Modeling and simulation of intracellular dynamics: choosing an appropriate framework.

Wolkenhauer O, Ullah M, Kolch W, Cho KH.

IEEE Trans Nanobioscience. 2004 Sep;3(3):200-7.

PMID:
15473072
18.

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

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