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Systems biology driven software design for the research enterprise.

Boyle J, Cavnor C, Killcoyne S, Shmulevich I.

BMC Bioinformatics. 2008 Jun 25;9:295.PMID: 18578887 [PubMed - indexed for MEDLINE]Related articlesFree article

caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

Oster S, Langella S, Hastings S, Ervin D, Madduri R, Phillips J, Kurc T, Siebenlist F, Covitz P, Shanbhag K, Foster I, Saltz J.

J Am Med Inform Assoc. 2008 Mar-Apr;15(2):138-49. Epub 2007 Dec 20.PMID: 18096909 [PubMed - indexed for MEDLINE]Related articlesFree article

The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.

Phillips J, Chilukuri R, Fragoso G, Warzel D, Covitz PA.

BMC Med Inform Decis Mak. 2006 Jan 6;6:2.PMID: 16398930 [PubMed - indexed for MEDLINE]Related articlesFree article

Talisman--rapid application development for the grid.

Oinn TM.

Bioinformatics. 2003;19 Suppl 1:i212-4.PMID: 12855460 [PubMed - indexed for MEDLINE]Related articlesFree article

An object-oriented programming system for the integration of internet-based bioinformatics resources.

Beveridge A.

Appl Bioinformatics. 2006;5(1):29-39.PMID: 16539535 [PubMed - indexed for MEDLINE]Related articles

caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability.

Komatsoulis GA, Warzel DB, Hartel FW, Shanbhag K, Chilukuri R, Fragoso G, Coronado S, Reeves DM, Hadfield JB, Ludet C, Covitz PA.

J Biomed Inform. 2008 Feb;41(1):106-23. Epub 2007 Apr 2.PMID: 17512259 [PubMed - indexed for MEDLINE]Related articlesFree article

Biowep: a workflow enactment portal for bioinformatics applications.

Romano P, Bartocci E, Bertolini G, De Paoli F, Marra D, Mauri G, Merelli E, Milanesi L.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S19.PMID: 17430563 [PubMed - indexed for MEDLINE]Related articlesFree article

The discovery net system for high throughput bioinformatics.

Rowe A, Kalaitzopoulos D, Osmond M, Ghanem M, Guo Y.

Bioinformatics. 2003;19 Suppl 1:i225-31.PMID: 12855463 [PubMed - indexed for MEDLINE]Related articlesFree article

Biological data integration using Semantic Web technologies.

Pasquier C.

Biochimie. 2008 Apr;90(4):584-94. Epub 2008 Feb 21.PMID: 18294970 [PubMed - indexed for MEDLINE]Related articles

Visualising biological data: a semantic approach to tool and database integration.

Pettifer S, Thorne D, McDermott P, Marsh J, Villéger A, Kell DB, Attwood TK.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S19.PMID: 19534744 [PubMed - indexed for MEDLINE]Related articlesFree article

The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches.

Yu ET, Hawkins A, Kuntz ID, Rahn LA, Rothfuss A, Sale K, Young MM, Yang CL, Pancerella CM, Fabris D.

J Proteome Res. 2008 Nov;7(11):4848-57. Epub 2008 Sep 26.PMID: 18817429 [PubMed - indexed for MEDLINE]Related articlesFree article

Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example.

Kano Y, Nguyen N, Saetre R, Yoshida K, Miyao Y, Tsuruoka Y, Matsubayashi Y, Ananiadou S, Tsujii J.

Pac Symp Biocomput. 2008:616-27.PMID: 18229720 [PubMed - indexed for MEDLINE]Related articlesFree article

caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.

Saltz J, Oster S, Hastings S, Langella S, Kurc T, Sanchez W, Kher M, Manisundaram A, Shanbhag K, Covitz P.

Bioinformatics. 2006 Aug 1;22(15):1910-6. Epub 2006 Jun 9.PMID: 16766552 [PubMed - indexed for MEDLINE]Related articlesFree article

Grid-based onto-technologies provide an effective instrument for biomedical research.

Joutchkov A, Tverdokhlebov N, Strizh I, Arnautov S, Golitsyn S.

Stud Health Technol Inform. 2005;112:37-46.PMID: 15923714 [PubMed - indexed for MEDLINE]Related articles

AlzPharm: integration of neurodegeneration data using RDF.

Lam HY, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH.

BMC Bioinformatics. 2007 May 9;8 Suppl 3:S4.PMID: 17493287 [PubMed - indexed for MEDLINE]Related articlesFree article

The GENIUS web portal--an easy way to access the Grid.

Andronico G, Barbera R, Falzone A, Lo Re G, Pulvirenti A, Rodolico A.

Methods Inf Med. 2005;44(2):215-20.PMID: 15924179 [PubMed - indexed for MEDLINE]Related articles

Advancing translational research with the Semantic Web.

Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH.

BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2. Review.PMID: 17493285 [PubMed - indexed for MEDLINE]Related articlesFree article

BioSPICE: access to the most current computational tools for biologists.

Garvey TD, Lincoln P, Pedersen CJ, Martin D, Johnson M.

OMICS. 2003 Winter;7(4):411-20.PMID: 14683613 [PubMed - indexed for MEDLINE]Related articles

BioMoby extensions to the Taverna workflow management and enactment software.

Kawas E, Senger M, Wilkinson MD.

BMC Bioinformatics. 2006 Nov 30;7:523.PMID: 17137515 [PubMed - indexed for MEDLINE]Related articlesFree article

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).

Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B.

Mol Oncol. 2009 Feb;3(1):9-17. Epub 2008 Dec 9.PMID: 19383362 [PubMed - indexed for MEDLINE]Related articles