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Results: 14

1.

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T.

J Biomed Semantics. 2011 Aug 2;2:4. doi: 10.1186/2041-1480-2-4.

PMID:
21806842
[PubMed]
Free PMC Article
2.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.

PMID:
20727200
[PubMed]
Free PMC Article
3.

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

Li P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, Owen S, Withers D, Oinn T, Pocock MR, Goble CA, Oliver SG, Kell DB.

BMC Bioinformatics. 2008 Aug 7;9:334. doi: 10.1186/1471-2105-9-334.

PMID:
18687127
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The Taverna Interaction Service: enabling manual interaction in workflows.

Lanzén A, Oinn T.

Bioinformatics. 2008 Apr 15;24(8):1118-20. doi: 10.1093/bioinformatics/btn082. Epub 2008 Mar 12.

PMID:
18337261
[PubMed - indexed for MEDLINE]
Free Article
5.

Automated manipulation of systems biology models using libSBML within Taverna workflows.

Li P, Oinn T, Soiland S, Kell DB.

Bioinformatics. 2008 Jan 15;24(2):287-9. Epub 2007 Dec 1.

PMID:
18056069
[PubMed - indexed for MEDLINE]
Free Article
6.

SPINE bioinformatics and data-management aspects of high-throughput structural biology.

Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, Guillemot F, Hamer R, Ben Jelloul M, Laskowski RA, Laurent T, Longhi S, Lopez R, Luchinat C, Malet H, Mochel T, Morris RJ, Moulinier L, Oinn T, Pajon A, Peleg Y, Perrakis A, Poch O, Prilusky J, Rachedi A, Ripp R, Rosato A, Silman I, Stuart DI, Sussman JL, Thierry JC, Thompson JD, Thornton JM, Unger T, Vaughan B, Vranken W, Watson JD, Whamond G, Henrick K.

Acta Crystallogr D Biol Crystallogr. 2006 Oct;62(Pt 10):1184-95. Epub 2006 Sep 19. Review.

PMID:
17001095
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
16845108
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Exploring Williams-Beuren syndrome using myGrid.

Stevens RD, Tipney HJ, Wroe CJ, Oinn TM, Senger M, Lord PW, Goble CA, Brass A, Tassabehji M.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i303-10.

PMID:
15262813
[PubMed - indexed for MEDLINE]
Free Article
9.

Taverna: a tool for the composition and enactment of bioinformatics workflows.

Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P.

Bioinformatics. 2004 Nov 22;20(17):3045-54. Epub 2004 Jun 16.

PMID:
15201187
[PubMed - indexed for MEDLINE]
Free Article
10.

Talisman--rapid application development for the grid.

Oinn TM.

Bioinformatics. 2003;19 Suppl 1:i212-4.

PMID:
12855460
[PubMed - indexed for MEDLINE]
Free Article
11.

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R.

Genome Res. 2003 Apr;13(4):662-72. Epub 2003 Mar 12.

PMID:
12654719
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Interactive InterPro-based comparisons of proteins in whole genomes.

Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E.

Bioinformatics. 2002 Feb;18(2):374-5.

PMID:
11847096
[PubMed - indexed for MEDLINE]
Free Article
13.

InterPro--an integrated documentation resource for protein families, domains and functional sites.

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM; InterPro Consortium.

Bioinformatics. 2000 Dec;16(12):1145-50.

PMID:
11159333
[PubMed - indexed for MEDLINE]
Free Article
14.

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM.

Nucleic Acids Res. 2001 Jan 1;29(1):37-40.

PMID:
11125043
[PubMed - indexed for MEDLINE]
Free PMC Article

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