XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 279-

  Wagener, Johannes ^a   Spjuth, Ola ^b   Willighagen, Egon L ^b   Wikberg, Jarl E S ^b  

^a UNIVERSITY OF MUNICH   (Germany)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DISTRIBUTED DATABASE SYSTEMS; HTTP; HYPERTEXT SYSTEMS; INTERNET PROTOCOLS; SEMANTICS; WEBSITES;

ASYNCHRONOUS COMMUNICATION; ASYNCHRONOUS INVOCATION; ASYNCHRONOUS WEB SERVICE; EXTENSIBLE MESSAGING AND PRESENCE PROTOCOLS; INPUT AND OUTPUTS; REPRESENTATIONAL STATE TRANSFER; SIMPLE OBJECT ACCESS PROTOCOLS; WEB SERVICE TECHNOLOGY;

WEB SERVICES;

ARTICLE; BIOINFORMATICS; CLIENT SERVER APPLICATION; COMPUTER GRAPHICS; COMPUTER LANGUAGE; COMPUTER NETWORK; COMPUTER PROGRAM; INFORMATION PROCESSING; INFORMATION SERVICE; INTERNET PROTOCOL; ONLINE SYSTEM;

EID: 70449384378     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-279     Document Type: Article

References (59)

1. Stockinger H, Attwood T, Chohan SN, Côté R, Cudré-Mauroux P, Falquet L, Fernandes P, Finn RD, Hupponen T, Korpelainen E, Labarga A, Laugraud A, Lima T, Pafilis E, Pagni M, Pettifer S, Phan I, Rahman N. Experience using web services for biological sequence analysis. Brief Bioinform 2008, 9:493-505. 10.1093/bib/bbn029, 18621748.
2. Stein L. Creating a bioinformatics nation. Nature 2002, 417:119-120. 10.1038/417119a, 12000935.
3. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, 37:D5-15. 10.1093/nar/gkn741, 2686545, 18940862.
4. Miyazaki S, Sugawara H, Ikeo K, Gojobori T, Tateno Y. DDBJ in the stream of various biological data. Nucleic Acids Res 2004, 32:D31-4. 10.1093/nar/gkh127, 308861, 14681352.
5. Labarga A, Valentin F, Anderson M, Lopez R. Web services at the European bioinformatics institute. Nucleic Acids Res 2007, 35:W6-11. 10.1093/nar/gkm291, 1933145, 17576686.
6. Sugawara H, Miyazaki S. Biological SOAP servers and web services provided by the public sequence data bank. Nucleic Acids Res 2003, 31:3836-3839. 10.1093/nar/gkg558, 168965, 12824432.
7. Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004, 20:3045-3054. 10.1093/bioinformatics/bth361, 15201187.
8. Fiers MWEJ, Burgt A, Datema E, de Groot JCW, van Ham RCHJ. High-throughput bioinformatics with the Cyrille2 pipeline system. BMC Bioinformatics 2008, 9:96. 10.1186/1471-2105-9-96, 2268656, 18269742.
9. Hoon S, Ratnapu KK, Chia J, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, Stupka E. Biopipe: a flexible framework for protocol-based bioinformatics analysis. Genome Res 2003, 13:1904-1915. 403782, 12869579.
10. Fisher P, Hedeler C, Wolstencroft K, Hulme H, Noyes H, Kemp S, Stevens R, Brass A. A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis. Nucleic Acids Res 2007, 35:5625-5633. 10.1093/nar/gkm623, 2018629, 17709344.
11. Wilkinson MD, Links M. BioMOBY: an open source biological web services proposal. Brief Bioinform 2002, 3:331-341. 10.1093/bib/3.4.331, 12511062.
12. Neerincx PBT, Leunissen JAM. Evolution of web services in bioinformatics. Brief Bioinform 2005, 6:178-188. 10.1093/bib/6.2.178, 15975226.
13. BioMoby Consortium Interoperability with Moby 1.0--it's better than sharing your toothbrush!. Brief Bioinform 2008, 9:220-231. 10.1093/bib/bbn003, 18238804.
14. Jain E, Phan I, Duvaud S, Gasteiger E, Redaschi N, Martin MJ, McGarvey P, Bairoch A. Design and Implementation of the UniProt Website. Nature Precedings 2008, , http://hdl.handle.net/10101/npre.2008.2611.1
15. Web Application Description Language. , https://wadl.dev.java.net/
16. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. BioMart--biological queries made easy. BMC Genomics 2009, 10:22. 10.1186/1471-2164-10-22, 2649164, 19144180.
17. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L. The distributed annotation system. BMC Bioinformatics 2001, 2:7. 10.1186/1471-2105-2-7, 58584, 11667947.
18. SOAP Over Java Message Service 1.0. , http://www.w3.org/TR/2008/WD-soapjms-20081121
19. SOAP Version 1.2 Email Binding. , http://www.w3.org/TR/2002/NOTE-soap12-email-20020703
20. Web Services Resource 1.2 (WS-Resource). , http://docs.oasis-open.org/wsrf/wsrf-ws_resource-1.2-spec-os.pdf
21. Web Services Glossary. , http://www.w3.org/TR/2004/NOTE-ws-gloss-20040211/
22. Vaquero LM, Rodero-Merino L, Caceres J, Lindner M. A break in the clouds: towards a cloud definition. SIGCOMM Comput Commun Rev 2009, 39:50-55.
23. About XMPP. , http://xmpp.org/about/
24. XMPP Standards Foundation. , http://xmpp.org/xsf/
25. XEP-0244: IO Data. , http://xmpp.org/extensions/xep-0244.html
26. XEP-0030: Service Discovery. , http://xmpp.org/extensions/xep-0030.html
27. XMPP Web Services for Java. , http://xws4j.sourceforge.net/
28. The Second Stable Version of the EMBL Nucleotide Sequence Database XML Schema. , http://www.ebi.ac.uk/embl/schema/EMBL_Services_V1.1.xsd
29. Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RKJ, Laursen K, Oliver SG, Paton NW, Sansone S, Sarkans U, Stoeckert CJJ, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol 2007, 25:1127-1133. 10.1038/nbt1347, 17921998.
30. Kottmann R, Gray T, Murphy S, Kagan L, Kravitz S, Lombardot T, Field D, Glöckner FO. A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS 2008, 12:115-121. 10.1089/omi.2008.0A10, 18479204.
31. Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 2007, 5:44. 10.1186/1741-7007-5-44, 2189715, 17925023.
32. 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 J, 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. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. 10.1093/bioinformatics/btg015, 12611808.
33. UniProt Consortium The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009, 37:D169-74. 10.1093/nar/gkn664, 2686606, 18836194.
34. Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JES. Proteochemometric modeling of HIV protease susceptibility. BMC Bioinformatics 2008, 9:181. 10.1186/1471-2105-9-181, 2375133, 18402661.
35. Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E. The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. J Chem Inf Comput Sci 2003, 43:493-500.
36. Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL. Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. Curr Pharm Des 2006, 12:2111-2120. 10.2174/138161206777585274, 16796559.
37. Murray-Rust P, Rzepa HS. Chemical Markup, XML, and the Worldwide Web. 1. Basic principles. J Chem Inf Comput Sci 1999, 39:928-42.
38. Holliday GL, Murray-Rust P, Rzepa HS. Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions. J Chem Inf Model 2006, 46:145-157. 10.1021/ci0502698, 16426051.
39. Kuhn S, Helmus T, Lancashire RJ, Murray-Rust P, Rzepa HS, Steinbeck C, Willighagen EL. Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data. J Chem Inf Model 2007, 47:2015-2034. 10.1021/ci600531a, 17887743.
40. Adams N, Winter J, Murray-Rust P, Rzepa HS. Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language. J Chem Inf Model 2008, 48:2118-2128. 10.1021/ci8002123, 18991372.
41. Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JES. Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics 2007, 8:59. 10.1186/1471-2105-8-59, 1808478, 17316423.
42. Wallner B, Larsson P, Elofsson A. Pcons.net: protein structure prediction meta server. Nucleic Acids Res 2007, 35:W369-74. 10.1093/nar/gkm319, 1933226, 17584798.
43. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res 2009, 37:D211-5. 10.1093/nar/gkn785, 2686546, 18940856.
44. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948. 10.1093/bioinformatics/btm404, 17846036.
45. The EMBRACE Service Registry. , http://www.embraceregistry.net/
46. BioCatalogue: Providing a Curated Catalogue of Life Science Web Services. , http://biocatalogue.org/
47. Kaarthik S, Kunal V, Amit S. Discovery of Web Services in a Federated Registry Environment. Proceedings of the IEEE International Conference on Web Services 2004, 270.
48. OASIS Web Service Security (WSS) TC. , http://www.oasis-open.org/committees/wss
49. Extensible Messaging and Presence Protocol (XMPP): Core. , http://www.ietf.org/rfc/rfc3920.txt
50. Extensible Messaging and Presence Protocol (XMPP): Instant Messaging and Presence. , http://www.ietf.org/rfc/rfc3921.txt
51. XMPP Software: Libraries. , http://xmpp.org/software/libraries.shtml
52. XEP-0050: Ad-Hoc Commands. , http://xmpp.org/extensions/xep-0050.html
53. JABBER Stream Objects. , https://jso.dev.java.net/
54. XMLBeans. , http://xmlbeans.apache.org/
55. Ejabberd - the Erlang Jabber/XMPP Daemon. , http://www.ejabberd.im/
56. Willighagen E. Processing CML conventions in Java. Internet J Chem 2001, 4:4+.
57. Workflow Entry: Run an XMPP Cloud Service. , http://www.myexperiment.org/workflows/631?version=2
58. Dong X, Gilbert KE, Guha R, Heiland R, Kim J, Pierce ME, Fox GC, Wild DJ. Web service infrastructure for chemoinformatics. J Chem Inf Model 2007, 47:1303-1307. 10.1021/ci6004349, 17602467.
59. CDK-Taverna. , http://www.cdk-taverna.de/