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Volumn 9, Issue 1, 2008, Pages 57-68

Automation of in-silico data analysis processes through workflow management systems

Author keywords

Automation of retrieval and analysis processes; Biological data integration; Ontologies; Web services; Workflow management systems; XML

Indexed keywords

AUTOMATION; CLASSIFICATION; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER MODEL; COMPUTER NETWORK; COMPUTER PROGRAM; COMPUTER SYSTEM; DATA ANALYSIS; DATA COLLECTION METHOD; DATA EXTRACTION; FREQUENCY ANALYSIS; GENETIC DATABASE; GENOMICS; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION TECHNOLOGY; INTERNET; MEDICAL INFORMATION SYSTEM; MEDICAL RESEARCH; METHODOLOGY; MOLECULAR BIOLOGY; PROTEOMICS; REVIEW; SEMANTICS; ALGORITHM; BIOLOGY; DATA BASE; FACTUAL DATABASE; SYSTEM ANALYSIS;

EID: 38049150833     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbm056     Document Type: Review
Times cited : (49)

References (52)
  • 1
    • 0037246058 scopus 로고    scopus 로고
    • ArrayExpress-a public repository for microarray gene expression data at the EBI
    • Brazma A, Parkinson H, Sarkans U, et al. ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003;31:68-71.
    • (2003) Nucleic Acids Res , vol.31 , pp. 68-71
    • Brazma, A.1    Parkinson, H.2    Sarkans, U.3
  • 2
    • 0037112032 scopus 로고    scopus 로고
    • Nucleotide sequence database policies
    • Brunak S, Danchin A, Hattori M, et al. Nucleotide sequence database policies. Science 2002;298:1333.
    • (2002) Science , vol.298 , pp. 1333
    • Brunak, S.1    Danchin, A.2    Hattori, M.3
  • 3
    • 0037220165 scopus 로고    scopus 로고
    • The UMD-p53 database: New mutations and analysis tools
    • Béroud C, Soussi T. The UMD-p53 database: New mutations and analysis tools. Hum Mutat 2003;21:176-81.
    • (2003) Hum Mutat , vol.21 , pp. 176-181
    • Béroud, C.1    Soussi, T.2
  • 4
    • 0036258111 scopus 로고    scopus 로고
    • The IARC TP53 Database: New online mutation analysis and recommendations to users
    • Olivier M, Eeles R, Hollstein M, et al. The IARC TP53 Database: new online mutation analysis and recommendations to users. Hum Mutat 2002;19:607-14.
    • (2002) Hum Mutat , vol.19 , pp. 607-614
    • Olivier, M.1    Eeles, R.2    Hollstein, M.3
  • 5
    • 3843084078 scopus 로고    scopus 로고
    • The COSMIC (catalogue of somatic mutations in cancer) database and website
    • Bamford S, Dawson E, Forbes S, et al. The COSMIC (catalogue of somatic mutations in cancer) database and website. Br J Cancer 2004;91:355-8.
    • (2004) Br J Cancer , vol.91 , pp. 355-358
    • Bamford, S.1    Dawson, E.2    Forbes, S.3
  • 6
    • 33846088142 scopus 로고    scopus 로고
    • The molecular biology database collection: 2007 update
    • Galperin MY. The molecular biology database collection: 2007 update. Nucleic Acids Res 2007;35:D3-D4.
    • (2007) Nucleic Acids Res , vol.35
    • Galperin, M.Y.1
  • 7
    • 0029967362 scopus 로고    scopus 로고
    • Etzold T, Ulyanov A, Argos P. SRS: Information retrieval system for molecular biology data banks. Meth Enzymol 1996;266:114-28.
    • Etzold T, Ulyanov A, Argos P. SRS: Information retrieval system for molecular biology data banks. Meth Enzymol 1996;266:114-28.
  • 8
    • 0005014105 scopus 로고    scopus 로고
    • Bioinformatics and extended markup language (XML)
    • Guerrini VH, Jackson D. Bioinformatics and extended markup language (XML). Online J Bioinform 2000;1:1-13.
    • (2000) Online J Bioinform , vol.1 , pp. 1-13
    • Guerrini, V.H.1    Jackson, D.2
  • 10
    • 38049168457 scopus 로고    scopus 로고
    • Romano, P. (ed) Towards a bioinformatics integrated network environment. In: Proceedings of NETTAB 2001 Workshop on 'XML and CORBA, Genova, May 17-18, 2001 (available from the editor)
    • Romano, P. (ed) Towards a bioinformatics integrated network environment. In: Proceedings of NETTAB 2001 Workshop on 'XML and CORBA, Genova, May 17-18, 2001 (available from the editor)
  • 11
    • 38049143536 scopus 로고    scopus 로고
    • Polymorphism Markup Language (PML) for the interoperability of data on SNPs and other sequence variations
    • December 16-18, Yokohama Pacifico, Japan
    • Sugawara H, Mizushima H, Kano T, et al. Polymorphism Markup Language (PML) for the interoperability of data on SNPs and other sequence variations. In: 15th International Conference on Genome Informatics, December 16-18, 2004, Yokohama Pacifico, Japan.
    • (2004) 15th International Conference on Genome Informatics
    • Sugawara, H.1    Mizushima, H.2    Kano, T.3
  • 14
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
    • Hucka M, Finney A, Sauro, HM, et al. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 2003;19:524-31.
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3
  • 15
    • 33751216367 scopus 로고    scopus 로고
    • XML schemas for common bioinformatic data types and their application in workflow systems
    • Seibel PN, Kruger J, Hartmeier S, et al. XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics 2006;7:490.
    • (2006) BMC Bioinformatics , vol.7 , pp. 490
    • Seibel, P.N.1    Kruger, J.2    Hartmeier, S.3
  • 16
    • 0037046558 scopus 로고    scopus 로고
    • Creating a bioinformatics nation
    • Stein L. Creating a bioinformatics nation. Nature 2002;417: 119-20.
    • (2002) Nature , vol.417 , pp. 119-120
    • Stein, L.1
  • 17
    • 0037433718 scopus 로고    scopus 로고
    • Open bioinformatics (editorial)
    • Jamison DC. Open bioinformatics (editorial). Bioinformatics 2003;19:679-80.
    • (2003) Bioinformatics , vol.19 , pp. 679-680
    • Jamison, D.C.1
  • 18
    • 21044459901 scopus 로고    scopus 로고
    • Evolution of web services in bioinformatics
    • Neenncx PB, Leunissen JA. Evolution of web services in bioinformatics. Breif Bioinform 2005;6:178-88.
    • (2005) Breif Bioinform , vol.6 , pp. 178-188
    • Neenncx, P.B.1    Leunissen, J.A.2
  • 21
    • 24644521025 scopus 로고    scopus 로고
    • GeneCruiser: A web service for the annotation of microarray data
    • Liefeld T, Reich M, Gould J, et al. GeneCruiser: A web service for the annotation of microarray data. Bioinformatics 2005;21 3681-2.
    • (2005) Bioinformatics , vol.21 , pp. 3681-3682
    • Liefeld, T.1    Reich, M.2    Gould, J.3
  • 22
    • 21344453433 scopus 로고    scopus 로고
    • Biosphere: The interoperation of web services in microarray cluster analysis
    • Cheung K-H, de Knikker R, Guo Y, et al. Biosphere: The interoperation of web services in microarray cluster analysis. Appl Bioinformatics 2004;3:253-6.
    • (2004) Appl Bioinformatics , vol.3 , pp. 253-256
    • Cheung, K.-H.1    de Knikker, R.2    Guo, Y.3
  • 23
    • 27344435089 scopus 로고    scopus 로고
    • The role of informatics in the coordinated management of biological resources collections
    • Romano P, Kracht M, Manniello MA, et al. The role of informatics in the coordinated management of biological resources collections. Appl Bioinformatics 2005;4: 175-86.
    • (2005) Appl Bioinformatics , vol.4 , pp. 175-186
    • Romano, P.1    Kracht, M.2    Manniello, M.A.3
  • 24
    • 33947220977 scopus 로고    scopus 로고
    • Web services and workflow management for biological resources
    • doi:10.1186/1471-2105-6-S4-S24
    • Romano P, Marra D, Milanesi L. Web services and workflow management for biological resources. BMC Bioinformatics 2005;6 S24(doi:10.1186/1471-2105-6-S4-S24).
    • (2005) BMC Bioinformatics , vol.6
    • Romano, P.1    Marra, D.2    Milanesi, L.3
  • 25
    • 38049102662 scopus 로고    scopus 로고
    • Senger M, Rice P, Oinn T. Soaplab. A unified sesame door to analysis tools, In: Simon J Cox (ed) Proceedings, UK e-Science, All Hands Meeting 2003, pp. 509-13. University of Southampton, Southampton, UK. ISBN: 1-904425-11-9 (meeting held on September 2-4, 2003, in Nottingham, UK).
    • Senger M, Rice P, Oinn T. Soaplab. A unified sesame door to analysis tools, In: Simon J Cox (ed) Proceedings, UK e-Science, All Hands Meeting 2003, pp. 509-13. University of Southampton, Southampton, UK. ISBN: 1-904425-11-9 (meeting held on September 2-4, 2003, in Nottingham, UK).
  • 26
    • 0037935183 scopus 로고    scopus 로고
    • BioMOBY: An open-source biological web services proposal
    • Wilkinson MD, Links M. BioMOBY: An open-source biological web services proposal. Brief Bioinform 2002;3: 331-41.
    • (2002) Brief Bioinform , vol.3 , pp. 331-341
    • Wilkinson, M.D.1    Links, M.2
  • 27
    • 27244434525 scopus 로고    scopus 로고
    • BioMOBY successfully integrates distributed heterogeneous bioinformatics web services. The PlaNet exemplar case
    • Wilkinson M, Schoof H, Ernst R, et al. BioMOBY successfully integrates distributed heterogeneous bioinformatics web services. The PlaNet exemplar case. Plant Physiol 2005;138:5-17.
    • (2005) Plant Physiol , vol.138 , pp. 5-17
    • Wilkinson, M.1    Schoof, H.2    Ernst, R.3
  • 28
    • 34249847873 scopus 로고    scopus 로고
    • Semantic web service provision: A realistic framework for bioinformatics programmers
    • Gordon PM, Trinh Q, Sensen CW. Semantic web service provision: A realistic framework for bioinformatics programmers. Bioinformatics 2007;23:1178-80.
    • (2007) Bioinformatics , vol.23 , pp. 1178-1180
    • Gordon, P.M.1    Trinh, Q.2    Sensen, C.W.3
  • 30
    • 34248195885 scopus 로고    scopus 로고
    • Biowep: A workflow enactment portal for bioinformatics applications
    • Romano P, Bartocci E, Bertolini G, et al. Biowep: A workflow enactment portal for bioinformatics applications. BMC Bioinformatics 2007;8:S19.
    • (2007) BMC Bioinformatics , vol.8
    • Romano, P.1    Bartocci, E.2    Bertolini, G.3
  • 31
    • 33746753308 scopus 로고    scopus 로고
    • Mahoui M, Ben-Miled Z, Srinivasan S, et al. SIBIOS Ontology: A robust package for the integration and pipelining of bioinformatics services. In: Proceedings of the Third International Workshop on Data Integration in the Life Sciences DILS 2006, July 20-22, 2006, Hinxton, UK, Springer Lecture Notes in Bioinformatics LNBI 4075, 2006, pp. 104-13, Springer Verlag Berlin Heidelberg 2006,
    • Mahoui M, Ben-Miled Z, Srinivasan S, et al. SIBIOS Ontology: A robust package for the integration and pipelining of bioinformatics services. In: Proceedings of the Third International Workshop on Data Integration in the Life Sciences DILS 2006, July 20-22, 2006, Hinxton, UK, Springer Lecture Notes in Bioinformatics LNBI 4075, 2006, pp. 104-13, Springer Verlag Berlin Heidelberg 2006,
  • 33
    • 0037163144 scopus 로고    scopus 로고
    • Design and implementation of microarray gene expression markup language (MAGE-ML)
    • Spellman PT, Miller M, Stewart J, et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 2002;3:0046.1-0046.9.
    • (2002) Genome Biol , vol.3
    • Spellman, P.T.1    Miller, M.2    Stewart, J.3
  • 34
    • 18344396568 scopus 로고    scopus 로고
    • Minimum information about a microarray experiment (MIAME) - toward standards for microarray data
    • Brazma A, Hingamp P, Quackenbush J, et al. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat Genet 2001;29: 365-71.
    • (2001) Nat Genet , vol.29 , pp. 365-371
    • Brazma, A.1    Hingamp, P.2    Quackenbush, J.3
  • 35
    • 0043026713 scopus 로고    scopus 로고
    • Biopipe: A flexible framework for protocol-based bioinformatics analysis
    • Hoon S, Ratnapu KK, Chia JM, et al. Biopipe: A flexible framework for protocol-based bioinformatics analysis. Genome Res 2003;13 1904-15.
    • (2003) Genome Res , vol.13 , pp. 1904-1915
    • Hoon, S.1    Ratnapu, K.K.2    Chia, J.M.3
  • 36
    • 10244255212 scopus 로고    scopus 로고
    • Taverna: A tool for the composition and enactment of bioinformatics workflows
    • Oinn T, Addis M, Ferris J, et al. Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004;20:3045-54.
    • (2004) Bioinformatics , vol.20 , pp. 3045-3054
    • Oinn, T.1    Addis, M.2    Ferris, J.3
  • 37
    • 33747833111 scopus 로고    scopus 로고
    • Taverna: A tool for building and running workflows of services
    • Hull D, Wolstencroft K, Stevens R, et al. Taverna: A tool for building and running workflows of services. Nucleic Acids Res 2006;W729-W32.
    • (2006) Nucleic Acids Res
    • Hull, D.1    Wolstencroft, K.2    Stevens, R.3
  • 38
    • 0345359315 scopus 로고    scopus 로고
    • MyGrid: Personalised bioinformatics on the information grid
    • Stevens R, Robinson A, Goble C. MyGrid: Personalised bioinformatics on the information grid. Bioinformatics 2003; 19:i302-i304.
    • (2003) Bioinformatics , vol.19
    • Stevens, R.1    Robinson, A.2    Goble, C.3
  • 39
    • 33845637822 scopus 로고    scopus 로고
    • BioMoby extensions to the taverna workflow management and enactment software
    • Kawas E, Senger M, Wilkinson MD. BioMoby extensions to the taverna workflow management and enactment software. BMC Bioinformatics 2006;7:523.
    • (2006) BMC Bioinformatics , vol.7 , pp. 523
    • Kawas, E.1    Senger, M.2    Wilkinson, M.D.3
  • 40
    • 26444577571 scopus 로고    scopus 로고
    • Feta: A light-weight architecture for user oriented semantic service discovery
    • The Semantic Web: Research and Applications, Lecture Notes in Comp. Sci, Springer, pp
    • Lord,P. Alper P, Wroe C, et al. Feta: A light-weight architecture for user oriented semantic service discovery. In: The Semantic Web: Research and Applications, Lecture Notes in Comp. Sci. LNCS 2005, Vol. 3532, Springer, pp. 17-31.
    • (2005) LNCS , vol.3532 , pp. 17-31
    • Lord, P.1    Alper, P.2    Wroe, C.3
  • 42
    • 25444520762 scopus 로고    scopus 로고
    • Wildfire: Distributed, grid-enabled workflow construction and execution
    • Tang F, Chua CL, Ho LY, et al. Wildfire: Distributed, grid-enabled workflow construction and execution. BMC Bioinformatics 2005;6 69.
    • (2005) BMC Bioinformatics , vol.6 , pp. 69
    • Tang, F.1    Chua, C.L.2    Ho, L.Y.3
  • 43
    • 0141617541 scopus 로고    scopus 로고
    • The design of Jemboss: A graphical user interface to EMBOSS
    • Carver T, Bleasby A. The design of Jemboss: A graphical user interface to EMBOSS. Bioinformatics 2003;19:1837-43.
    • (2003) Bioinformatics , vol.19 , pp. 1837-1843
    • Carver, T.1    Bleasby, A.2
  • 45
    • 22944475836 scopus 로고    scopus 로고
    • Taylor I, Wang I, Shields M, et al. Distributed computing with Triana on the grid. concurrency and computation. Practice and Experience 2005;17:1197-14.
    • Taylor I, Wang I, Shields M, et al. Distributed computing with Triana on the grid. concurrency and computation. Practice and Experience 2005;17:1197-14.
  • 48
    • 29644434815 scopus 로고    scopus 로고
    • Pegasus: A framework for mapping complex scientific workflows onto distributed systems
    • Deelman E, Singba G, Sua M-H, et al. Pegasus: A framework for mapping complex scientific workflows onto distributed systems. Scientific Programming 2005;13:219-37.
    • (2005) Scientific Programming , vol.13 , pp. 219-237
    • Deelman, E.1    Singba, G.2    Sua, M.-H.3
  • 49
    • 2942544409 scopus 로고    scopus 로고
    • Pegasys: Software for executing and integrating analyses of biological sequences
    • Shah SP, He DY, Sawkins JN, et al. Pegasys: Software for executing and integrating analyses of biological sequences. BMC Bioinformatics 2004;5:40.
    • (2004) BMC Bioinformatics , vol.5 , pp. 40
    • Shah, S.P.1    He, D.Y.2    Sawkins, J.N.3
  • 50
    • 34248198746 scopus 로고    scopus 로고
    • BioWMS: A web based workflow management system for bioinformatics
    • Bartocci E, Corradini F, Merelli E, et al. BioWMS: A web based workflow management system for bioinformatics. BMC Bioinformatics 2007;8:S2.
    • (2007) BMC Bioinformatics , vol.8
    • Bartocci, E.1    Corradini, F.2    Merelli, E.3
  • 51
    • 85142176695 scopus 로고    scopus 로고
    • Navas-Delgado I, del Mar Rojano-Munoz M, Ramirez S, et al. Intelligent client for integrating bioinformatics services. Bioinformatics 2006;22:106-11.
    • Navas-Delgado I, del Mar Rojano-Munoz M, Ramirez S, et al. Intelligent client for integrating bioinformatics services. Bioinformatics 2006;22:106-11.
  • 52
    • 33646134618 scopus 로고    scopus 로고
    • Adapters, shims, and glue - service interoperability for in silico experiments
    • Radetzki U, Leser U, Schulze-Rauschenbach SC, et al. Adapters, shims, and glue - service interoperability for in silico experiments. Bioinformatics 2006;22:1137-43.
    • (2006) Bioinformatics , vol.22 , pp. 1137-1143
    • Radetzki, U.1    Leser, U.2    Schulze-Rauschenbach, S.C.3


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