메뉴 건너뛰기




Volumn 23, Issue 3, 2007, Pages 497-509

Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences

Author keywords

Client server; Distributed systems; Integrated environments; Semantics; User interface; Web base services; Workflow management

Indexed keywords

CLIENT SERVER COMPUTER SYSTEMS; COMPUTATIONAL METHODS; COMPUTER AIDED SOFTWARE ENGINEERING; DISTRIBUTED COMPUTER SYSTEMS; USER INTERFACES; WORLD WIDE WEB;

EID: 33750809488     PISSN: 0167739X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.future.2006.07.011     Document Type: Article
Times cited : (31)

References (68)
  • 3
    • 33750843754 scopus 로고    scopus 로고
    • A.L. Bazinet, D.S. Myers, J. Fuetsch, M.P. Cummings, Grid services base library: A high-level, procedural application programming interface for writing Globus-based Grid services, Future Gener. Comput. Syst. (in press). doi:10.1016/j.future.2006.07.009
  • 4
    • 0034523499 scopus 로고    scopus 로고
    • Masker Aid: A performance enhancement to RepeatMasker
    • Bedell J., Korf I., and Gish W. Masker Aid: A performance enhancement to RepeatMasker. Bioinformatics 16 (2000) 1040-1041
    • (2000) Bioinformatics , vol.16 , pp. 1040-1041
    • Bedell, J.1    Korf, I.2    Gish, W.3
  • 6
    • 33750818877 scopus 로고    scopus 로고
    • Bio Grid Service Ontology, http://www.flacp.fujitsulabs.com/tce/ontologies/2005/08/BioGridService.owl
  • 7
    • 33750799808 scopus 로고    scopus 로고
    • Bioinformatic Workflow Builder Interface, http://www.alphaworks.ibm.com/tech/biowbi
  • 8
    • 0030030777 scopus 로고    scopus 로고
    • Evolutionary biology of platyhelminths comes of age: The role of molecular phylogenetics
    • Blair D., Campos A., Cummings M.P., and Laclette J.P. Evolutionary biology of platyhelminths comes of age: The role of molecular phylogenetics. Parasitol. Today 12 (1996) 66-71
    • (1996) Parasitol. Today , vol.12 , pp. 66-71
    • Blair, D.1    Campos, A.2    Cummings, M.P.3    Laclette, J.P.4
  • 9
    • 33750808648 scopus 로고    scopus 로고
    • BLAST Semantic Web service description, http://www.flacp.fujitsulabs.com/sylee/BLAST.owl
  • 10
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • Brudno M., Do C., Cooper G., Kim M., Davydov E., Green E., Sidow A., and Batzoglou S. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13 (2003) 721-731
    • (2003) Genome Res. , vol.13 , pp. 721-731
    • Brudno, M.1    Do, C.2    Cooper, G.3    Kim, M.4    Davydov, E.5    Green, E.6    Sidow, A.7    Batzoglou, S.8
  • 11
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genome DNA
    • Burge C., and Karlin S. Prediction of complete gene structures in human genome DNA. J. Mol. Biol. 268 (1997) 78-94
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 12
    • 0032132835 scopus 로고    scopus 로고
    • Phylogenetic relationships of Platyhelminthes based on 18S ribosomal gene sequences
    • Campos A., Cummings M.P., Reyes J.L., and Laclette J.P. Phylogenetic relationships of Platyhelminthes based on 18S ribosomal gene sequences. Mol. Phylogenet. Evol. 10 (1998) 1-10
    • (1998) Mol. Phylogenet. Evol. , vol.10 , pp. 1-10
    • Campos, A.1    Cummings, M.P.2    Reyes, J.L.3    Laclette, J.P.4
  • 17
    • 0028082064 scopus 로고
    • Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae)
    • Cummings M.P., King L.M., and Kellogg E.A. Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae). Mol. Biol. Evol. 11 (1994) 1-8
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 1-8
    • Cummings, M.P.1    King, L.M.2    Kellogg, E.A.3
  • 18
    • 27744543065 scopus 로고    scopus 로고
    • Magic bullets and golden rules: Data sampling in molecular phylogenetics
    • Cummings M.P., and Meyer A. Magic bullets and golden rules: Data sampling in molecular phylogenetics. Zoology 108 (2005) 329-336
    • (2005) Zoology , vol.108 , pp. 329-336
    • Cummings, M.P.1    Meyer, A.2
  • 19
    • 0038000616 scopus 로고    scopus 로고
    • Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms
    • Cummings M.P., Nugent J.M., Olmstead R.G., and Palmer J.D. Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. Curr. Genet. 43 (2003) 131-138
    • (2003) Curr. Genet. , vol.43 , pp. 131-138
    • Cummings, M.P.1    Nugent, J.M.2    Olmstead, R.G.3    Palmer, J.D.4
  • 20
    • 0033153406 scopus 로고    scopus 로고
    • Genes and other samples of DNA sequence data for phylogenetic inference
    • Cummings M.P., Otto S.P., and Wakeley J. Genes and other samples of DNA sequence data for phylogenetic inference. Biol. Bull. 196 (1999) 345-350
    • (1999) Biol. Bull. , vol.196 , pp. 345-350
    • Cummings, M.P.1    Otto, S.P.2    Wakeley, J.3
  • 21
    • 33750836659 scopus 로고    scopus 로고
    • T. de Boer, AJAX Command Definition (ACD files). http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Acd/
  • 22
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 23
    • 33750798752 scopus 로고    scopus 로고
    • EFetch, http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html
  • 24
    • 0031732094 scopus 로고    scopus 로고
    • A computer program for aligning a cDNA sequence with a genomic DNA sequence
    • Florea L., Hartzell G., Zhang Z., Rubin G., and Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8 (1998) 967-974
    • (1998) Genome Res. , vol.8 , pp. 967-974
    • Florea, L.1    Hartzell, G.2    Zhang, Z.3    Rubin, G.4    Miller, W.5
  • 25
    • 0033735445 scopus 로고    scopus 로고
    • Phylogenetic relationships of Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI
    • Förster H., Cummings M.P., and Coffey M.D. Phylogenetic relationships of Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI. Mycol. Res. 104 (2000) 1055-1061
    • (2000) Mycol. Res. , vol.104 , pp. 1055-1061
    • Förster, H.1    Cummings, M.P.2    Coffey, M.D.3
  • 26
    • 0035983980 scopus 로고    scopus 로고
    • Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala)
    • García-Verela M., Cummings M.P., Pérez-Ponce de León G., Gardner S.L., and Laclette J.P. Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala). Mol. Phylogenet. Evol. 23 (2002) 288-292
    • (2002) Mol. Phylogenet. Evol. , vol.23 , pp. 288-292
    • García-Verela, M.1    Cummings, M.P.2    Pérez-Ponce de León, G.3    Gardner, S.L.4    Laclette, J.P.5
  • 28
    • 33750803184 scopus 로고    scopus 로고
    • Globus Toolkit, http://www.globus.org/toolkit/
  • 29
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 30
    • 33750807424 scopus 로고    scopus 로고
    • N. Hashmi, S. Lee, M.P. Cummings, Abstracting workflows: Unifying bioinformatics task conceptualization and specification through semantic Web services, in: W3C Workshop on Semantic Web for Life Sciences, Cambridge, MA, USA, 2004
  • 31
    • 0030623944 scopus 로고    scopus 로고
    • A. Krogh, Two methods for improving performance of an HMM and their application for gene finding, in: Proc. Int. Conf. Intell. Syst. Mol. Biol., vol. 5, 1997, pp. 179-186
  • 33
    • 33750827759 scopus 로고    scopus 로고
    • S. Lee, N. Hashmi, J. Hendler, B. Parsia, Bio-STEER: An application of Task Computing - the Semantic Web meets Grid computing, Technical Report FLA-PCR-TM-3, Pervasive Computing Research, Fujitsu Laboratories of America, Inc., 2004
  • 34
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe T., and Eddy S. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (1997) 955-964
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.1    Eddy, S.2
  • 35
    • 0031350056 scopus 로고    scopus 로고
    • NEXUS: An extensible file format for systematic information
    • Maddison D.R., Swofford D.L., and Maddison W.P. NEXUS: An extensible file format for systematic information. Syst. Biol. 46 (1997) 590-621
    • (1997) Syst. Biol. , vol.46 , pp. 590-621
    • Maddison, D.R.1    Swofford, D.L.2    Maddison, W.P.3
  • 36
    • 1242319545 scopus 로고    scopus 로고
    • Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families
    • Mark Welch D.B., Cummings M.P., Hillis D.M., and Meselson M. Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families. Proc. Natl. Acad. Sci. USA 101 (2004) 1622-1625
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 1622-1625
    • Mark Welch, D.B.1    Cummings, M.P.2    Hillis, D.M.3    Meselson, M.4
  • 37
    • 0030474204 scopus 로고    scopus 로고
    • DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater Cladophora (Chlorophyta)
    • Marks J.C., and Cummings M.P. DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater Cladophora (Chlorophyta). J. Phycol. 32 (1996) 1035-1042
    • (1996) J. Phycol. , vol.32 , pp. 1035-1042
    • Marks, J.C.1    Cummings, M.P.2
  • 40
    • 33750831774 scopus 로고    scopus 로고
    • Mindswap, http://www.mindswap.org/2004/ontolink/
  • 41
    • 0042101429 scopus 로고    scopus 로고
    • Necessity is the mother of invention: A simple Grid computing system using commodity tools
    • Myers D.S., and Cummings M.P. Necessity is the mother of invention: A simple Grid computing system using commodity tools. J. Parallel. Distr. Com. 63 (2003) 578-589
    • (2003) J. Parallel. Distr. Com. , vol.63 , pp. 578-589
    • Myers, D.S.1    Cummings, M.P.2
  • 42
    • 13444292888 scopus 로고    scopus 로고
    • Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions
    • Neel M.C., and Cummings M.P. Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions. BMC Evol. Biol. 4 (2004) 15
    • (2004) BMC Evol. Biol. , vol.4 , pp. 15
    • Neel, M.C.1    Cummings, M.P.2
  • 44
    • 33750833708 scopus 로고    scopus 로고
    • OWL-S, http://www.daml.org/services/owl-s/1.0/
  • 45
    • 0035282695 scopus 로고    scopus 로고
    • GeneSplicer: A new computational method for splice site prediction
    • Pertea M., Lin X., and Salzberg S. GeneSplicer: A new computational method for splice site prediction. Nucleic Acids Res. 29 (2001) 1185-1190
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1185-1190
    • Pertea, M.1    Lin, X.2    Salzberg, S.3
  • 46
    • 0033639232 scopus 로고    scopus 로고
    • A case for evolutionary genomics and the comprehensive examination of sequence biodiversity
    • Pollock D.D., Eisen J.A., Doggett N.A., and Cummings M.P. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol. Biol. Evol. 17 (2000) 1776-1788
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1776-1788
    • Pollock, D.D.1    Eisen, J.A.2    Doggett, N.A.3    Cummings, M.P.4
  • 47
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • Posada D., and Crandall K.A. Modeltest: Testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 48
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • Rice P., Longden I., and Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16 (2000) 276-277
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 49
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 50
    • 33750835319 scopus 로고    scopus 로고
    • QT, http://www.trolltech.com/products/qt/index.html
  • 52
    • 33750809136 scopus 로고    scopus 로고
    • Simple Object Access Protocol, http://www.w3.org/tr/soap
  • 53
    • 33750823927 scopus 로고    scopus 로고
    • E. Sirin, J. Hendler, B. Parsia, Semi-automatic composition of Web services using semantic descriptions, in: Web Services: Modeling, Architecture and Infrastructure workshop in ICEIS, Angers, France, 2003
  • 54
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 55
    • 11044234605 scopus 로고    scopus 로고
    • Z. Song, Y. Labrou, R. Masuoka, Dynamic service discovery and management in Task Computing, in: First Annual International Conference on Mobile and Ubiquitous Systems: Networking and Services, MobiQuitous'04, Boston, MA, USA, 2003
  • 56
    • 0345359315 scopus 로고    scopus 로고
    • myGrid: Personalised Bioinformatics on the Information Grid
    • Proceedings of 11th International Conference on Intelligent Systems in Molecular Biology, 2003, Brisbane, Australia
    • Stevens R., Robinson A., and Goble C.A. myGrid: Personalised Bioinformatics on the Information Grid. Proceedings of 11th International Conference on Intelligent Systems in Molecular Biology, 2003, Brisbane, Australia. Bioinformatics 19 Suppl. 1 (2003) i302-i304
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Stevens, R.1    Robinson, A.2    Goble, C.A.3
  • 57
    • 33750821643 scopus 로고    scopus 로고
    • D.L. Swofford, PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4, Sinauer Associates. Sunderland, MA, USA
  • 58
    • 33750824495 scopus 로고    scopus 로고
    • E. Sirin, B. Parsia, B. Cuenca Grau, A. Kalyanpur, Y. Katz, Pellet: A Practical OWL-DL Reasoner, http://www.mindswap.org/papers/PelletJWS.pdf
  • 59
    • 33750839973 scopus 로고    scopus 로고
    • Task Computing, http://taskcomputing.org
  • 60
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 61
    • 33750827758 scopus 로고    scopus 로고
    • Universal Plug and Play, http://www.upnp.org
  • 62
    • 33750806748 scopus 로고    scopus 로고
    • Washington University BLAST 2.0, http://blast.wustl.edu/blast/README.html
  • 63
    • 33750805720 scopus 로고    scopus 로고
    • Wildfire, http://wildfire.bii.a-star.edu.sg/wildfire/
  • 64
    • 33750829171 scopus 로고    scopus 로고
    • Wildfire/GEL, http://Web.bii.a-star.edu.sg/~francis/wildfiregel/
  • 65
    • 33750819598 scopus 로고    scopus 로고
    • W3C Resource Description Framework, http://www.w3.org/rdf
  • 66
    • 33750830185 scopus 로고    scopus 로고
    • W3C Web-Ontology (WebOnt) Working Group, http://www.w3.org/2001/sw/Webont
  • 67
    • 33750839525 scopus 로고    scopus 로고
    • W3C Web Services Description Working Group, http://www.w3.org/2002/ws/desc
  • 68
    • 31444436554 scopus 로고    scopus 로고
    • A taxonomy of scientific workflow systems for Grid computing
    • Yu J., and Buyya R. A taxonomy of scientific workflow systems for Grid computing. SIGMOD Rec. 34 (2005) 44-49
    • (2005) SIGMOD Rec. , vol.34 , pp. 44-49
    • Yu, J.1    Buyya, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.