The BioExtract Server: A web-based bioinformatic workflow platform

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Lushbough, Carol M ^a   Jennewein, Douglas M ^a   Brendel, Volker P ^b,c  

^a University of South Dakota   (United States)

^b Department of Genetics Development and Cell Biology and   (United States)

^c Iowa State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETIC ANALYSIS; INFORMATION SYSTEM; MOLECULAR BIOLOGY; NUCLEIC ACID DATABASE; PRIORITY JOURNAL; PROTEIN DATABASE; WORKFLOW;

DATABASES, GENETIC; GENOMICS; INTERNET; SOFTWARE; SYSTEMS INTEGRATION; WORKFLOW;

EID: 79960008613     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr286     Document Type: Article

References (19)

1. Gil, Y., Deelman, E., Ellisman, M., Fahringer, T., Fox, G., Gannon, D., Goble, C., Livny, M., Moreau, L. and Myers, J. (2007) Examining the challenges of scientific workflows. IEEE Comput., 40, 24-32.
2. Mesirov, J.P. (2010) Computer science. Accessible reproducible research. Science, 327, 415-416.
3. Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S. et al. (2010) BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res., 38, W689-W694.
4. Goble, C.R.D. (2008) Curating scientific web services and workflow. EDUCAUSE Rev., 43, 10-11.
5. Lushbough, C., Bergman, M.K., Lawrence, C.J., Jennewein, D. and Brendel, V. (2010) BioExtract server-an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data. IEEE/ACM Trans. Comput. Biol. Bioinform., 7, 12-24.
6. Goble, C., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M. and Li, P. (2010) myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res., 38, W677-W682.
7. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)
8. Abouelhoda, M.I., Kurtz, S. and Ohlebusch, E. (2004) Replacing suffix trees with enhanced suffix arrays. J. Dis. Algor., 2, 53-86.
9. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G. and Thompson, J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500. (Pubitemid 37442184)
10. Xing, L. and Brendel, V. (2001) Multi-query sequence BLAST output examination with MuSeqBox. Bioinformatics, 17, 744-745. (Pubitemid 32851385)
11. Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M.R., Li, P. and Oinn, T. (2006) Taverna: a tool for building and running workflows of services. Nucleic Acids Res., 34, W729-732. (Pubitemid 44529867)
12. Ludäscher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger, E., Jones, M., Lee, E.A., Tao, J. and Zhao, Y. (2006) Scientific workflow management and the Kepler system. Concurr. Comput. Pract. Exp., 18, 1039-1065. (Pubitemid 44258497)
13. Harrison, A., Taylor, I., Wang, I. and Shields, M. (2008) WS-RF workflow in Triana. Int. J. High Perform. Comput. Appl., 22, 268-283.
14. Fursov, M.Y., Oshchepkov, D.Y. and Novikova, O.S. (2009) UGENE: interactive computational schemes for genome analysis. Proc. Fifth Moscow Int. Congress Biotechnol., 3, 14-15.
15. Barga, R., Jackson, J., Araujo, N., Guo, D., Gautam, N. and Simmhan, Y. (2008) The Trident Scientific Workflow Workbench eScience, 2008. IEEE Fourth International Conference, pp. 317-318.
16. Oinn, T., Li, P., Kell, D.B., Goble, C., Goderis, A., Greenwood, M., Hull, D., Stevens, R., Daniele, T. and Zhao, J. (2006) Taverna/ myGrid: aligning a workflow system with the life sciences community. In Taylor, I., Deelman, E., Gannon, D. and Shields, M. (eds), Workflows in e-Science. Springer, New York, pp. 300-319.
17. Reich, M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P. and Mesirov, J.P. (2006) GenePattern 2.0. Nat. Genet., 38, 500-501.
18. Neron, B., Menager, H., Maufrais, C., Joly, N., Maupetit, J., Letort, S., Carrere, S., Tuffery, P. and Letondal, C. (2009) Mobyle: a new full web bioinformatics framework. Bioinformatics, 25, 3005-3011.
19. Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.