Conveyor: A workflow engine for bioinformatic analyses

Bioinformatics

Volumn 27, Issue 7, 2011, Pages 903-911

  Linke, Burkhard ^a   Giegerich, Robert ^a   Goesmann, Alexander ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BIOLOGY; COMPUTER PROGRAM; ESCHERICHIA COLI; GENETICS; GENOMICS; MOLECULAR GENETICS; WORKFLOW;

COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; WORKFLOW;

EID: 79953305104     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr040     Document Type: Article

References (20)

1. Altintas,I. et al. (2004) Kepler: an extensible system for design and execution of scientific workflows. In Proceedings of Scientific and Statistical Database Management, 21-23 June 2004, Santorini Island, Greece. IEEE Computer Society, pp. 423-424.
2. Altschul,S. et al. (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Benson,D.A. et al. (2010) GenBank. Nucleic Acids Res., 38, D46-D51.
4. Consortium,T.U. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
5. Deelman,E. et al. (2005) Pegasus: a framework for mapping complex scientific workflows onto distributed systems. Scientific Program. J., 13, 219-237.
6. Delcher,A. et al. (1999) Improved microbial gene identification with glimmer. Nucleic Acids Res., 27, 4636.
7. Edgar,R.C. (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
8. Goecks,J. et al. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
9. Goodstadt,L. (2010) Ruffus: a lightweight Python library for computational pipelines. Bioinformatics, 26, 2778-2779.
10. Hull,D. et al. (2006) Taverna: a tool for building and running workflows of services. Nucleic Acids Res., 34, 729-732.
11. Kalaš,M. et al. (2010) BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics, 26, i540.
12. Li,H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078.
13. Neron,B. et al. (2009) Mobyle: a new full web bioinformatics framework. Bioinformatics, 25, 3005.
14. Romano,P. (2007) Automation of in-silico data analysis processes through workflow management systems. Brief. Bioinformatics, 9, 57-68.
15. Seibel,P. et al. (2006) XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics, 7, 490.
16. Smedley,D. et al. (2008) Solutions for data integration in functional genomics: a critical assessment and case study. Brief. Bioinformatics, 9, 532-544.
17. Thompson,J. et al. (1994) 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, 4673.
18. Troeger,P. et al. (2007) Standardization of an api for distributed resource management systems. In Proceedings of the IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2007), 14-17 May 2007, Rio de Janeiro, IEEE Computer Society, Brazil, pp. 619-626.
19. Wassink,I. et al. (2009)Analysing scientific workflows:why workflows not only connect web services. In 2009 Congress on Services-I, July 6-10, 2009, Los Angeles, California, USA, IEEE Computer Society, pp. 314-321.
20. Wilkinson,M. et al. (2008) Interoperability with Moby 1.0 it's better than sharing your toothbrush. Brief. Bioinformatics, 9, 220-231.