Designing and executing scientific workflows with a programmable integrator

Bioinformatics

Volumn 20, Issue 13, 2004, Pages 2092-2100

  Chagoyen, Monica ^a   Kurul, M E ^b   De Alarcon P A ^c   Carazo, J M ^a   Gupta, A ^b  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Integromics   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER LANGUAGE; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; HUMAN; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL;

EID: 4544238649     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth209     Document Type: Article

References (16)

1. Ailamaki,A., Ioannidis,Y.E. and Livny,M. (1998) Scientific workflow management by database management. Stat. Sci. Database Manage., 190-199.
2. Altschul,S.F., Madden,T.L., Schäffer,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.
3. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Ceratti,L., Corpet,F., Croning,M.D. et al. (2000) InterPro - an integrated documentation resource for protein families, domains and functional sites. Bioinformatics, 16, 1145-1150.
4. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
5. Bairoch,A. (2000) The ENZYME database in 2000. Nucleic Acids Res., 28, 304-305.
6. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
7. Crescenzi,V. and Mecca,G. (1998) Grammars have exceptions. Information Systems, 23, 539-565.
8. Gupta,A., Ludäscher,B., Martone,M.E. et al. (2003) BIRN-M: a semantic mediator for solving real-world neuroscience problems. Proceedings of ACM SIGMOD 2003, San Diego, CA, p. 678.
9. Henrick,K. and Thornton,J.M. (1998) PQS: a protein quaternary structure file server. Trends Biochem. Sci., 23, 358-361.
10. Ludäscher,B., Altintas,I. and Gupta,A. (2003) Compiling abstract scientific workflows into web service workflows. Proceedings of the 15th International Conference Science Statistical Database Management (SSDBM), Cambridge, MA, pp. 251-254.
11. Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
12. Shen,M. and Sala,C. (2001) PDZ domains and the organization of supramolecular complexes. Annu. Rev. Neurosci., 24, 1-29.
13. Stein,L.D. (2003) Integrating biological databases. Nat. Rev. Genet., 4, 337-345.
14. Stevens,R., Goble,C., Baker,P. and Brass,A. (2001) A classification of tasks in bioinformatics. Bioinformatics, 17, 180-188.
15. Valdar,W.S.J. and Thornton,J.M. (2001) Protein-Protein interfaces: analysis of amino acid conservation in homodimers. Proteins, 42, 108-124.
16. XQuery 1.0 (2003) An XML Query Language W3C Working Draft.