Seven variations of an alignment workflow - An illustration of agile process design and management in bio-jETI

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4983 LNBI, Issue , 2008, Pages 445-456

  Lamprecht, Anna Lena ^a,b   Margaria, Tiziana ^c   Steffen, Bernhard ^a  

^a TU DORTMUND UNIVERSITY   (Germany)

^b Center of Applied Proteomics   (Germany)

^c UNIVERSITY OF POTSDAM   (Germany)

Author keywords

Bioinformatics workflows; Model driven development; Service orchestration; Web services

Indexed keywords

ALIGNMENT; BIOCOMMUNICATIONS; BIOINFORMATICS; INFORMATION SCIENCE; MANAGEMENT; PROCESS DESIGN;

AGILE PROCESSING; BIOINFORMATICS ANALYSIS; BIOINFORMATICS WORKFLOWS; INTERNATIONAL SYMPOSIUM; MODEL-DRIVEN DEVELOPMENT; MULTIPLE SEQUENCE ALIGNMENT; SERVICE ORCHESTRATION; VARIATIONS OF; WEB SERVICES;

PROCESS ENGINEERING;

EID: 49949095003     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-79450-9_42     Document Type: Conference Paper

References (27)

1. Margaria, T., Kubczak, C., Steffen, B.: Bio-jETI: A Service Integration, Design, and Provisioning Platform for Orchestrated Bioinformatics Processes. BMC Bioinformatics (to appear)
2. Jörges, S., Kubczak, C., Nagel, R., Margaria, T., Steffen, B.: Model-Driven Development with the jABC. In: Bin, E., Ziv, A., Ur, S. (eds.) HVC 2006. LNCS, vol. 4383, Springer, Heidelberg (2007)
3. Margaria, T., Nagel, R., Steffen, B.: JETI: A Tool for Remote Tool Integration. In: Halbwachs, N., Zuck, L.D. (eds.) TACAS 2005. LNCS, vol. 3440, pp. 557-562. Springer, Heidelberg (2005)
4. Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M.R., Wipat, A., Li, P.: Taverna: A tool for the composition and enactment of bioinformatics workflows, bioinformatics 20(17), 3045-3054 (2004)
5. Hull, D., Wolstencroft, K., Stevens, R., Goble, C.A., Pocock, M.R., Li, P., Oinn, T.: Taverna: A tool for building and running workflows of services. Nucleic Acids Research 34(Web-Server-Issue), 729-732 (2006)
6. Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludäscher, B., Mock, S.: Kepler: An Extensible System for Design and Execution of Scientific Workflows. In: SSDBM, pp. 423-424 (2004)
7. Garvey, T.D., Lincoln, P., Pedersen, C.J., Martin, D., Johnson, M.: BioSPICE: Access to the Most Current Computational Tools for Biologists. OMICS - A Journal of Integrative Biology 7(4), 411-420 (2003)
8. Majithia, S., Shields, M.S., Taylor, I.J., Wang, I.: Triana: A Graphical Web Service Composition and Execution Toolkit. In: Proceedings of the IEEE International Conference on Web Services (ICWS 2004), pp. 514-524. IEEE Computer Society, Los Alamitos (2004)
9. Taylor, I., Shields, M., Wang, I., Harrison, A.: The Triana Workflow Environment: Architecture and Applications. In: Taylor, I., Deelman, E., Gannon, D., Shields, M. (eds.) Workflows for e-Science, Secaucus, NJ, USA, pp. 320-339. Springer, New York (2007)
10. Deelman, E., Singh, G., Su, M.-H., Blythe, J., Gil, Y., Kesselman, C., Mehta, G., Vahi, K., Berriman, G.B., Good, J., Laity, A.C., Jacob, J.C., Katz, D.S.: Pgasus: A framework for mapping complex scientific workflows onto distributed systems. Scientific Programming 13(3), 219-237 (2005)
11. Chebotko, A., Lin, C., Fei, X., Lai, Z., Lu, S., Hua, J., Fotouhi, F.: View: A visual scientific workflow management system. In: IEEE SCW, pp. 207-208. IEEE Computer Society, Los Alamitos (2007)
12. Polanski, A.: Sequence Alignment. In: Bioinformatics, pp. 155-156. Springer, Heidelberg (2007)
13. Thompson, J.D., Higgins, D.G., 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(22), 4673-4680 (1994)
14. Hartmeier, S., Krüger, J., Giegerich, R.: Webservices and Workflows on the Bielefeld Bioinformatics Server: Practices and Problems. In: Proceedings of NETTAB 2007 Workshop: A Semantic Web for Bioinformatics (2007)
15. DDBJ: Web API for Bioinformatics (2007), http://xml.nig.ac.jp/wsdl/index. jsp 16. Pillai, S., Silventoinen, V., Kallio, K., Senger, M., Sobhany, S., Tate, J., Velankar, S., Golovin, A., Henrick, K., Rice, P., Stoehr, P., Lopez, R.: SOAP-based services provided by the European Bioinformatics Institute. Nucleic Acids Research 33(1), 25 (2005)
16. Labarga, A., Pilai, S., Valentin, F., Anderson, M., Lopez, R.: Web services at the European Bioinformatics Institute. EMBnet.news 11(4), 18-23 (2005)
17. Labarga, A., Valentin, F., Anderson, M., Lopez, R.: Web Services at the European Bioinformatics Institute. Nucleic Acids Research Web Server Issue (2007)
18. Zmasek, C.M., Eddy, S.R.: ATV: Display and manipulation of annotated phylogenetic trees. Bioinformatics 17(4), 383-384 (2001)
19. Lamprecht, A.-L., Margaria, T., Steffen, B.: GeneFisher-P: Variations of Gene-Fisher as Processes in Bio-jETI. In: Proceedings of NETTAB 2007 Workshop: A Semantic Web for Bioinformatics (2007)
20. Seibel, P.N., Krüger, J., Hartmeier, S., Schwarzer, K., Löwenthal, K., Mersch, H., Dandekar, T., Giegerich, R.: XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics 7, 490 (2006)
21. BioJava Project: Main Page - BioJava, http:'//biojava.org
22. Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: Variations of GeneFisher as Processes in BiojETI. BMC Bioinformatics (to appear)
23. Margaria, T., Kubczak, C., Njoku, M., Steffen, B.: Model-Based Design of Distributed Collaborative Bioinformatics Processes in the jABC. In: Proc. ICECCS 2006, IEEE International Conference on Engineering of Complex Computer Systems (August 2006)
24. Kubczak, C., Margaria, T., Fritsch, A., Steffen, B.: Biological LC/MS Preprocessing and Analysis with jABC, jETI and xcms. In: Proceedings of the 2nd International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (ISoLA 2006), Paphos, Cyprus, pp. 308-313. IEEE Computer Society Press, Los Alamitos (2006)
25. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T.: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research 13, 2498-2504 (2003)
26. Margaria, T., Steffen, B.: Ltl guided planning: Revisiting automatic tool composition in eti. In: SEW, pp. 214-226. IEEE Computer Society, Los Alamitos (2007)
27. SWS Challenge: Challenge on Automating Web Services Mediation, Choreography and Discovery, http://sws-challehge.org/