GeneFisher-P: Variations of GeneFisher as processes in Bio-jETI

BMC Bioinformatics

Volumn 9, Issue SUPPL. 4, 2008, Pages

  Lamprecht, Anna Lena ^a   Margaria, Tiziana ^b   Steffen, Bernhard ^a   Sczyrba, Alexander ^c   Hartmeier, Sven ^c   Giegerich, Robert ^c  

^a TU DORTMUND UNIVERSITY   (Germany)

^b UNIVERSITY OF POTSDAM   (Germany)

^c BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS TOOLS; FLEXIBLE PROCESS; HETEROGENEOUS SOURCES; PROCESS DEFINITION; PROCESS ORIENTATION; REMOTE RESOURCES; SEAMLESS INTEGRATION; SERVICE-ORIENTED APPROACHES;

BIOINFORMATICS; WEB SERVICES; WEBSITES;

TOOLS;

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; APPLICATION SERVICE PROVIDER; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; HUMAN COMPUTER INTERACTION; INFORMATION PROCESSING; INFORMATION TECHNOLOGY; INTERMETHOD COMPARISON; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROCESS CONTROL; SEQUENCE ALIGNMENT; WEB BROWSER; ALGORITHM; DNA SEQUENCE; GENE TARGETING; GENETICS; METHODOLOGY; MOLECULAR GENETICS;

PRIMER DNA;

ALGORITHMS; BASE SEQUENCE; DNA PRIMERS; GENE TARGETING; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 44649175821     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S4-S13     Document Type: Article

References (37)

1. Saiki RK Scharf S Faloona F Mullis KB Horn GT Erlich HA Arnheim N Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia Science 1985, 230(4732):1350-1354 10.1126/science.2999980 2999980
2. Giegerich R Meyer F Schleiermacher C GeneFisher - Software Support for the Detection of Postulated Genes Proceedings of the 4th International Conference on Intelligent Systems for Molecular Biology St. Louis, Washington, USA: AAAI States DJ, Agarwal P, Gaasterland T, Hunter L, Smith RF 1996:68-77
3. Meyer F Schleiermacher C GeneFisher - Interactive PCR Primer Design http://bibiserv.techfak.uni-bielefeld.de/genefisher/.
4. Thompson J Higgins D Gibson T CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 1994, 22(22):4673-4680 308517 7984417 10.1093/nar/22.22.4673
5. Stoye J Moulton V Dress A DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment Computer Applications in the Biosciences 1997, 13(6):625-626 9475994
6. Hagemeier D GeneFisher2 - an AJAX based implementation of GeneFisher Bachelor's thesis University Bielefeld, Faculty of Technology 2006
7. BiBiServ - Bielefeld University Bioinformatics Server http://bibiserv.techfak.uni-bielefeld.de/.
8. Steffen P Voss B Rehmsmeier M Reeder J Giegerich R RNAshapes: An integrated RNA analysis package based on abstract shapes Bioinformatics 2006, 22(4):500-503 10.1093/bioinformatics/btk010 16357029
9. Rehmsmeier M Steffen P Höchsmann M Giegerich R Fast and effective prediction of microRNA/target duplexes RNA 2004, 10:1507-1517 1370637 15383676 10.1261/rna.5248604
10. Hartmeier S Krüger J Löwenthal K Mersch H BioDOM - Hobit XML formats made easy http://bibiserv.techfak.uni-bielefeld.de/biodomws/ welcome.html.
11. Seibel P Schwarzer K Krüger J Hartmeier S Löwenthal K Mersch H Dandekar T Giegerich R XML schemas for common bioinformatic data types and their application in workflow systems BMC Bioinformatics 2006, 7:490 2001303 17087823 10.1186/1471-2105-7-490
12. Steffen B Narayan P Full Lifecycle Support for End-to-End Processes IEEE Computer 2007 Special Issue on Service Orientation
13. Wagner C Margaria T Pagendarm HG Comparative Analysis of Tools for automated Software Re-Engineering purposes Proceedings of the 2nd International Symposium on Leveraging Applications of Formal Methods, Verification and Validation Cyprus: IEEE Computer Society Press Margaria T, Phillipou A, Steffen B, IEEE, Paphos 2006
14. jABC Framework http://jabc.cs.uni-dortmund.de.
15. Jörges S Kubczak C Nagel R Margaria T Steffen B Model-Driven Development with the jABC Proceedings of the 2nd International Haifa Verification Conference Israel: IBM Bin E, Ziv A, Ur S, Haifa 2006
16. Margaria T Kubczak C Njoku M Steffen B Model-Based Design of Distributed Collaborative Bioinformatics Processes in the jABC Proceedings of the 11th IEEE International Conference on Engineering of Complex Computer Systems Stanford, California, USA: IEEE Computer Society 2006
17. Kubczak C Margaria T Fritsch A Steffen B Biological LC/MS Preprocessing and Analysis with jABC, jETI and xcms Proceedings of the 2nd International Symposium on Leveraging Applications of Formal Methods, Verification and Validation Cyprus: IEEE Computer Society Press Margaria T, Phillipou A, Steffen B, IEEE, Paphos 2006:308-313
18. Margaria T Steffen B Service Engineering: Linking Business and IT IEEE Computer 2006:53-63 Issue for the 60th anniversary of the Computer Society
19. Margaria T Steffen B Aggressive Model Driven Development for the Management of Service Evolution Annual Review of Communication 2004:57
20. Oinn T Addis M Ferris J Marvin D Senger M Greenwood M Carver T Glover K Pocock MR Wipat A Li P Taverna: A tool for the composition and enactment of bioinformatics workflows Bioinformatics 2004, 20(17) 3045-3054 10.1093/bioinformatics/bth361 15201187
21. Bio-jETI - jETI for Bioinformatics http://jeti.cs.uni-dortmund.de/ biojeti/.
22. Margaria T Kubczak C Steffen B Bio-jETI: A Service Integration, Design, and Provisioning Platform for Orchestrated Bioinformatics Processes BMC Bioinformatics 2008, 9(Suppl 4):S12
23. BiBiServ - ClustalW http://bibiserv.techfak.uni-bielefeld.de/clustalw/.
24. BiBiServ - DCA http://bibiserv.techfak.uni-bielefeld.de/dca/.
25. Hartmeier S Krüger J Löwenthal K Mersch H SequenceML - BioSchemas http://bioschemas.sourceforge.net/index.php/SequenceML.
26. BiBiServ - BioDOMWS http://bibiserv.techfak.uni-bielefeld.de/biodomws/.
27. Margaria T Nagel R Steffen B jETI: A Tool for Remote Tool Integration Proceedings of the 11th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Volume 3440 of U.K.: Springer Halbwachs N, Zuck LD, Edinburgh 2005:557-562 Lecture Notes in Computer Science
28. jETI - Java Electronic Tool Integration Platform http://jeti.cs.uni-dortmund.de/.
29. 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 2005, 33(1):W25-W28 1160251 15980463 10.1093/nar/gki491
30. Labarga A Pilai S Valentin F Anderson M Lopez R Web services at EBI EMBnet.news 2005, 11(4):18-23
31. Web Services at the EBI http://www.ebi.ac.uk/Tools/webservices/.
32. services:dBfetch [EBI web services] http://www.ebi.ac.uk/Tools/ webservices/services/dbfetch.
33. services:cLustalw [EBI web services] http://www.ebi.ac.uk/Tools/ webservices/services/clustalw.
34. Clarke EM Grumberg O Peled DA Model Checking The MIT Press 1999
35. Taverna project website http://taverna.sourceforge.net/.
36. BioSPICE Member Site https://biospice.sourceforge.net/.
37. WebLab Homepage http://weblab.cbi.pku.edu.cn/.