MAPI: A software framework for distributed biomedical applications

Journal of Biomedical Semantics

Volumn 4, Issue 1, 2013, Pages

  Karlsson, Johan ^a   Trelles, Oswaldo ^a  

^a UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

Service oriented architectures; Software framework; Web service integration

Indexed keywords

EID: 84880078373     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-4-4     Document Type: Article

References (31)

1. Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA: BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res 2010,38(suppl 2):689-694.
2. Siegel E, Channin D: Integrating the healthcare enterprise: a primer. Radiographics 2001,21(5):1339.
3. Wolinsky H: The thousand-dollar genome. Genetic brinkmanship or personalized medicine? EMBO Rep 2007,8(10):900.
4. Sheth A, et al.: Active semantic electronic medical record. Proceedings of the 5th International Semantic Web Conference 2006, 913-926.
5. SOAP: Specification. http://www.w3.org/TR/soap/
6. Fielding R, Taylor R: Principled design of the modern web architecture. ACM Trans Internet Technol 2002,2(2):115-150.
7. FASTA: format. http://zhanglab.ccmb.med.umich.edu/FASTA/
8. Bilofsky H, Burks C: The GenBank® genetic sequence data bank. Nucleic Acids Res 1988,16(5):1861-1863.
9. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2010,38(6):1767-1771.
10. Karlsson J, Martín-Requena V, Ríos J, Trelles O: Workflow composition and enactment using jORCA. Lect Notes Comput Sci 2010, 6415:328-339.
11. Gilbert D: Sequence file format conversion with command-line readseq. Curr Protoc Bioinformatics 2002. Appendix 1E. [ http://dx.doi.org/10.1002/0471250953.bia01es00 ]
12. Ramirez S, Karlsson J, Trelles O: MAPI: towards the integrated exploitation of bioinformatics web services. BMC Bioinforma 2011, 12:419.
13. Perez-Iratxeta C, Andrade-Navarro MA, Wren JD: Evolving research trends in bioinformatics. Brief Bioinform 2007,8(2):88-95.
14. Wilkinson MD, et al.: Interoperability with Moby 1.0 - it's better than sharing your toothbrush. Brief Bioinform 2008,9(3):220-231.
15. Labarga A, Valentin F, Anderson M, Lopez R: Web services at the European Bioinformatics Institute. Nucleic Acids Res 2007,35(suppl 2):6-11.
16. Kwon Y, Shigemoto Y, Kuwana Y, Sugawara H: Web API for biology with a workflow navigation system. Nucleic Acids Res 2009,37(2):11-16.
17. Oinn T, et al.: Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004,20(17):3045-3054.
18. Instituto Nacional de Bioinformática http://www.inab.org
19. Advancing Clinico Genomic Trials http://eu-acgt.org/
20. Martín-Requena V, Ríos J, García M, Ramírez S, Trelles O: jORCA: easily integrating bioinformatics Web Service. Bioinformatics 2010,26(4):553-559.
21. Rios J, Karlsson J, Trelles O: Magallanes: A web services discovery and automatic workflow composition tool. BMC Bioinforma 2009,10(1):334.
22. Flipper http://www.bitlab-es.com/flipper/
23. Martínez A, Gordon P, Sensen C, Trelles OTowards closing the gap between user data and standardized input, Network Tools and Applications in Biology (NETTAB 2009; 2009. Towards closing the gap between user data and standardized input, Network Tools and Applications in Biology (NETTAB 2009; 2009.
24. Hull D, Stevens R, Lord P, Wroe C, Goble C: Treating shimantic web syndrome with ontologies. 2004. [AKT Workshop on Semantic Web Services]
25. Karlsson J, Torreño O, Ramet D, Klambauer G, Cano M, Trelles O: Enabling large-scale bioinformatics data analysis with cloud computing. ISPA 2012 International Workshop on Heterogeneous Architectures and Computing 2012, 640-645.
26. Foster I: The globus toolkit for grid computing. Proceedings of First IEEE/ACM International Symposium on Cluster Computing and the Grid 2001, 2.
27. OASIS UDDI http://www.oasis-open.org/standardsuddiv3.0.2
28. Lord P, Alper P, Wroe C, Goble CA: Feta: A light-weight architecture for user oriented semantic service discovery. Proc Eur Semant Web Conf 2005, 3532:17-31.
29. Oren E, Wahler A, Schreder B, Balaban A, Zaremba M: Demonstrating WSMX-least cost supply management. Proceedings of the Workshop on WSMO Implementations 2004.
30. Wilkinson MD, Vandervalk B, McCarthy L: The Semantic Automated Discovery and Integration (SADI) web service design-pattern, API and reference implementation. J Biomed Semant 2011, 2:8.
31. Goecks J, Nekrutenko A, Taylor J, The Galaxy Team: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11:R86.