Intuitive bioinformatics for genomics applications: Omega-brigid workflow framework

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

Volumn 5518 LNCS, Issue PART 2, 2009, Pages 1084-1091

  Díaz, David ^a   Gálvez, Sergio ^a   Falgueras, Juan ^a   Caballero, Juan Antonio ^b   Hernández, Pilar ^c   Claros, Gonzalo ^a   Dorado, Gabriel ^b  

^a UNIVERSITY OF MÁLAGA   (Spain)

^b UNIVERSITY OF CÓRDOBA   (Spain)

^c INSTITUTO DE AGRICULTURA SOSTENIBLE   (Spain)

Author keywords

GUI; Online services; Plugins; Resource integration; SNP; Workflow

Indexed keywords

BIOINFORMATICS APPLICATIONS; CODE-WRITING; COMPUTING PLATFORM; COST-EFFICIENT; DIFFERENT PROCESS; FILE FORMATS; GENOMIC DATA; GENOMICS; HARDWARE PLATFORM; LARGE AMOUNTS OF DATA; LIFE-SCIENCES; MASSIVELY PARALLEL COMPUTING; OLIVE OIL; ON-LINE SERVICE; OPERATING SYSTEMS; PLUG-INS; RESOURCE INTEGRATION; WORK-FLOWS;

COMPUTER APPLICATIONS; COMPUTER OPERATING SYSTEMS; COMPUTER PROGRAMMING; CONCENTRATION (PROCESS); ENTERPRISE RESOURCE MANAGEMENT; GRAPHICAL USER INTERFACES; NEURAL NETWORKS; PARALLEL ARCHITECTURES; SOFT COMPUTING; VEGETABLE OILS;

BIOINFORMATICS;

EID: 77952564869     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-02481-8_164     Document Type: Conference Paper

References (17)

1. Dorado, G., Falgueras, J., Claros, M.G., Gálvez, S., Hernández, P.: Bioinformatics: from command-line to GUI and multithreading. In: EU Science Forum, Heidelberg, Germany (2006)
2. Dorado, G., Vásquez, V., Rey, I., Luque, F., Jiménez, I., Morales, A., Gálvez, M., Sáiz, J., Sánchez, A., Hernández, P.: Sequencing ancient and modern genomes (Review). Archaeobios 2, 75-80 (2008)
3. Emmerich, W., Wolf, A.L. (eds.): CD 2004. LNCS, vol.3083. Springer, Heidelberg (2004)
4. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., et al.: Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948 (2006)
5. Kumar, S., Dudley, J.: Bioinformatics software for biologists in the genomics era. Bioinformatics 23, 1713-1717 (2007)
6. Bridget, S., David, G.: A compositional formalization of connector wrappers. In: Proceedings of the 25th Int. Conf. on Software Engineering. EEE Computer Society Technical Council on Software Engineering, Portland, Oregon, pp. 374-384 (2003)
7. Lopes, A., Wermelinger, M., Fiadeiro, J.: A Compositional Approach to Connector Construction. In: Cerioli, M., Reggio, G. (eds.) WADT 2001 and CoFI WG Meeting 2001. LNCS, vol.2267, pp. 201-220. Springer, Heidelberg (2002)
8. Bridget Carragher, C.S.P.F.J.S.: Software Tools for Macromolecular Microscopy. Journal of Structural Biology 157, 1-2 (2007)
9. Díaz, D., Dorado, G., Hernández, P., Castillo, A., Claros, G., Falgueras, J., Gálvez, S.: Bioinformatics Approaches for Olive Oil Quality Control. In: Plant Genomics European Meetings (Plant GEM 6). P 06.9. Tenerife, Spain (2007)
10. Cervantes, H., Charleston-Villalobos, S.: Using a workflow engine in a plugin-based product line architecture. In: Gorton, I., Heineman, G.T., Crnkovi?, I., Schmidt, H.W., Stafford, J.A., Szyperski, C., Wallnau, K. (eds.) CBSE 2006. LNCS, vol.4063, pp. 198-205. Springer, Heidelberg (2006)
11. Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48(3), 443-453 (1970)
12. Pocock, M., et al.: BioJava: Open Source Components for Bioinformatics. ACM SIGBIO Newsletter 20, 10-12 (2000)
13. Hernández, P., de la Rosa, R., Rallo, L., Martín, A., Dorado, G.: First evidence of a retrotransposon- like element in olive (Olea europaea): implications in plant variety identification by SCAR-marker development. In: TAG Theoretical and Applied Genetics, vol.102, pp. 1082-1087. Springer, Heidelberg (2001)
14. 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, 3045-3054 (2004)
15. Altintas I., Berkley C., Jaeger E., Jones M., Ludäscher B., Mock S.: Kepler: An Extensible System for Design and Execution of Scientific Workflows. 16th International Conf. on Scientific and Statistical Database Management, Proceedings, 423-424 (2004)
16. Fiers, M., van der Burgt, A., Datema, E., de Groot, J., van Ham, R.: High-throughput bioinformatics with the Cyrille2 pipeline system. BMC Bioinformatics 9, 96 (2008)
17. Falgueras, J., Lara, A., Cantón, F., Pérez-Trabado, G., Claros, G.: SeqTrim - A Validation and Trimming Tool for All Purpose Sequence Reads. In: Advances in Soft Computing, vol.44, pp. 353-360. Springer, Heidelberg (2008)