Abstract
The recent developments in life sciences and technology have produced large amounts of data in an extremely fast and cost-efficient way which require the development of new algorithms, coupled with massively parallel computing. Besides, biologists are usually non-programmers, thus demanding intuitive computer applications that are easy to use by means of a friendly GUI. In addition, different algorithms, databases and other tools usually lie on incompatible file formats, applications, operating systems and hardware platforms. It is therefore of paramount importance to overcome such limitations, so that bioinformatics becomes much more widely used amongst biologists. The main goal of our research project is to unify many of these existing bioinformatics applications and resources (local and remote) in one easy-to-use environment, independent of the computing platform, being a concentrator resource tool with a friendly interface. To achieve this, we propose a tool based on a new, open, free and well-documented architecture called Biomniverso. Two main elements make up such a tool: its kernel (Omega), which supplies services specifically adapted to allow the addition of new bioinformatics functionalities by means of plugins (like Minerva, which makes easy to detect SNP amongst a set of genomic data to discover fraudulent olive oil), and the interface (Brigid), which allows even non-programmer laboratory scientists to chain different processes into workflows and customize them without code writing.
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References
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)
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)
Emmerich, W., Wolf, A.L. (eds.): CD 2004. LNCS, vol. 3083. Springer, Heidelberg (2004)
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)
Kumar, S., Dudley, J.: Bioinformatics software for biologists in the genomics era. Bioinformatics 23, 1713–1717 (2007)
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)
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)
Bridget Carragher, C.S.P.F.J.S.: Software Tools for Macromolecular Microscopy. Journal of Structural Biology 157, 1–2 (2007)
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)
Cervantes, H., Charleston-Villalobos, S.: Using a workflow engine in a plugin-based product line architecture. In: Gorton, I., Heineman, G.T., Crnković, I., Schmidt, H.W., Stafford, J.A., Szyperski, C., Wallnau, K. (eds.) CBSE 2006. LNCS, vol. 4063, pp. 198–205. Springer, Heidelberg (2006)
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)
Pocock, M., et al.: BioJava: Open Source Components for Bioinformatics. ACM SIGBIO Newsletter 20, 10–12 (2000)
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)
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)
Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludäscher, B., Mock, S.: Kepler: An Extensible System for Design and Execution of Scientific Workflows. In: 16th International Conf. on Scientific and Statistical Database Management, Proceedings, pp. 423–424 (2004)
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)
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)
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Díaz, D. et al. (2009). Intuitive Bioinformatics for Genomics Applications: Omega-Brigid Workflow Framework. In: Omatu, S., et al. Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. IWANN 2009. Lecture Notes in Computer Science, vol 5518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02481-8_164
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DOI: https://doi.org/10.1007/978-3-642-02481-8_164
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