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An Extensible Framework for Genomic and Metagenomic Analysis

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8826))

Abstract

Computational tools for supporting the management of scientific experiments are fundamental for the modern science. These tools must be easy to use, extensible and robust. This paper presents a framework for managing bioinformatics’ experiments, focusing on analysis of genomic and metagenomic data. The developed system is based on an extension of a scientific workflows management system combined with the development of specific tools related to genomic and metagenomic data analysis.

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References

  1. Agrawal, R., Srikant, R.: Fast algorithms for mining association rules in large databases. In: International Conference On Very Large Data Bases (VLDB 1994), pp. 487–499. Morgan Kaufmann Publishers, Inc. (1994)

    Google Scholar 

  2. Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludascher, B., Mock, S.: Kepler: An extensible system for design and execution of scientific workflows. In: Proceedings of the 16th International Conference on Scientific and Statistical Database Management, Washington, DC, USA, pp. 423–424 (2004)

    Google Scholar 

  3. Andrioli, L.P., Digiampietri, L.A., de Barros, L.P., Machado-Lima, A.: Huckebein is part of a combinatorial repression code in the anterior blastoderm. Developmental Biology 361(1), 177–185 (2012)

    Article  Google Scholar 

  4. Angly, F.E., Fields, C.J., Tyson, G.W.: The bio-community perl toolkit for microbial ecology. Bioinformatics (2014)

    Google Scholar 

  5. Callahan, S.P., Freire, J., Santos, E., Scheidegger, C.E., Silva, C.T., Vo, H.T.: Managing the evolution of dataflows with VisTrails. In: Proceedings of the 22nd International Conference on Data Engineering Workshops, p. 71 (2006)

    Google Scholar 

  6. Curcin, V., Ghanem, M.: Scientific workflow systems - can one size fit all? In: Biomedical Engineering Conference, CIBEC 2008, pp. 1–9 (2008)

    Google Scholar 

  7. Deelman, E., Gannon, D., Shields, M., Taylor, I.: Workflows and e-science: An overview of workflow system features and capabilities. Future Generation Computer Systems 25(5), 528–540 (2009)

    Article  Google Scholar 

  8. Digiampietri, L.A., Araujo, J.C., Ostroski, E.H., Santiago, C.R.N., Perez-Alcazar, J.J.: Combinando workflows e semantica para facilitar o reuso de software. Revista de Informatica Teorica e Aplicada: RITA 20, 73–89 (2013)

    Google Scholar 

  9. Goecks, J., Nekrutenko, A., Taylor, J., Team, T.G.: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 11(8), R86 (2010)

    Google Scholar 

  10. Hey, T., Tansley, S., Tolle, K. (eds.): The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, Redmond (2009)

    Google Scholar 

  11. Long, D., Fox, M.: The 3rd International Planning Competition: Results and Analysis. Journal of Artificial Intelligence Research 20, 1–59 (2003)

    Article  MATH  Google Scholar 

  12. Lu, S., Zhang, J.: Collaborative scientific workflows. In: IEEE International Conference on Web Services, ICWS 2009, pp. 527–534 (2009)

    Google Scholar 

  13. Mangalam, H.: The bio* toolkits - A brief preview. Briefings in Bioinformatics 3(3), 296–302 (2002)

    Article  Google Scholar 

  14. Martins, L.F., Antunes, L.P., Pascon, R.C., de Oliveira, J.C.F., Digiampietri, L.A., Barbosa, D., Peixoto, B.M., Vallim, M.A., Viana-Niero, C., Ostroski, E.H., et al.: Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms. Plos One 8(4), e61928 (2013)

    Google Scholar 

  15. Medeiros, C., Perez-Alcazar, J., Digiampietri, L., Pastorello, G., Santanche, A., Torres, R., Madeira, E., Bacarin, E.: WOODSS and the Web: Annotating and Reusing Scientific Workflows. ACM SIGMOD Record 34(3), 18–23 (2005)

    Article  Google Scholar 

  16. Oliveira, F.T.: Um sistema de recomendacao para composicao de workflows. Master’s thesis, COPPE/UFRJ (2010)

    Google Scholar 

  17. Rao, J., Su, X.: A survey of automated web service composition methods. In: Cardoso, J., Sheth, A.P. (eds.) SWSWPC 2004. LNCS, vol. 3387, pp. 43–54. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  18. Setubal, J., Meidanis, J.: Introduction to Computational Molecular Biology. PWS Publishing Company, Boston (1997)

    Google Scholar 

  19. Taylor, I., Shields, M., Wang, I., Harrison, A.: Visual grid workflow in triana. Journal of Grid Computing 3(3-4), 153–169 (2005)

    Article  Google Scholar 

  20. Zuniga, J.C., PrezAlczar, J.J., Digiampietri, L.A., Barbin, S.E.: A loosely coupled architecture for automatic composition of web services applications. International Journal of Metadata, Semantics and Ontologies 9(3), 241–251 (2014)

    Article  Google Scholar 

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Digiampietri, L.A., Pereira, V.M.Y., Costa, C.I., dos Santos Júnior, G.J., Stefanini, F.M., Santiago, C.R.N. (2014). An Extensible Framework for Genomic and Metagenomic Analysis. In: Campos, S. (eds) Advances in Bioinformatics and Computational Biology. BSB 2014. Lecture Notes in Computer Science(), vol 8826. Springer, Cham. https://doi.org/10.1007/978-3-319-12418-6_1

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  • DOI: https://doi.org/10.1007/978-3-319-12418-6_1

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-12417-9

  • Online ISBN: 978-3-319-12418-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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