BioInfoWF – WEB SERVICES AND WEB INTERFACES GENERATOR FOR BIOINFORMATICS ANALYSIS
Abstract
The BioinfoWF (Bioinformatics WorkFlow) system for automated generation of Web interface and Web services for bioinformatics programs. Each program module used in the system has metadescription in XML. The metadescriptions are used for automated generation of Web interface and Web services that can be used further in bioinformatics workflows. Computational modules can be organized in workflows. The tool we have developed significantly simplify the design and publication of modules for bioinformatics data analysis via the internet and their availability for scientific communities. The developed system makes is distributed under GNU GPL. The Source codes and documentation for BioinfoWF are available at http://bioinfowf.bionet.nsc.ru.
About the Authors
M. A. Genaev
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
E. G. Komyshev
Novosibirsk National Research State University, Novosibirsk, Russia
Russian Federation
Russian Federation
K. V. Gunbin
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
D. A. Afonnikov
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Novosibirsk National Research State University, Novosibirsk, Russia
Russian Federation
Russian Federation
References
1. Гунбин К.В., Генаев М.А., Турнаев И.И., Афонников Д.А. Компьютерная система анализа режимов молекулярной эволюции генов и белков: анализ эволюции циклинов B // Вестн. Томского гос. ун-та. Биология. 2011. 4. С. 175–189.
2. Bhagat J., Tanoh F., Nzuobontane E. et al. BioCatalogue: a universal catalogue of Web services for the life sciences // Nucl. Acids Res. 2010. V. 38. Р. 689–694.
3. Deelman E., Gannon D., Shields M., Taylor I. Workfl ows and e-Science: An overview of workfl ow system features and capabilities // Future Generation Computer Systems. 2009. V. 25. Р. 528–540.
4. Dereeper A., Guignon V., Blanc G. et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist // Nucl. Acids Res. 2008. V. 36. Р. 465–469.
5. Fernald G.H., Capriotti E., Daneshjou R. et al. Bioinformatics challenges for personalized medicine // Bioinformatics. 2011. V. 27. Р. 1741–1748.
6. Goble C.A., Bhagat J., Aleksejevs S. et al. myExperiment: a repository and social network for the sharing of bioinformatics workfl ows // Nucl. Acids Res. 2010. V. 38. Р. 677–682.
7. Goecks J., Nekrutenko A., Taylor J., Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences // Genome Biol. 2010. 11:R86.
8. Gunbin K.V., Suslov V.V., Genaev M.A., Afonnikov D.A. Computer system for analysis of molecular evolution modes (SAMEM): analysis of molecular evolution modes at deep inner branches of the phylogenetic tree // In Silico Biol. 2012. In press.
9. Gunbin K.V., Suslov V.V., Turnaev I.I. et al. Molecular evolution of cyclin proteins in animals and fungi // BMC Evol. Biol. 2011. V. 11. P. 224.
10. Hartmann A., Czauderna T., Hoffmann R. et al. HTPheno: an image analysis pipeline for high-throughput plant phenotyping // BMC Bioinformatics. 2011. V. 12. P. 148.
11. Moore J.H., Asselbergs F.W., Williams S.M. Bioinformatics challenges for genome-wide association studies // Bioinformatics. 2010. V. 26. Р. 445–455.
12. Oinn T., Addis M., Ferris J. et al. Taverna: a tool for the composition and enactment of bioinformatics workfl ows // Bioinformatics. 2004. V. 20. Р. 3045–3054.
13. Pop M., Salzberg S.L. Bioinformatics challenges of new sequencing technology // Trends Genet. 2008. V. 24. Р. 142–149.
14. Pupko T., Pe’er I., Hasegawa M. et al. A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of fi ve gene families // Bioinformatics. 2002. V. 18. Р. 1116–1123.
15. Sánchez R., Serra F., Tárraga J. et al. Phylemon 2.0: a suite of Web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing // Nucl. Acids Res. 2011. V. 39. Р. 470–474.
16. Smith N.G. Are radical and conservative substitution rates useful statistics in molecular evolution? // J. Mol. Evol. 2003. V. 57. Р. 467–478.
17. Zhang J. Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes // J. Mol. Evol. 2000. V. 50. Nо. 1. P. 56–68.
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