DISTRIBUTED RESTful WEB SERVICES FOR RECONSTRUCTION AND ANALYSIS OF GENE NETWORKS
Abstract
This paper describes a RESTful Web service-based distributed software system, which focuses on the reconstruction of gene networks by integrating data from heterogeneous data sources, including databases of molecular-genetic interactions, metabolic and signaling pathways, gene networks, etc.
About the Authors
N. L. Podkolodnyy
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
A. V. Semenychev
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
D. A. Rasskazov
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
V. G. Borowsky
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
E. A. Ananko
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
E. V. Ignatieva
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
N. N. Podkolodnaya
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
O. A. Podkolodnaya
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
N. A. Kolchanov
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Novosibirsk National Research State University, Novosibirsk, Russia
National Research Centre «Kurchatov Institute», Moscow, Russia
Russian Federation
Russian Federation
References
1. Гринвальд Р., Стаковьяк Р., Стерн Д. Oracle 11g. Основы. СПб.: Символ-плюс, 2009. 464 с.
2. Кайт Т. Oracle для профессионалов: архитектура, программирование и особенности версий 9i, 10g и 11g. «ВИЛЬЯМС», 2011. 848 с.
3. Колчанов Н.А., Ананько Е.А., Колпаков Ф.А. и др. Генные сети // Молекуляр. биология. 2000. Т. 34. № 4. С. 533–544.
4. Ananko E.A., Podkolodny N.L., Stepanenko I.L. et al. GeneNet in 2005 // Nucl. Acids Res. 2005. V. 33. D425–D427.
5. Aranda B., Achuthan P., Alam-Faruque Y. et al. The IntAct molecular interaction database in 2010 // Nucl. Acids Res. 2009. V. 38. D525–D531.
6. Caspi R., Altman T., Dale J.M. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases // Nucl. Acids Res. 2010. V. 38. P. 473–479.
7. Chatr-Aryamontri A., Ceol A., Palazzi L.M. et al. MINT: the Molecular INTeraction database // Nucl. Acids Res. 2007. V. 35. P. 572–574.
8. Croft D., O’Kelly G., Wu G., Haw R. et al. Reactome: a database of reactions, pathways and biological processes // Nucl. Acids Res. 2011. V. 39. P. 691–697.
9. Csárdi G., Nepusz T. The igraph software package for complex network research // Intern. J. Complex Syst. 2006a. V. 1695.
10. Csárdi G., Nepusz T. igraph Reference Manual // 29-33 Konkoly-Thege Miklуs road, Budapest H-1121, Hungary, 509 p. 2006b. http://igraph.sourceforge.net/doc/igraphdocs.pdf
11. Galperin M.Y., Fernández-Suárez X.M. The 2012 nucleic acids research database issue and the online molecular biology database collection // Nucl. Acids Res. 2011. V. 40. D1-D8.
12. Kolchanov N.A., Ignatieva E.V., Podkolodnaya O.A. et al. TRRD: Technology for extraction, storage, and use of knowledge about the structural-functional organization of the transcriptional regulatory regions in the eukaryotic genes // Intell. Data Anal. 2008. V. 12. No. 5. P. 443–461.
13. Kolpakov F.A., Ananko E.A., Kolesov G.B., Kolchanov N.A. GeneNet: a database for gene networks and its automated visualization // Bioinformatics. 1998. V. 14. No. 6. P. 529–537.
14. Newman M.E.J. Finding community structure in networks using the eigenvectors of matrices // Phys. Rev. 2006. E 74, 036104.
15. Richardson L., Ruby S. RESTful Web Services. O’Relly Media. Inc., 1005 Gravensein Highway North, Sebastopol, CA, 2007. 420 c.
16. Schaefer C.F., Anthony K., Krupa S. et al. PID: the pathway interaction database // Nucl. Acids Res. 2009. V. 37. P. 674–679.
17. Scheer M., Grote A., Chang A. et al. BRENDA, the enzyme information system in 2011 // Nucl. Acids Res. 2011. V. 39. P. 670–676.
18. Schreier S. Modeling RESTful applications // Proc. WS-REST ‘11 Proceedings of the Second Intern. Workshop on RESTful Design. ACM, NY, USA, 2011. P. 15–21.
19. Subbu Allamaraju RESTful Web Servises Cookbook. O’Relly Media, Inc. 2010. 293 с.
20. Valverde F., Pastor O. Dealing with REST Services in Modeldriven Web Engineering Methods // V Jornadas Científi co-Técnicas en Servicios Web y SOA, JSWEB. 2009.
21. Wrzodek C., Drager A., Zell A. KEGG translator: visualizing and converting the KEGG PATHWAY database to various formats // Bioinformatics. 2011. V. 27. No. 16. P. 2314–2315.
Review
Views:
509
Email this article 