BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services

BMC Research Notes

JMiguel Ortega¹  Ricardo A Vialle¹  Henrique Velloso¹ 

[1] Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil

关键词: HPC;    Bioinformatics;    Web services;   

Others  :  1232449
DOI  :  10.1186/s13104-015-1190-0

 received in 2014-08-27, accepted in 2015-05-20,  发布年份 2015

【 摘 要 】

Background

Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal.

Results

Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients.

Conclusions

Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

【 授权许可】

   
2015 Velloso et al.

【 图 表 】

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【 参考文献 】

• [1]Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M: Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014, 42:D199-D205.
• [2]The universal protein resource (UniProt) in 2010 Nucleic Acids Res 2009, 38:D142-D148.
• [3]Gasteiger E: ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003, 31:3784-3788.
• [4]Neerincx PBT, Leunissen JAM: Evolution of web services in bioinformatics. Brief Bioinform 2005, 6:178-188.
• [5]McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, et al.: Analysis tool web services from the EMBL-EBI. Nucleic Acids Res 2013, 41:W597-W600.
• [6]Acland A, Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2014, 42:D7-D17.
• [7]Eckart JD, Sobral BWS: A life scientist’s gateway to distributed data management and computing: the PathPort/ToolBus framework. OMICS 2003, 7:79-88.
• [8]Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K: DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res 2009, 38:D33-D38.
• [9]Katayama T, Nakao M, Takagi T: TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics web services. Nucleic Acids Res 2010, 38:W706-W711.
• [10]Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, et al.: BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res 2010, 38:W689-W694.
• [11]Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, et al.: Taverna: a tool for building and running workflows of services. Nucleic Acids Res 2006, 34:W729-W732.
• [12]Altintas I, Berkley C, Jaeger E, Jones M, Ludascher B, Mock S (2004) Kepler: an extensible system for design and execution of scientific workflows. In: Proceedings 16th International Conference on Scientific and Statistical Database Management 2004
• [13]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(8):R86. BioMed Central Full Text
• [14]Romano P, Bartocci E, Bertolini G, et al.: Biowep: a workflow enactment portal for bioinformatics applications. BMC Bioinform 2007, 8(Suppl 1):S19. BioMed Central Full Text
• [15]BioVel (2015). http://www.biovel.eu. Accessed 23 Mar 2015
• [16]Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, et al.: myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res 2010, 38(suppl 2):W677-W682.
• [17]Löytynoja A, Goldman N: An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci USA 2005, 102:10557-10562.
• [18]Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
• [19]Barbosa-Silva A, Satagopam VP, Schneider R, Ortega JM: Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. BMC Bioinform 2008, 9:141. BioMed Central Full Text