Implementation and evaluation of a Java based computational grid for bioinformatics applications

Author

Yang, Chao-Tung ; Hsiung, Yi-Chun ; Kan, Heng-Chuan

Author_Institution

Dept. of Comput. Sci. & Inf. Eng., Tunghai Univ., Taichung City, Taiwan

Volume

1

fYear

2005

fDate

28-30 March 2005

Firstpage

298

Abstract

In the present study, THUBioGrid, an experimental distributed computing application for bioinformatics (BioGrid) is proposed. THUBioGrid incorporates directory services (data and software), grid computing methods (security, authentication, data transport and remote jobs), and gene sequence/genomic data processing methods. It uses Java CoG Kit plus bioinformatics Java packages to perform various computational tasks. The performance of THUBioGrid has been tested by executing the FASTA and mpiBLAST programs for protein sequence alignment applications. Results demonstrate the speed-up effects with increasing number of processors used in the computations.

Keywords

Java; biology computing; genetics; grid computing; message passing; middleware; proteins; sequences; FASTA program; Java CoG Kit; Java based computational grid; THUBioGrid platform; bioinformatics applications; directory service; distributed computing; genomic data processing; message passing; middleware; mpiBLAST program; protein sequence alignment; Application software; Authentication; Bioinformatics; Data processing; Data security; Distributed computing; Genomics; Grid computing; Java; Packaging; BioGrid; FASTA; Grid Computing; Java CoG; mpiBLAST;

fLanguage

English

Publisher

ieee

Conference_Titel

Advanced Information Networking and Applications, 2005. AINA 2005. 19th International Conference on

ISSN

1550-445X

Print_ISBN

0-7695-2249-1

Type

conf

DOI

10.1109/AINA.2005.209

Filename

1423508