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Implementing a Bioinformatics Workflow in a Parallel and Distributed Environment

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Parallel and Distributed Computing: Applications and Technologies (PDCAT 2004)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 3320))

Abstract

This paper illustrates a bioinformatics workflow and its execution in a parallel and distributed environment. Our paper is organized into two main parts. The first part describes a bioinformatics study of a genome wide analysis based on full length human transcripts (cDNA information) to determine gene expression in various tissues. The second part is the execution of the workflow in a parallel and distributed environment. We show the embarrassingly parallel structure of the workflow, its implementation in a distributed cluster environment and the efficiency that can be achieved by automation of the workflow through a parallel scripting language.

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References

  1. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C.: Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)

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  2. Strausberg, R.L., Feingold, E.A., Klausner, R.D., Collins, F.S.: The Mammalian Gene Collection. Science 286, 455–457 (1999)

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  3. Chua, C.L., Tang, F., Issac, P., Krishnan, A.: GEL: Grid Execution Language. Journal of Parallel and Distributed Computing (2004) (to be submitted)

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Author information

Authors and Affiliations

  1. Bioinformatics Institute, 30 Biopolis St, #07-01 Matrix, 138671, Singapore

    Ching-Lian Chua, Francis Tang, Yun-Ping Lim, Liang-Yoong Ho & Arun Krishnan

Authors
  1. Ching-Lian Chua
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  2. Francis Tang
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  3. Yun-Ping Lim
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  4. Liang-Yoong Ho
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  5. Arun Krishnan
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Editor information

Editors and Affiliations

  1. Nanyang Centre for Supercomputing and Visualisation School of Mechanical and Production Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639 798, Singapore

    Kim-Meow Liew

  2. School of Computer Science, The University of Adelaide,  

    Hong Shen

  3. Asia Pacific Science and Technology Center, Sun Microsystems Inc., 50 Nanyang Avenue, N3-1c-10, 639798, Singapore

    Simon See

  4. School of Computer Engineering, Nanyang Technological University, 639798, Singapore

    Wentong Cai

  5. Southwest Jiaotong University,  

    Pingzhi Fan

  6. Tohoku University ,  

    Susumu Horiguchi

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© 2004 Springer-Verlag Berlin Heidelberg

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Cite this paper

Chua, CL., Tang, F., Lim, YP., Ho, LY., Krishnan, A. (2004). Implementing a Bioinformatics Workflow in a Parallel and Distributed Environment. In: Liew, KM., Shen, H., See, S., Cai, W., Fan, P., Horiguchi, S. (eds) Parallel and Distributed Computing: Applications and Technologies. PDCAT 2004. Lecture Notes in Computer Science, vol 3320. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30501-9_1

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  • DOI: https://doi.org/10.1007/978-3-540-30501-9_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-24013-6

  • Online ISBN: 978-3-540-30501-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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