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An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs

Nature Methods volume 2, page 563 (2005)Cite this article

To the editor:

The emergence of computational biology continues to yield the advancement of diverse algorithmic methodology. Each new advance has typically used unique sources of biological information or applied faster, more accurate heuristics. But identifying the right bioinformatics program for any particular experiment continues to be burdensome as each program's performance is a function of biological context. This is further complicated as most programs can require specialized hardware, large compute resources and disparate software dependencies. It is our hypothesis that a community-driven approach to program discovery, use and assessment will increase the accessibility and relevance of these programs to a wide range of end users. We have developed an open-source, decentralized peer-to-peer platform for bioinformatics analysis, called Chinook, which allows researchers across the globe to freely integrate and access diverse command-line programs, computational resources and databases. We have demonstrated Chinook's utility to the assessment of programs used for transcription factor binding site discovery.

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Figure 1: Chinook platform.

References

  1. Montgomery, S.B. et al. Genome Res. 14, 956–962 (2004).

    Article  CAS  Google Scholar 

  2. Wilkinson, M.D. & Links, M. Brief Bioinform. 3, 331–341 (2002).

    Article  Google Scholar 

  3. States, D. J. Nature 417, 588 (2002).

    Article  CAS  Google Scholar 

  4. Birney, E. et al. Genome Res. 14, 925–928 (2004).

    Article  CAS  Google Scholar 

  5. Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. & Lenhard, B. Nucleic Acids Res. 32, D91–D94 (2004).

    Article  CAS  Google Scholar 

  6. Tompa, M. et al. Nat. Biotechnol. 23, 137–144 (2005).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Canada's Michael Smith Genome Sciences Centre, 570 W. 7th Avenue, Vancouver, V5Z 4S6, British Columbia, Canada

    Stephen B Montgomery, Tony Fu, Jun Guan, Keven Lin & Steven J M Jones

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  1. Stephen B Montgomery
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  2. Tony Fu
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  3. Jun Guan
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  4. Keven Lin
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  5. Steven J M Jones
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Montgomery, S., Fu, T., Guan, J. et al. An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs. Nat Methods 2, 563 (2005). https://doi.org/10.1038/nmeth0805-563

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