Agile parallel bioinformatics workflow management using Pwrake View Full Text


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Article Info

DATE

2011-09-08

AUTHORS

Hiroyuki Mishima, Kensaku Sasaki, Masahiro Tanaka, Osamu Tatebe, Koh-ichiro Yoshiura

ABSTRACT

BackgroundIn bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows.FindingsWe implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows.ConclusionsPwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles may facilitate sharing workflows among the scientific community. Workflows for GATK and Dindel are available at http://github.com/misshie/Workflows. More... »

PAGES

331

References to SciGraph publications

  • 2010-07. Gfarm Grid File System in NEW GENERATION COMPUTING
  • 2009-07-16. An introduction to scripting in Ruby for biologists in BMC BIOINFORMATICS
  • 2004-04-19. Pegasys: software for executing and integrating analyses of biological sequences in BMC BIOINFORMATICS
  • 2003-07. Workflow Patterns in DISTRIBUTED AND PARALLEL DATABASES
  • 2008-02-12. High-throughput bioinformatics with the Cyrille2 pipeline system in BMC BIOINFORMATICS
  • 2005-10. A haplotype map of the human genome in NATURE
  • 2007-03-08. Biowep: a workflow enactment portal for bioinformatics applications in BMC BIOINFORMATICS
  • 2011-02-25. A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines in BMC BIOINFORMATICS
  • 2008-05-28. Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs in BMC BIOINFORMATICS
  • 2010-10-27. A map of human genome variation from population-scale sequencing in NATURE
  • 2010-10-24. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing in NATURE GENETICS
  • 2003-03. Mapping Abstract Complex Workflows onto Grid Environments in JOURNAL OF GRID COMPUTING
  • 2007-03-08. BioWMS: a web-based Workflow Management System for bioinformatics in BMC BIOINFORMATICS
  • 2006-05-30. Agile methods in biomedical software development: a multi-site experience report in BMC BIOINFORMATICS
  • 2010-08-25. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences in GENOME BIOLOGY
  • 2011-04-10. A framework for variation discovery and genotyping using next-generation DNA sequencing data in NATURE GENETICS
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    DIMENSIONS

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    PUBMED

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