Citation
Ilkay Altintas, Daniel Crawl. "bioKepler: A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data". Talk or presentation, 16, October, 2015; Presented at the Eleventh Biennial Ptolemy Miniconference, Berkeley.

Abstract
The enormous data growth due to next-generation gene sequences places unprecedented demands on traditional single-processor bioinformatics algorithms. Efficient and comprehensive analysis of the generated data requires distributed and parallel processing capabilities. Based on this motivation and our previous experiences in bioinformatics and distributed scientific workflows, we have created a Kepler suite called “bioKepler” (biokepler.org), that facilitates the development of Kepler workflows for integrated execution of bioinformatics applications in distributed environments. To develop such an environment, we build scientific workflow components to execute a set of bioinformatics tools using distributed data-parallel execution patterns. Once customized, these components are executed on multiple distributed platforms including various Cloud and HPC computing platforms. bioKepler contains a set of Kepler actors, called “bioActors”. There are two sets of bioActors: bioKepler and Bio-Linux. The bioActors inside bioKepler are configured with specific inputs, outputs, parameters, and documentation. These bioActors are specialized for running bioinformatics tools along with Kepler directors for distributed data-parallel (DDP) execution on Hadoop, Spark, and Stratosphere engines. Over 40 example workflows (http://biokepler.org/demos) demonstrating how to use these actors and directors have been packaged in the first release of bioKepler. The Bio-Linux bioActors, however, are mostly “unconfigured” with only a single input and output. These actors represent most of the 500+ biology-related tools that come with the Bio-Linux distribution (environmentalomics.org/bio-linux/). Due to this large number of bioActors, the current bioKepler release doesn’t provide configured inputs, outputs, etc., for each of these bioActors. However, users can manually create and configure them by using the Execution Choice configuration dialog. The bioActors under either bioKepler or Bio-Linux are grouped into major categories such as Alignment, Assembly, Clustering, RNA-seq, etc. To locate a bioActor, e.g., bwa, you can browse the bioActor tree or directly search from the Kepler search panel. Additionally, we have created bioKepler virtual machine images for Amazon EC2 and Docker, which includes bioKepler suite and 500+ bioinformatics tools.

Electronic downloads

• Altintas_BioKepler_PtolemyMiniconference_16Oct15.pdf · application/pdf · 4379 kbytes

• HTML

  Ilkay Altintas, Daniel Crawl. <a
  href="http://chess.eecs.berkeley.edu/pubs/1130.html"><i>bioKepler:
  A Comprehensive Bioinformatics Scientific Workflow Module
  for Distributed Analysis of Large-Scale Biological
  Data</i></a>, Talk or presentation,  16,
  October, 2015; Presented at the <a
  href="http://ptolemy.eecs.berkeley.edu/conferences/15/"
  >Eleventh Biennial Ptolemy Miniconference</a>,
  Berkeley.

• Plain text

  Ilkay Altintas, Daniel Crawl. "bioKepler: A
  Comprehensive Bioinformatics Scientific Workflow Module for
  Distributed Analysis of Large-Scale Biological Data".
  Talk or presentation,  16, October, 2015; Presented at the
  <a
  href="http://ptolemy.eecs.berkeley.edu/conferences/15/"
  >Eleventh Biennial Ptolemy Miniconference</a>,
  Berkeley.

• BibTeX

  @presentation{AltintasCrawl15_BioKeplerComprehensiveBioinformaticsScientificWorkflow,
      author = {Ilkay Altintas and Daniel Crawl},
      title = {bioKepler: A Comprehensive Bioinformatics
                Scientific Workflow Module for Distributed
                Analysis of Large-Scale Biological Data},
      day = {16},
      month = {October},
      year = {2015},
      note = {Presented at the <a
                href="http://ptolemy.eecs.berkeley.edu/conferences/15/"
                >Eleventh Biennial Ptolemy Miniconference</a>,
                Berkeley},
      abstract = {The enormous data growth due to next-generation
                gene sequences places unprecedented demands on
                traditional single-processor bioinformatics
                algorithms. Efficient and comprehensive analysis
                of the generated data requires distributed and
                parallel processing capabilities. Based on this
                motivation and our previous experiences in
                bioinformatics and distributed scientific
                workflows, we have created a Kepler suite called
                �bioKepler� (biokepler.org), that facilitates
                the development of Kepler workflows for integrated
                execution of bioinformatics applications in
                distributed environments. To develop such an
                environment, we build scientific workflow
                components to execute a set of bioinformatics
                tools using distributed data-parallel execution
                patterns. Once customized, these components are
                executed on multiple distributed platforms
                including various Cloud and HPC computing
                platforms. bioKepler contains a set of Kepler
                actors, called �bioActors�. There are two sets
                of bioActors: bioKepler and Bio-Linux. The
                bioActors inside bioKepler are configured with
                specific inputs, outputs, parameters, and
                documentation. These bioActors are specialized for
                running bioinformatics tools along with Kepler
                directors for distributed data-parallel (DDP)
                execution on Hadoop, Spark, and Stratosphere
                engines. Over 40 example workflows
                (http://biokepler.org/demos) demonstrating how to
                use these actors and directors have been packaged
                in the first release of bioKepler. The Bio-Linux
                bioActors, however, are mostly �unconfigured�
                with only a single input and output. These actors
                represent most of the 500+ biology-related tools
                that come with the Bio-Linux distribution
                (environmentalomics.org/bio-linux/). Due to this
                large number of bioActors, the current bioKepler
                release doesn�t provide configured inputs,
                outputs, etc., for each of these bioActors.
                However, users can manually create and configure
                them by using the Execution Choice configuration
                dialog. The bioActors under either bioKepler or
                Bio-Linux are grouped into major categories such
                as Alignment, Assembly, Clustering, RNA-seq, etc.
                To locate a bioActor, e.g., bwa, you can browse
                the bioActor tree or directly search from the
                Kepler search panel. Additionally, we have created
                bioKepler virtual machine images for Amazon EC2
                and Docker, which includes bioKepler suite and
                500+ bioinformatics tools. },
      URL = {http://chess.eecs.berkeley.edu/pubs/1130.html}
  }
  

Posted by Christopher Brooks on 19 Oct 2015.
Groups: ptolemy
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