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Bio-Cirrus: A Framework for Running Legacy Bioinformatics Applications with Cloud Computing Resources

  • Tor Johan Mikael Karlsson
  • Óscar Torreño Tirado
  • Daniel Ramet
  • Juan Lago
  • Juan Falgueras Cano
  • Noura Chelbat
  • Oswaldo Trelles
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7903)

Abstract

Technological advances in biological and biomedical data acquisition are creating mountains of data. Existing legacy applications are unable to process this data without using new strategies. However, some workloads in bioinformatics are easily parallelized by splitting the data, running legacy applications in parallel and then join the partial results into one final result. In this paper, we present Bio-Cirrus, a software package which facilitates this process. Our software consists of a user-friendly client (jORCA) for accessing Web Services and enacting workflows, and a module (Mr. Cirrus) for processing the data with a map/reduce style approach. Bio-Cirrus binaries and documentation are freely available at http://www.bitlab-es.com/cloud under the Creative Commons Attribution-No Derivative Works 2.5 Spain License and its source code is available under request. (GPL v3 license).

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Tor Johan Mikael Karlsson
    • 1
  • Óscar Torreño Tirado
    • 1
  • Daniel Ramet
    • 1
  • Juan Lago
    • 4
  • Juan Falgueras Cano
    • 2
  • Noura Chelbat
    • 3
  • Oswaldo Trelles
    • 1
  1. 1.Department of Computer ArchitectureUniversity of MálagaMálagaSpain
  2. 2.Department of Languages and Computer SciencesUniversity of MálagaMálagaSpain
  3. 3.Institute for BioinformaticsJohannes Kepler UniversityLinzAustria
  4. 4.Fundacion Iavante, Consejeria de Salud, Junta de AndalucíaSpain

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