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Data-Intensive Computing Infrastructure Systems for Unmodified Biological Data Analysis Pipelines

  • Lars Ailo Bongo
  • Edvard Pedersen
  • Martin Ernstsen
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8623)

Abstract

Biological data analysis is typically implemented using a deep pipeline that combines a wide array of tools and databases. These pipelines must scale to very large datasets, and consequently require parallel and distributed computing. It is therefore important to choose a hardware platform and underlying data management and processing systems well suited for processing large datasets. There are many infrastructure systems for such data-intensive computing. However, in our experience, most biological data analysis pipelines do not leverage these systems.

We give an overview of data-intensive computing infrastructure systems, and describe how we have leveraged these for: (i) scalable fault-tolerant computing for large-scale biological data; (ii) incremental updates to reduce the resource usage required to update large-scale compendium; and (iii) interactive data analysis and exploration. We provide lessons learned and describe problems we have encountered during development and deployment. We also provide a literature survey on the use of data-intensive computing systems for biological data processing. Our results show how unmodified biological data analysis tools can benefit from infrastructure systems for data-intensive computing.

Keywords

data-intensive computing biological data analysis flexible pipelines infrastructure systems 

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Lars Ailo Bongo
    • 1
  • Edvard Pedersen
    • 1
  • Martin Ernstsen
    • 2
  1. 1.Department of Computer Science and Center for BioinformaticsUniversity of TromsøTromsøNorway
  2. 2.Now at Kongsberg Satellite Services ASTromsøNorway

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