The Wasp System: An open source environment for managing and analyzing genomic data

Andrew S. McLellan, Robert A. Dubin, Qiang Jing, Pilib Ó Broin, David Moskowitz, Masako Suzuki, R. Brent Calder, Joseph Hargitai, Aaron Golden, John M. Greally

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

The challenges associated with the management, analysis and interpretation of assays based on massively-parallel sequencing (MPS) are both individually complex and numerous. We describe what we believe to be the appropriate solution, one that represents a departure from traditional computational biology approaches. The Wasp System is an open source, distributed package written in Spring/J2EE that creates a foundation for development of an end-to-end solution for MPS-based experiments or clinical tests. Recognizing that one group will be unable to solve these challenges in isolation, we describe a nurtured open source development model that will allow the software to be collectively used, shared and developed. The ultimate goal is to emulate resources such as the Virtual Observatory of the astrophysics community, enabling computationally-inexpert scientists and clinicians to explore and interpret their MPS data. Here we describe the current implementation and development of the Wasp System and the roadmap for its community development.

Original languageEnglish (US)
Pages (from-to)345-351
Number of pages7
JournalGenomics
Volume100
Issue number6
DOIs
StatePublished - Dec 2012

Fingerprint

High-Throughput Nucleotide Sequencing
Wasps
Social Planning
Computational Biology
Software

Keywords

  • Database
  • Distributed
  • LIMS
  • Massively-parallel sequencing
  • Open source
  • Workflow

ASJC Scopus subject areas

  • Genetics

Cite this

The Wasp System : An open source environment for managing and analyzing genomic data. / McLellan, Andrew S.; Dubin, Robert A.; Jing, Qiang; Broin, Pilib Ó; Moskowitz, David; Suzuki, Masako; Calder, R. Brent; Hargitai, Joseph; Golden, Aaron; Greally, John M.

In: Genomics, Vol. 100, No. 6, 12.2012, p. 345-351.

Research output: Contribution to journalArticle

McLellan, AS, Dubin, RA, Jing, Q, Broin, PÓ, Moskowitz, D, Suzuki, M, Calder, RB, Hargitai, J, Golden, A & Greally, JM 2012, 'The Wasp System: An open source environment for managing and analyzing genomic data', Genomics, vol. 100, no. 6, pp. 345-351. https://doi.org/10.1016/j.ygeno.2012.08.005
McLellan, Andrew S. ; Dubin, Robert A. ; Jing, Qiang ; Broin, Pilib Ó ; Moskowitz, David ; Suzuki, Masako ; Calder, R. Brent ; Hargitai, Joseph ; Golden, Aaron ; Greally, John M. / The Wasp System : An open source environment for managing and analyzing genomic data. In: Genomics. 2012 ; Vol. 100, No. 6. pp. 345-351.
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