QMachine: commodity supercomputing in web browsers

Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Canc...

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Vydané v:BMC bioinformatics Ročník 15; číslo 1; s. 176
Hlavní autori: Wilkinson, Sean R, Almeida, Jonas S
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 09.06.2014
BioMed Central Ltd
Springer Nature B.V
Predmet:
Algorithms
Analysis
Big data
Bioinformatics
Biomedical and Life Sciences
Cancer
Cloud computing
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Design
Genetic aspects
Genome
Genomes
Genomics - methods
Humans
Life Sciences
Methods
Microarrays
Research Article
Sequence analysis (applications)
Software
Software Design
Streptococcus infections
Streptococcus pneumoniae
Streptococcus pneumoniae - genetics
Studies
Technology application
Volunteers
Web Browser
Crowdsourcing
Cloud computing
PaaS
JavaScript
Web service
Distributed computing
Sequence analysis
MapReduce
ISSN:1471-2105, 1471-2105
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Popis
Shrnutí:Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. Results QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running “download and install” software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. Conclusions QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-15-176