The case for cloud computing in genome informatics
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Correspondence: Lincoln D Stein lincoln.stein@gmail.com
Genome Biology 2010, 11:207 doi:10.1186/gb-2010-11-5-207
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Software
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community Konstantinos Krampis, Tim Booth, Brad Chapman, Bela Tiwari, Mesude Bicak, Dawn Field, Karen Nelson BMC Bioinformatics 2012, 13:42 (19 March 2012) Cloud BioLinux includes over 135 pre-configured bioinformatics tools for sequence alignment, clustering, assembly, display and phylogeny, aimed at reducing costs to researchers of maintaining and configuring hardware, and encouraging sharing of codebase.
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Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke BMC Bioinformatics 2011, 12:356 (30 August 2011) Cloud Virtual Resource (CloVR) is a new desktop application for large-scale sequence analysis using remote computing resources that provides several automated pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis.
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Opinion
The real cost of sequencing: higher than you think! Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein Genome Biology 2011, 12:125 (25 August 2011) The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
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Software
Cistrome: an integrative platform for transcriptional regulation studies Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu Genome Biology 2011, 12:R83 (22 August 2011) A Galaxy-based web application for integrative analysis of ChIP data
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Proceedings
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics Ronald C Taylor BMC Bioinformatics 2010, 11(Suppl 12):S1 (21 December 2010) |
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Software
Cloud-scale RNA-sequencing differential expression analysis with Myrna Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010) This article is part of a collection on Cloud computing tools and... Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
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