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Cloud computing tools and analyses

Collection published: 7 September 2010

The next generation sequencing 'problem', namely the generation of huge datasets that are unwieldy for analyses and expensive and problematic to store, has been remedied by the advent of cloud computing, where one rents hardware or storage space. This phenomenon has revolutionized genomic analyses and brought large-scale genomics within reach of smaller labs. The following articles - which will be updated in an ongoing basis - showcase tools and examples of studies that use such technologies.

		Research Sequencing and analysis of an Irish human genome Pin Tong, James GD Prendergast, Amanda J Lohan, Susan M Farrington, Simon Cronin, Nial Friel, Dan G Bradley, Orla Hardiman, Alex Evans, James F Wilson, Brendan Loftus Genome Biology 2010, 11:R91 (7 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first Irish human genome was sequenced to 11-fold coverage. Over 3 million SNPs and nearly 200,000 indels are identified.
		Software Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team Genome Biology 2010, 11:R86 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy computing platform allows researchers to share data and data analysis workflows, facilitating easily reproducible analyses.
		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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
		Correspondence Translational bioinformatics in the cloud: an affordable alternative Joel T Dudley, Yannick Pouliot, Rong Chen, Alexander A Morgan, Atul J Butte Genome Medicine 2010, 2:51 (6 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Cloud-based analysis offers a valid alternative both in terms of performance and cost to local computational clusters for the integration and analysis of large-scale genomic datasets relevant for translational research.
		Methodology article Cloud computing for comparative genomics Dennis P Wall, Parul Kudtarkar, Vincent A Fusaro, Rimma Pivovarov, Prasad Patil, Peter J Tonellato BMC Bioinformatics 2010, 11:259 (18 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Review The case for cloud computing in genome informatics Lincoln D Stein Genome Biology 2010, 11:207 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 3 comments \| Editor’s summary With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics.
		Review Cloud computing in pharmaceutical R&D: Business risks and mitigations K Geiger Current Opinion in Drug Discovery & Development 2010, 13:279-285 (30 April 2010) Full text \| PDF
		Software Searching for SNPs with cloud computing Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.
		Methodology article XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services Johannes Wagener, Ola Spjuth, Egon L Willighagen, Jarl ES Wikberg BMC Bioinformatics 2009, 10:279 (4 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central

		Research Sequencing and analysis of an Irish human genome Pin Tong, James GD Prendergast, Amanda J Lohan, Susan M Farrington, Simon Cronin, Nial Friel, Dan G Bradley, Orla Hardiman, Alex Evans, James F Wilson, Brendan Loftus Genome Biology 2010, 11:R91 (7 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first Irish human genome was sequenced to 11-fold coverage. Over 3 million SNPs and nearly 200,000 indels are identified.
		Software Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team Genome Biology 2010, 11:R86 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy computing platform allows researchers to share data and data analysis workflows, facilitating easily reproducible analyses.
		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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
		Correspondence Translational bioinformatics in the cloud: an affordable alternative Joel T Dudley, Yannick Pouliot, Rong Chen, Alexander A Morgan, Atul J Butte Genome Medicine 2010, 2:51 (6 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Cloud-based analysis offers a valid alternative both in terms of performance and cost to local computational clusters for the integration and analysis of large-scale genomic datasets relevant for translational research.
		Methodology article Cloud computing for comparative genomics Dennis P Wall, Parul Kudtarkar, Vincent A Fusaro, Rimma Pivovarov, Prasad Patil, Peter J Tonellato BMC Bioinformatics 2010, 11:259 (18 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Review The case for cloud computing in genome informatics Lincoln D Stein Genome Biology 2010, 11:207 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 3 comments \| Editor’s summary With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics.
		Review Cloud computing in pharmaceutical R&D: Business risks and mitigations K Geiger Current Opinion in Drug Discovery & Development 2010, 13:279-285 (30 April 2010) Full text \| PDF
		Software Searching for SNPs with cloud computing Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.
		Methodology article XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services Johannes Wagener, Ola Spjuth, Egon L Willighagen, Jarl ES Wikberg BMC Bioinformatics 2009, 10:279 (4 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central