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%% BioMed_Central_Bib_Style_v1.01
\begin{thebibliography}{10}
\providecommand{\url}[1]{[#1]}
\providecommand{\urlprefix}{}
\bibitem{venterdublin}
\emph{Syntetic Biology, Euroscience Open Forum 2012}.
\bibitem{Schrodinger1992}
\emph{What is life?: With mind and matter and autobiographical sketches}.
Cambridge University Press 1992.
\bibitem{Gibson2010}
Gibson D, Glass J, Lartigue C, Noskov V, Chuang R, Algire M, Benders G,
Montague M, Ma L, Moodie M: \textbf{Creation of a bacterial cell controlled
by a chemically synthesized genome}. \emph{science} 2010,
\textbf{329}(5987):52--56.
\bibitem{Rusch2007}
Rusch D, Halpern A, Sutton G, Heidelberg K, Williamson S, Yooseph S, Wu D,
Eisen J, Hoffman J, Remington K: \textbf{The Sorcerer II global ocean
sampling expedition: northwest Atlantic through eastern tropical Pacific}.
\emph{PLoS biology} 2007, \textbf{5}(3):e77.
\bibitem{Nelson2010}
Nelson K, Weinstock G, Highlander S, Worley K, Creasy H, Wortman J, Rusch D,
Mitreva M, Sodergren E, Chinwalla A: \textbf{A catalog of reference genomes
from the human microbiome}. \emph{Science (New York, NY)} 2010,
\textbf{328}(5981):994.
\bibitem{Mason2012}
Mason C, Elemento O: \textbf{Faster sequencers, larger datasets, new
challenges}. \emph{Genome Biology} 2012.
\bibitem{Illumina}
Illumina I: \textbf{Technical Specifications of Illumina Sequencers}.
\bibitem{solid5500}
Inc AB: \textbf{The SOLiD 5500 sequencing system.}
\bibitem{PacBio}
Inc PB: \textbf{PacBio RS sequencing technology}.
\bibitem{Loman2012a}
Loman N, Misra R, Dallman T: \textbf{Performance comparison of benchtop
high-throughput sequencing platforms} 2012.
\bibitem{Mardis2008}
Mardis E: \textbf{Next-generation DNA sequencing methods}. \emph{Annu. Rev.
Genomics Hum. Genet.} 2008, \textbf{9}:387--402.
\bibitem{gogol2012overview}
Gogol-D{\"o}ring A, Chen W, et~al.: \textbf{An overview of the analysis of next
generation sequencing data}. \emph{Methods in Molecular Biology} 2012,
\textbf{802}:249--257.
\bibitem{altschul1990basic}
Altschul S, Gish W, Miller W, Myers E, Lipman D, et~al.: \textbf{Basic local
alignment search tool}. \emph{Journal of molecular biology} 1990,
\textbf{215}(3):403--410.
\bibitem{johnson2008ncbi}
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden T:
\textbf{NCBI BLAST: a better web interface}. \emph{Nucleic acids research}
2008, \textbf{36}(suppl 2):W5--W9.
\bibitem{Pruitt2009}
Pruitt K, Tatusova T, Klimke W, Maglott D: \textbf{NCBI Reference Sequences:
current status, policy and new initiatives}. \emph{Nucleic acids research}
2009, \textbf{37}(suppl 1):D32--D36.
\bibitem{schaller1997moore}
Schaller R: \textbf{Moore's law: past, present and future}. \emph{Spectrum,
IEEE} 1997, \textbf{34}(6):52--59.
\bibitem{ncbi}
\textbf{National Center for Biotechnology
Information:}\urlprefix\url{[http://www.ncbi.nlm.nih.gov]}.
\bibitem{sra}
Information NCFB: \textbf{Sequence Read Archive}.
\bibitem{awsec2}
Services AW: \textbf{Elastic Compute Cloud (EC2)}.
\bibitem{ec2price}
Services AW: \textbf{EC2 Pricing}.
\bibitem{ec2regions}
\textbf{Amazon EC2 Cloud global regions}.
\bibitem{clarke2012}
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B,
Preuss D, Leinonen R, Shumway M: \textbf{The 1000 Genomes Project: data
management and community access}. \emph{nature methods} 2012,
\textbf{9}(5):459--462.
\bibitem{1000tube1}
Krampis K: \textbf{Accessing 1000 Human Genomes Data with Cloud BioLinux}.
\bibitem{1000tube2}
Krampis K: \textbf{Accessing 1000 Human Genomes Data with Cloud BioLinux}.
\bibitem{Krampis2012}
Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE:
\textbf{Cloud BioLinux: pre-configured and on-demand bioinformatics computing
for the genomics community}. \emph{BMC Bioinformatics} 2012, \textbf{13}:42.
\bibitem{sourceforge}
\textbf{SourceForge open-source code repository}.
\bibitem{github}
Inc G: \textbf{Open-Source code repository}.
\bibitem{Subramaniam1998Biology}
Subramaniam S: \textbf{The biology workbench---A seamless database and analysis
environment for the biologist}. \emph{Proteins} 1998, \textbf{32}:1--2.
\bibitem{Letondal2001Web}
Letondal C: \textbf{A Web interface generator for molecular biology programs in
Unix}. \emph{Bioinformatics} 2001, \textbf{17}:73--82.
\bibitem{Sarachu2005WEMBOSS}
Sarachu M, Colet M: \textbf{wEMBOSS: a web interface for EMBOSS}.
\emph{Bioinformatics} 2005, \textbf{21}(4):540--541.
\bibitem{Neron2009Mobyle}
Neron B, and H Menager, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S,
Tuffery P, Letondal C: \textbf{Mobyle: a new full web bioinformatics
framework Bioinformatics}. \emph{Bioinformatics} 2009,
\textbf{25}(22):3005--3011.
\bibitem{Cattley2007BioManager}
Cattley S, Arthur JW: \textbf{BioManager: the use of a bioinformatics web
application as a teaching tool in undergraduate bioinformatics training}.
\emph{Briefings in Bioinformatics} 2007, \textbf{8}(6):457--465.
\bibitem{Lushbough2008Implementing}
Lushbough CM, Bergman MK, Lawrence C, Jennewein D, Volker B:
\textbf{Implementing bioinformatic workflows within the BioExtract Server}.
\emph{International Journal of Computational Biology and Drug Design} 2008,
\textbf{1}(3):302--312.
\bibitem{Grigoriev2012}
Grigoriev I, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A,
Minovitsky S, Nikitin R, Ohm R: \textbf{The Genome Portal of the Department
of Energy Joint Genome Institute}. \emph{Nucleic Acids Research} 2012,
\textbf{40}(D1):D26--D32.
\bibitem{Altintas2010}
\emph{Camera 2.0: A data-centric metagenomics community infrastructure driven
by scientific workflows}, IEEE 2010.
\bibitem{Hunter2011}
Hunter C, Cochrane G, Apweiler R, Hunter S: \textbf{The EBI Metagenomics
Archive, Integration and Analysis Resource}. \emph{Handbook of Molecular
Microbial Ecology I} 2011, :333--340.
\bibitem{Aziz2010}
Aziz R: \textbf{Subsystems-based servers for rapid annotation of genomes and
metagenomes}. \emph{BMC Bioinformatics} 2010, \textbf{11}(Suppl 4):O2.
\bibitem{Goecks2010}
Goecks J, Nekrutenko A, Taylor J: \textbf{Galaxy: a comprehensive approach for
supporting accessible, reproducible, and transparent computational research
in the life sciences}. \emph{Genome Biol} 2010, \textbf{11}(8):R86.
\bibitem{Angiuoli2011}
Angiuoli S, Matalka M, Gussman A, Galens K, Vangala M, Riley D, Arze C, White
J, White O, Fricke W: \textbf{CloVR: A virtual machine for automated and
portable sequence analysis from the desktop using cloud computing}. \emph{BMC
Bioinformatics} 2011, \textbf{12}:356.
\bibitem{Altintas2011}
\emph{Distributed workflow-driven analysis of large-scale biological data using
biokepler}, ACM 2011.
\bibitem{galaxywiki}
team Gd: \textbf{Galaxy Bioinformatics Wiki}.
\bibitem{Afgan2010}
Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J: \textbf{Galaxy
CloudMan: delivering cloud compute clusters}. \emph{BMC Bioinformatics} 2010,
\textbf{11}(Suppl 12):S4.
\bibitem{console}
Services AW: \textbf{Amazon Cloud Console}.
\bibitem{euca}
\textbf{Eucalyptus Open Source Cloud
Platform:}\urlprefix\url{[http://open.eucalyptus.com]}.
\bibitem{openstack}
\textbf{OpenStack Open Source Cloud
Platform:}\urlprefix\url{[http://www.openstack.org]}.
\bibitem{googlegroup}
Groups G: .
\bibitem{fabric}
framework CBD: .
\bibitem{genomespace}
\textbf{Broad Institute Genomespace
portal:}\urlprefix\url{[http://www.genomespace.org]}.
\bibitem{d2010seqware}
D~OConnor B, Merriman B, Nelson S: \textbf{SeqWare Query Engine: storing and
searching sequence data in the cloud}. \emph{BMC bioinformatics} 2010,
\textbf{11}(Suppl 12):S2.
\bibitem{basespace}
\textbf{Illumina BaseSpace:}\urlprefix\url{[http://basespace.illumina.com]}.
\bibitem{dnanexus}
\textbf{DNANexus Inc.:}\urlprefix\url{[http://www.dnanexus.com]}.
\bibitem{Wilkening2009}
\emph{Using clouds for metagenomics: A case study}, IEEE 2009.
\bibitem{Uhlig2005}
Uhlig R, Neiger G, Rodgers D, Santoni A, Martins F, Anderson A, Bennett S, Kagi
A, Leung F, Smith L: \textbf{Intel virtualization technology}.
\emph{Computer} 2005, \textbf{38}(5):48--56.
\bibitem{Dudley2010}
Dudley JT, Butte AJ: \textbf{In silico research in the era of cloud computing}.
\emph{Nature biotechnology} 2010, \textbf{28}(11):1181--1185.
\bibitem{ebs}
\textbf{Elastic Block Store:}\urlprefix\url{[http://aws.amazon.com/ebs]}.
\bibitem{aws}
\textbf{Amazon Web Services:}\urlprefix\url{[http://aws.amazon.com]}.
\bibitem{s3}
\textbf{Simple Storage Service:}\urlprefix\url{[http://aws.amazon.com/s3]}.
\bibitem{awsforums}
\textbf{Amazon Web Services
Forums:}\urlprefix\url{[https://forums.aws.amazon.com]}.
\bibitem{ubuntucloud}
\textbf{Ubuntu Linux Operating
System:}\urlprefix\url{[http://www.ubuntu.com/Cloud]}.
\bibitem{openstackother}
\textbf{OpenStack Installation
Documentation:}\urlprefix\url{[http://docs.openstack.org/essex/openstack-compute/starter/content/CentOS-de1592.html]}.
\bibitem{eucalyptusother}
\textbf{Eucalyptus Cloud Installation
Packages:}\urlprefix\url{[http://www.eucalyptus.com/download/eucalyptus]}.
\bibitem{appengine}
\textbf{Google Apple Engine}.
\bibitem{azure}
\textbf{Microsoft Windows Azure}.
\bibitem{gogrid}
\textbf{Go Grid Cloud}.
\bibitem{flexiscale}
\textbf{Flexiscale Cloud}.
\bibitem{smartcloud}
\textbf{IBM SmartCloud}.
\bibitem{python}
\textbf{Python Programming Language}.
\bibitem{net}
\textbf{Microsoft .NET Framework}.
\bibitem{scriptaws}
\textbf{BioTeam: Scriptable Cloud Infrastructures}.
\bibitem{magellan}
\textbf{OpenStack at Magellan
Cloud:}\urlprefix\url{[http://www.alcf.anl.gov/magellan]}.
\bibitem{openstackinstalls}
\textbf{OpenStack Cloud
Installations:}\urlprefix\url{[http://openstack.org/user-stories/]}.
\bibitem{vbox}
\textbf{VirtualBox desktop virtualization
software:}\urlprefix\url{[http://www.virtualbox.org]}.
\bibitem{cblorg}
\textbf{Cloud BioLinux community
site:}\urlprefix\url{[http://www.cloudbiolinux.org]}.
\bibitem{awsgrants}
\textbf{Educational Grants:}\urlprefix\url{[http://aws.amazon.com/grants/]}.
\bibitem{awspublicdata}
\textbf{Community datasets
hosting:}\urlprefix\url{[http://aws.amazon.com/datasets]}.
\bibitem{aws1000gen}
\textbf{1000 Human Genomes dataset on the
cloud:}\urlprefix\url{[http://aws.amazon.com/1000genomes/]}.
\bibitem{awsflu}
\textbf{NCBI Flue sequence
datasets:}\urlprefix\url{[http://aws.amazon.com/datasets/2419]}.
\bibitem{awsensembl}
\textbf{Ensembl Human Genome
Annotation:}\urlprefix\url{[http://aws.amazon.com/datasets/3841]}.
\bibitem{cloudfront}
\textbf{Amazon CloudFront:}\urlprefix\url{[http://aws.amazon.com/cloudfront/]}.
\bibitem{fielding2000}
Fielding R: \textbf{Representational state transfer (REST)}.
\emph{Architectural Styles and the Design of Network-based Software
Architectures. University of California, Irvine} 2000, :120.
\bibitem{soap}
\textbf{Simple Object Access Protocol (SOAP):}.
\bibitem{s3developer}
Libraries SD: .
\bibitem{s3fox}
\textbf{Amazon Cloud Storage S3 Add-On}.
\bibitem{reduced}
\textbf{S3 Reduced Redudancy Storage}.
\bibitem{glacier}
\textbf{Amazon Glacier storage service}.
\bibitem{papazoglou2003}
\emph{Service-oriented computing: Concepts, characteristics and directions Web
Information Systems Engineering, 2003. WISE 2003. Proceedings of the Fourth
International Conference on}, IEEE 2003.
\bibitem{Stein2010}
Stein LD: \textbf{The case for cloud computing in genome informatics}.
\emph{Genome Biology} 2010, \textbf{11}(5):207.
\bibitem{bhardwaj2010cloud}
Bhardwaj S, Jain L, Jain S: \textbf{Cloud computing: A study of infrastructure
as a service (IAAS)}. \emph{International Journal of engineering and
information Technology} 2010, \textbf{2}:60--63.
\bibitem{instancetypes}
\textbf{Amazon EC2 Cloud instance types:}.
\bibitem{jackson2010}
Jackson K, Ramakrishnan L, Muriki K, Canon S, Cholia S, Shalf J, Wasserman H,
Wright N: \textbf{Performance analysis of high performance computing
applications on the amazon web services cloud}. In \emph{Cloud Computing
Technology and Science (CloudCom), 2010 IEEE Second International Conference
on}, IEEE 2010:159--168.
\bibitem{hill2009quantitative}
Hill Z, Humphrey M: \textbf{A quantitative analysis of high performance
computing with Amazon's EC2 infrastructure: The death of the local cluster?}
In \emph{Grid Computing, 2009 10th IEEE/ACM International Conference on},
IEEE 2009:26--33.
\bibitem{boden1995myrinet}
Boden N, Cohen D, Felderman R, Kulawik A, Seitz C, Seizovic J, Su W:
\textbf{Myrinet: A gigabit-per-second local area network}. \emph{Micro, IEEE}
1995, \textbf{15}:29--36.
\bibitem{infiniband2000infiniband}
Association IT: \emph{InfiniBand Architecture Specification: Release 1.0}.
InfiniBand Trade Association 2000.
\end{thebibliography}
\newcommand{\BMCxmlcomment}[1]{}
\BMCxmlcomment{
<refgrp>
<bibl id="B1">
<title><p>Syntetic Biology, Euroscience Open Forum 2012</p></title>
<aug>
<au><snm>Venter</snm><fnm>JC</fnm></au>
</aug>
<source>Syntetic Biology, Euroscience Open Forum 2012</source>
</bibl>
<bibl id="B2">
<title><p>What is life?: With mind and matter and autobiographical
sketches</p></title>
<publisher>Cambridge University Press</publisher>
<pubdate>1992</pubdate>
</bibl>
<bibl id="B3">
<title><p>Creation of a bacterial cell controlled by a chemically synthesized
genome</p></title>
<aug>
<au><snm>Gibson</snm><fnm>D.G.</fnm></au>
<au><snm>Glass</snm><fnm>J.I.</fnm></au>
<au><snm>Lartigue</snm><fnm>C.</fnm></au>
<au><snm>Noskov</snm><fnm>V.N.</fnm></au>
<au><snm>Chuang</snm><fnm>R.Y.</fnm></au>
<au><snm>Algire</snm><fnm>M.A.</fnm></au>
<au><snm>Benders</snm><fnm>G.A.</fnm></au>
<au><snm>Montague</snm><fnm>M.G.</fnm></au>
<au><snm>Ma</snm><fnm>L.</fnm></au>
<au><snm>Moodie</snm><fnm>M.M.</fnm></au>
</aug>
<source>science</source>
<pubdate>2010</pubdate>
<volume>329</volume>
<issue>5987</issue>
<fpage>52</fpage>
<lpage>56</lpage>
</bibl>
<bibl id="B4">
<title><p>The Sorcerer II global ocean sampling expedition: northwest
Atlantic through eastern tropical Pacific</p></title>
<aug>
<au><snm>Rusch</snm><fnm>D.B.</fnm></au>
<au><snm>Halpern</snm><fnm>A.L.</fnm></au>
<au><snm>Sutton</snm><fnm>G.</fnm></au>
<au><snm>Heidelberg</snm><fnm>K.B.</fnm></au>
<au><snm>Williamson</snm><fnm>S.</fnm></au>
<au><snm>Yooseph</snm><fnm>S.</fnm></au>
<au><snm>Wu</snm><fnm>D.</fnm></au>
<au><snm>Eisen</snm><fnm>J.A.</fnm></au>
<au><snm>Hoffman</snm><fnm>J.M.</fnm></au>
<au><snm>Remington</snm><fnm>K.</fnm></au>
</aug>
<source>PLoS biology</source>
<pubdate>2007</pubdate>
<volume>5</volume>
<issue>3</issue>
<fpage>e77</fpage>
</bibl>
<bibl id="B5">
<title><p>A catalog of reference genomes from the human
microbiome</p></title>
<aug>
<au><snm>Nelson</snm><fnm>K.E.</fnm></au>
<au><snm>Weinstock</snm><fnm>G.M.</fnm></au>
<au><snm>Highlander</snm><fnm>S.K.</fnm></au>
<au><snm>Worley</snm><fnm>K.C.</fnm></au>
<au><snm>Creasy</snm><fnm>H.H.</fnm></au>
<au><snm>Wortman</snm><fnm>J.R.</fnm></au>
<au><snm>Rusch</snm><fnm>D.B.</fnm></au>
<au><snm>Mitreva</snm><fnm>M.</fnm></au>
<au><snm>Sodergren</snm><fnm>E.</fnm></au>
<au><snm>Chinwalla</snm><fnm>A.T.</fnm></au>
</aug>
<source>Science (New York, NY)</source>
<pubdate>2010</pubdate>
<volume>328</volume>
<issue>5981</issue>
<fpage>994</fpage>
</bibl>
<bibl id="B6">
<title><p>Faster sequencers, larger datasets, new challenges</p></title>
<aug>
<au><snm>Mason</snm><fnm>CE</fnm></au>
<au><snm>Elemento</snm><fnm>O</fnm></au>
</aug>
<source>Genome Biology</source>
<pubdate>2012</pubdate>
</bibl>
<bibl id="B7">
<title><p>Technical Specifications of Illumina Sequencers</p></title>
<aug>
<au><snm>Illumina</snm><fnm>I</fnm></au>
</aug>
</bibl>
<bibl id="B8">
<title><p>The SOLiD 5500 sequencing system.</p></title>
<aug>
<au><snm>Inc.</snm><fnm>AB</fnm></au>
</aug>
</bibl>
<bibl id="B9">
<title><p>PacBio RS sequencing technology</p></title>
<aug>
<au><snm>Inc.</snm><fnm>PB</fnm></au>
</aug>
</bibl>
<bibl id="B10">
<title><p>Performance comparison of benchtop high-throughput sequencing
platforms</p></title>
<aug>
<au><snm>Loman</snm><fnm>NJ</fnm></au>
<au><snm>Misra</snm><fnm>RV</fnm></au>
<au><snm>Dallman</snm><fnm>TJ</fnm></au>
</aug>
<pubdate>2012</pubdate>
</bibl>
<bibl id="B11">
<title><p>Next-generation DNA sequencing methods</p></title>
<aug>
<au><snm>Mardis</snm><fnm>E.R.</fnm></au>
</aug>
<source>Annu. Rev. Genomics Hum. Genet.</source>
<pubdate>2008</pubdate>
<volume>9</volume>
<fpage>387</fpage>
<lpage>402</lpage>
</bibl>
<bibl id="B12">
<title><p>An overview of the analysis of next generation sequencing
data</p></title>
<aug>
<au><snm>Gogol D{\"o}ring</snm><fnm>A.</fnm></au>
<au><snm>Chen</snm><fnm>W.</fnm></au>
<au><cnm>others</cnm></au>
</aug>
<source>Methods in Molecular Biology</source>
<publisher>Springer</publisher>
<pubdate>2012</pubdate>
<volume>802</volume>
<fpage>249</fpage>
<lpage>-257</lpage>
</bibl>
<bibl id="B13">
<title><p>Basic local alignment search tool</p></title>
<aug>
<au><snm>Altschul</snm><fnm>S.F.</fnm></au>
<au><snm>Gish</snm><fnm>W.</fnm></au>
<au><snm>Miller</snm><fnm>W.</fnm></au>
<au><snm>Myers</snm><fnm>E.W.</fnm></au>
<au><snm>Lipman</snm><fnm>D.J.</fnm></au>
<au><cnm>others</cnm></au>
</aug>
<source>Journal of molecular biology</source>
<publisher>Elsevier Science</publisher>
<pubdate>1990</pubdate>
<volume>215</volume>
<issue>3</issue>
<fpage>403</fpage>
<lpage>-410</lpage>
</bibl>
<bibl id="B14">
<title><p>NCBI BLAST: a better web interface</p></title>
<aug>
<au><snm>Johnson</snm><fnm>M.</fnm></au>
<au><snm>Zaretskaya</snm><fnm>I.</fnm></au>
<au><snm>Raytselis</snm><fnm>Y.</fnm></au>
<au><snm>Merezhuk</snm><fnm>Y.</fnm></au>
<au><snm>McGinnis</snm><fnm>S.</fnm></au>
<au><snm>Madden</snm><fnm>T.L.</fnm></au>
</aug>
<source>Nucleic acids research</source>
<publisher>Oxford Univ Press</publisher>
<pubdate>2008</pubdate>
<volume>36</volume>
<issue>suppl 2</issue>
<fpage>W5</fpage>
<lpage>-W9</lpage>
</bibl>
<bibl id="B15">
<title><p>NCBI Reference Sequences: current status, policy and new
initiatives</p></title>
<aug>
<au><snm>Pruitt</snm><fnm>K.D.</fnm></au>
<au><snm>Tatusova</snm><fnm>T.</fnm></au>
<au><snm>Klimke</snm><fnm>W.</fnm></au>
<au><snm>Maglott</snm><fnm>D.R.</fnm></au>
</aug>
<source>Nucleic acids research</source>
<pubdate>2009</pubdate>
<volume>37</volume>
<issue>suppl 1</issue>
<fpage>D32</fpage>
<lpage>D36</lpage>
</bibl>
<bibl id="B16">
<title><p>Moore's law: past, present and future</p></title>
<aug>
<au><snm>Schaller</snm><fnm>R.R.</fnm></au>
</aug>
<source>Spectrum, IEEE</source>
<publisher>IEEE</publisher>
<pubdate>1997</pubdate>
<volume>34</volume>
<issue>6</issue>
<fpage>52</fpage>
<lpage>-59</lpage>
</bibl>
<bibl id="B17">
<title><p>National Center for Biotechnology Information:</p></title>
<url>http://www.ncbi.nlm.nih.gov</url>
</bibl>
<bibl id="B18">
<title><p>Sequence Read Archive</p></title>
<aug>
<au><snm>Information</snm><fnm>NCFB</fnm></au>
</aug>
</bibl>
<bibl id="B19">
<title><p>Elastic Compute Cloud (EC2)</p></title>
<aug>
<au><snm>Services</snm><fnm>AW</fnm></au>
</aug>
</bibl>
<bibl id="B20">
<title><p>EC2 Pricing</p></title>
<aug>
<au><snm>Services</snm><fnm>AW</fnm></au>
</aug>
</bibl>
<bibl id="B21">
<title><p>Amazon EC2 Cloud global regions</p></title>
</bibl>
<bibl id="B22">
<title><p>The 1000 Genomes Project: data management and community
access</p></title>
<aug>
<au><snm>Clarke</snm><fnm>L.</fnm></au>
<au><snm>Zheng Bradley</snm><fnm>X.</fnm></au>
<au><snm>Smith</snm><fnm>R.</fnm></au>
<au><snm>Kulesha</snm><fnm>E.</fnm></au>
<au><snm>Xiao</snm><fnm>C.</fnm></au>
<au><snm>Toneva</snm><fnm>I.</fnm></au>
<au><snm>Vaughan</snm><fnm>B.</fnm></au>
<au><snm>Preuss</snm><fnm>D.</fnm></au>
<au><snm>Leinonen</snm><fnm>R.</fnm></au>
<au><snm>Shumway</snm><fnm>M.</fnm></au>
</aug>
<source>nature methods</source>
<pubdate>2012</pubdate>
<volume>9</volume>
<issue>5</issue>
<fpage>459</fpage>
<lpage>462</lpage>
</bibl>
<bibl id="B23">
<title><p>Accessing 1000 Human Genomes Data with Cloud BioLinux</p></title>
<aug>
<au><snm>Krampis</snm><fnm>K.</fnm></au>
</aug>
</bibl>
<bibl id="B24">
<title><p>Accessing 1000 Human Genomes Data with Cloud BioLinux</p></title>
<aug>
<au><snm>Krampis</snm><fnm>K.</fnm></au>
</aug>
</bibl>
<bibl id="B25">
<title><p>Cloud BioLinux: pre-configured and on-demand bioinformatics
computing for the genomics community</p></title>
<aug>
<au><snm>Krampis</snm><fnm>K.</fnm></au>
<au><snm>Booth</snm><fnm>T.</fnm></au>
<au><snm>Chapman</snm><fnm>B.</fnm></au>
<au><snm>Tiwari</snm><fnm>B.</fnm></au>
<au><snm>Bicak</snm><fnm>M.</fnm></au>
<au><snm>Field</snm><fnm>D.</fnm></au>
<au><snm>Nelson</snm><fnm>K. E.</fnm></au>
</aug>
<source>BMC Bioinformatics</source>
<pubdate>2012</pubdate>
<volume>13</volume>
<fpage>42</fpage>
</bibl>
<bibl id="B26">
<title><p>SourceForge open-source code repository</p></title>
</bibl>
<bibl id="B27">
<title><p>Open-Source code repository</p></title>
<aug>
<au><snm>Inc</snm><fnm>G</fnm></au>
</aug>
</bibl>
<bibl id="B28">
<title><p>The biology workbench---A seamless database and analysis
environment for the biologist</p></title>
<aug>
<au><snm>Subramaniam</snm><fnm>S</fnm></au>
</aug>
<source>Proteins</source>
<pubdate>1998</pubdate>
<volume>32</volume>
<issue>1</issue>
<fpage>1</fpage>
<lpage>-2</lpage>
</bibl>
<bibl id="B29">
<title><p>A Web interface generator for molecular biology programs in
Unix</p></title>
<aug>
<au><snm>Letondal</snm><fnm>C</fnm></au>
</aug>
<source>Bioinformatics</source>
<pubdate>2001</pubdate>
<volume>17</volume>
<issue>1</issue>
<fpage>73</fpage>
<lpage>-82</lpage>
</bibl>
<bibl id="B30">
<title><p>wEMBOSS: a web interface for EMBOSS</p></title>
<aug>
<au><snm>Sarachu</snm><fnm>M</fnm></au>
<au><snm>Colet</snm><fnm>M</fnm></au>
</aug>
<source>Bioinformatics</source>
<pubdate>2005</pubdate>
<volume>21</volume>
<issue>4</issue>
<fpage>540</fpage>
<lpage>-541</lpage>
</bibl>
<bibl id="B31">
<title><p>Mobyle: a new full web bioinformatics framework
Bioinformatics</p></title>
<aug>
<au><snm>Neron</snm><fnm>B</fnm></au>
<au><snm>and</snm><fnm>H</fnm></au>
<au><snm>Maufrais</snm><fnm>C</fnm></au>
<au><snm>Joly</snm><fnm>N</fnm></au>
<au><snm>Maupetit</snm><fnm>J</fnm></au>
<au><snm>Letort</snm><fnm>S</fnm></au>
<au><snm>Carrere</snm><fnm>S</fnm></au>
<au><snm>Tuffery</snm><fnm>P</fnm></au>
<au><snm>Letondal</snm><fnm>C</fnm></au>
</aug>
<source>Bioinformatics</source>
<pubdate>2009</pubdate>
<volume>25</volume>
<issue>22</issue>
<fpage>3005</fpage>
<lpage>-3011</lpage>
</bibl>
<bibl id="B32">
<title><p>BioManager: the use of a bioinformatics web application as a
teaching tool in undergraduate bioinformatics training</p></title>
<aug>
<au><snm>Cattley</snm><fnm>S</fnm></au>
<au><snm>Arthur</snm><fnm>JW</fnm></au>
</aug>
<source>Briefings in Bioinformatics</source>
<pubdate>2007</pubdate>
<volume>8</volume>
<issue>6</issue>
<fpage>457</fpage>
<lpage>-465</lpage>
</bibl>
<bibl id="B33">
<title><p>Implementing bioinformatic workflows within the BioExtract
Server</p></title>
<aug>
<au><snm>Lushbough</snm><fnm>CM</fnm></au>
<au><snm>Bergman</snm><fnm>MK</fnm></au>
<au><snm>Lawrence</snm><fnm>C</fnm></au>
<au><snm>Jennewein</snm><fnm>D</fnm></au>
<au><snm>Volker</snm><fnm>B</fnm></au>
</aug>
<source>International Journal of Computational Biology and Drug
Design</source>
<pubdate>2008</pubdate>
<volume>1</volume>
<issue>3</issue>
<fpage>302</fpage>
<lpage>-312</lpage>
</bibl>
<bibl id="B34">
<title><p>The Genome Portal of the Department of Energy Joint Genome
Institute</p></title>
<aug>
<au><snm>Grigoriev</snm><fnm>I.V.</fnm></au>
<au><snm>Nordberg</snm><fnm>H.</fnm></au>
<au><snm>Shabalov</snm><fnm>I.</fnm></au>
<au><snm>Aerts</snm><fnm>A.</fnm></au>
<au><snm>Cantor</snm><fnm>M.</fnm></au>
<au><snm>Goodstein</snm><fnm>D.</fnm></au>
<au><snm>Kuo</snm><fnm>A.</fnm></au>
<au><snm>Minovitsky</snm><fnm>S.</fnm></au>
<au><snm>Nikitin</snm><fnm>R.</fnm></au>
<au><snm>Ohm</snm><fnm>R.A.</fnm></au>
</aug>
<source>Nucleic Acids Research</source>
<pubdate>2012</pubdate>
<volume>40</volume>
<issue>D1</issue>
<fpage>D26</fpage>
<lpage>D32</lpage>
</bibl>
<bibl id="B35">
<title><p>Camera 2.0: A data-centric metagenomics community infrastructure
driven by scientific workflows</p></title>
<aug>
<au><snm>Altintas</snm><fnm>I.</fnm></au>
<au><snm>Lin</snm><fnm>A.W.</fnm></au>
<au><snm>Chen</snm><fnm>J.</fnm></au>
<au><snm>Churas</snm><fnm>C.</fnm></au>
<au><snm>Gujral</snm><fnm>M.</fnm></au>
<au><snm>Sun</snm><fnm>S.</fnm></au>
<au><snm>Li</snm><fnm>W.</fnm></au>
<au><snm>Manansala</snm><fnm>R.</fnm></au>
<au><snm>Sedova</snm><fnm>M.</fnm></au>
<au><snm>Grethe</snm><fnm>J.S.</fnm></au>
</aug>
<source>Camera 2.0: A data-centric metagenomics community infrastructure
driven by scientific workflows</source>
<publisher>IEEE</publisher>
<pubdate>2010</pubdate>
<fpage>352</fpage>
<lpage>359</lpage>
</bibl>
<bibl id="B36">
<title><p>The EBI Metagenomics Archive, Integration and Analysis
Resource</p></title>
<aug>
<au><snm>Hunter</snm><fnm>C.</fnm></au>
<au><snm>Cochrane</snm><fnm>G.</fnm></au>
<au><snm>Apweiler</snm><fnm>R.</fnm></au>
<au><snm>Hunter</snm><fnm>S.</fnm></au>
</aug>
<source>Handbook of Molecular Microbial Ecology I</source>
<pubdate>2011</pubdate>
<fpage>333</fpage>
<lpage>340</lpage>
</bibl>
<bibl id="B37">
<title><p>Subsystems-based servers for rapid annotation of genomes and
metagenomes</p></title>
<aug>
<au><snm>Aziz</snm><fnm>R.</fnm></au>
</aug>
<source>BMC Bioinformatics</source>
<pubdate>2010</pubdate>
<volume>11</volume>
<issue>Suppl 4</issue>
<fpage>O2</fpage>
</bibl>
<bibl id="B38">
<title><p>Galaxy: a comprehensive approach for supporting accessible,
reproducible, and transparent computational research in the life
sciences</p></title>
<aug>
<au><snm>Goecks</snm><fnm>J.</fnm></au>
<au><snm>Nekrutenko</snm><fnm>A.</fnm></au>
<au><snm>Taylor</snm><fnm>J.</fnm></au>
</aug>
<source>Genome Biol</source>
<pubdate>2010</pubdate>
<volume>11</volume>
<issue>8</issue>
<fpage>R86</fpage>
</bibl>
<bibl id="B39">
<title><p>CloVR: A virtual machine for automated and portable sequence
analysis from the desktop using cloud computing</p></title>
<aug>
<au><snm>Angiuoli</snm><fnm>S.V.</fnm></au>
<au><snm>Matalka</snm><fnm>M.</fnm></au>
<au><snm>Gussman</snm><fnm>A.</fnm></au>
<au><snm>Galens</snm><fnm>K.</fnm></au>
<au><snm>Vangala</snm><fnm>M.</fnm></au>
<au><snm>Riley</snm><fnm>D.R.</fnm></au>
<au><snm>Arze</snm><fnm>C.</fnm></au>
<au><snm>White</snm><fnm>J.R.</fnm></au>
<au><snm>White</snm><fnm>O.</fnm></au>
<au><snm>Fricke</snm><fnm>W.F.</fnm></au>
</aug>
<source>BMC Bioinformatics</source>
<pubdate>2011</pubdate>
<volume>12</volume>
<issue>1</issue>
<fpage>356</fpage>
</bibl>
<bibl id="B40">
<title><p>Distributed workflow-driven analysis of large-scale biological data
using biokepler</p></title>
<aug>
<au><snm>Altintas</snm><fnm>I.</fnm></au>
</aug>
<source>Distributed workflow-driven analysis of large-scale biological data
using biokepler</source>
<publisher>ACM</publisher>
<pubdate>2011</pubdate>
<fpage>41</fpage>
<lpage>42</lpage>
</bibl>
<bibl id="B41">
<title><p>Galaxy Bioinformatics Wiki</p></title>
<aug>
<au><snm>team</snm><fnm>Gd</fnm></au>
</aug>
</bibl>
<bibl id="B42">
<title><p>Galaxy CloudMan: delivering cloud compute clusters</p></title>
<aug>
<au><snm>Afgan</snm><fnm>E.</fnm></au>
<au><snm>Baker</snm><fnm>D.</fnm></au>
<au><snm>Coraor</snm><fnm>N.</fnm></au>
<au><snm>Chapman</snm><fnm>B.</fnm></au>
<au><snm>Nekrutenko</snm><fnm>A.</fnm></au>
<au><snm>Taylor</snm><fnm>J.</fnm></au>
</aug>
<source>BMC Bioinformatics</source>
<pubdate>2010</pubdate>
<volume>11</volume>
<issue>Suppl 12</issue>
<fpage>S4</fpage>
</bibl>
<bibl id="B43">
<title><p>Amazon Cloud Console</p></title>
<aug>
<au><snm>Services</snm><fnm>AW</fnm></au>
</aug>
</bibl>
<bibl id="B44">
<title><p>Eucalyptus Open Source Cloud Platform:</p></title>
<url>http://open.eucalyptus.com</url>
</bibl>
<bibl id="B45">
<title><p>OpenStack Open Source Cloud Platform:</p></title>
<url>http://www.openstack.org</url>
</bibl>
<bibl id="B46">
<aug>
<au><snm>Groups</snm><fnm>G</fnm></au>
</aug>
</bibl>
<bibl id="B47">
<aug>
<au><snm>framework</snm><fnm>CBD</fnm></au>
</aug>
</bibl>
<bibl id="B48">
<title><p>Broad Institute Genomespace portal:</p></title>
<url>http://www.genomespace.org</url>
</bibl>
<bibl id="B49">
<title><p>SeqWare Query Engine: storing and searching sequence data in the
cloud</p></title>
<aug>
<au><snm>D OConnor</snm><fnm>B.</fnm></au>
<au><snm>Merriman</snm><fnm>B.</fnm></au>
<au><snm>Nelson</snm><fnm>S.F.</fnm></au>
</aug>
<source>BMC bioinformatics</source>
<publisher>BioMed Central Ltd</publisher>
<pubdate>2010</pubdate>
<volume>11</volume>
<issue>Suppl 12</issue>
<fpage>S2</fpage>
</bibl>
<bibl id="B50">