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77 new_gh_pages/applications.html
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="content-type" content="application/xhtml+xml; charset=windows-1252" />
+ <link media="screen" href="style.css" type="text/css" rel="stylesheet" />
+ </head>
+ <body>
+ <div class="post">
+ <h1 class="title">Applications</h1>
+ <div class="entry">
+ <p>CloudBioLinux raises the possibly of several applications to advance
+ Bioinformatics, many of which are already in development and
+ production:</p>
+ <p><span style="text-decoration: underline;"><span style="font-weight: bold;">
+ <a href="http://wiki.galaxyproject.org/CloudMan?action=show&amp;redirect=Admin%2FCloud" target="_blank">CloudMan</a>
+ </span></span></p>
+ <p>Written by Enis Afgan and the Galaxy Team, CloudMan is a manager that
+ uses CloudBioLinux as a platform to build a full SGE cluster
+ environment for hosting the Galaxy application. CloudMan also enables
+ Galaxy to run effectively by:</p>
+ <ul>
+ <li> Coordinating the cloud infrastructure needed by Galaxy.</li>
+ <li>Providing a framework for enabling applications to run on the
+ cloud and utilize the infrastructure's elasticity.</li>
+ <li>Providing a ready-to-run. dynamically scalable version of Galaxy
+ on Amazon AWS.</li>
+ </ul>
+ <p>Backed up by cloud environment provided by CloudMan, Galaxy can
+ utilize greater resources than the the traditional configuration of an
+ in-house installation. In addition, the scalability offered by cloud
+ computing via CloudMan spares users the concern of computing details
+ (i.e. number of nodes, etc), as CloudMan can optimize use of resources
+ to the workload in question. Many users and organizations may prefer
+ the cost of renting space and computational power to use the CloudMan-backed
+ Galaxy instance of a 3rd party over the costs of installing, and maintaining,
+ their own in-house instance.</p>
+ <p>The measure of CloudMan's benefits only increases when considering
+ Galaxy's own features of enabling users to add their own custom tools
+ and enabling the users of a common Galaxy deployment to share their data,
+ tools, pipelines, and workflows with one another.</p>
+ <p>Various pipelines have already been developed for Galaxy in
+ conjunction with CloudMan:</p>
+ <ul style="text-align: left;">
+ <li><span style="font-weight: bold;"><a href="http://172.17.31.104" target="_blank">Viral Assembly and Annotation</a></span></li>
+ <ul><li>This set of tools allows a user to assemble and/or annotate 454
+ sequence data (along with optional Sanger and Solexa) from any one
+ of several viral organisms. The annotation is displayed in an
+ extensive, graphical interface through which the user can easily
+ acquire more information.</li></ul>
+ <li><span style="font-weight: bold;">Prokaryote Assembly</span></li>
+ <ul><li>The JCVI prokaryotic genome annotation pipeline runs a
+ collection of scripts and programs allowing the identification of
+ genes as well as structural and functional annotation of those
+ genes. A variety of 3rd-party tools is run alongside novel scripts
+ that collect and analyze results.</li></ul>
+ <li><span style="font-weight: bold;">
+ <a href="http://bcbio.wordpress.com/2011/08/19/distributed-exome-analysis-pipeline-with-cloudbiolinux-and-cloudman/" target="_blank">Distributed Exome Analysis Pipeline</a>
+ </span></li>
+ <ul><li>A fully automated pipeline for processing high throughput exome
+ sequencing data. Using several 3rd-party tools, the pipeline
+ performs alignment, realignment, variant detection, and analysis
+ summary on input data.</li></ul>
+ </ul>
+ <p><span style="text-decoration: underline;"><span style="font-weight: bold;">
+ <a href="http://bcbio.wordpress.com/2011/11/29/making-next-generation-sequencing-analysis-pipelines-easier-with-biocloudcentral-and-galaxy-integration/" target="_blank">CloudBioCentral</a>
+ </span></span></p>
+ <p>An extension of CloudBioLinux, in response to feedback from the
+ CloudBioLinux community, CloudBioCentral is a web service that
+ launches CloudBioLinux and CloudMan clusters on Amazon Web Services
+ hardware. This removes all of the manual steps involved in setting up
+ security groups and launching a CloudBioLinux instance. A user only
+ needs to sign up for an AWS account; BioCloudCentral takes care of
+ everything else. The CloudBioCentral web interface itself can be found
+ <a href="https://biocloudcentral.herokuapp.com/launch" target="_blank">here</a>.</p>
+ </div>
+ </div>
+ </body>
+</html>
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97 new_gh_pages/cloudbiolinux_users.html
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
+
+ <div class="post">
+ <h1 class="title">CloudBioLinux Users</h1>
+ <div class="entry"><br />
+ <table width="100%" border="1"><tbody>
+ <tr>
+ <th style="text-align: center;">Name</th>
+ <th style="text-align: center;">Institutional Affiliation</th>
+ <th style="text-align: center;">CloudBioLinux Applications</th>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://cloudman.irb.hr/enis/" target="_blank">Enis Afgan</a></td>
+ <td style="text-align: center;">Ruder Boskovic Institute, Croatia</td>
+ <td style="text-align: center;">Scalable computing using Cloud BioLinux, on public and private clouds.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.linkedin.com/in/danielbrami" target="_blank">Daniel Brami</a></td>
+ <td style="text-align: center;">Synthetic Genomics Inc, CA, USA</td>
+ <td style="text-align: center;">Genome re-sequencing and read mapping, using Bowtie and TopHat in the Cloud BioLinux VM.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://bcbio.wordpress.com/" target="_blank">Brad Chapman</a></td>
+ <td style="text-align: center;">Bioinformatics Core at Harvard School of Public Health</td>
+ <td style="text-align: center;">Leveraging collection of tools in Cloud BioLinux VM to create data analysis pipelines.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.jcvi.org/cms/about/bios/jinman" target="_blank">Jason Inman</a></td>
+ <td style="text-align: center;">J Craig Venter Institute, MD, USA</td>
+ <td style="text-align: center;">Installation of JCVI Prokaryotic Genome Annotation Pipeline.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;">Jeff Kitrell</td>
+ <td style="text-align: center;">University of Nebraska Medical Center</td>
+ <td style="text-align: center;">Next-gen sequencing data analysis, leveraging tools pre-configured in the VM.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.jcvi.org/cms/about/bios/kkrampis" target="_blank">Konstantinos Krampis</a></td>
+ <td style="text-align: center;">J Craig Venter Institute, MD, USA</td>
+ <td style="text-align: center;">JCVI Representative for CloudBioLinux. Installation, development, and manteinance of JCVI CloudMan instances.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.linkedin.com/pub/raja-mazumder/5/615/74" target="_blank">Raja Mazmuder</a></td>
+ <td style="text-align: center;">Dept. of Biochemistry, George Washington Univ., DC, USA</td>
+ <td style="text-align: center;">Integration of Cloud BioLinux VM to the HIVE cloud platform used by GWU and FDA, and for cloud-in-a-box applications.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.jcvi.org/cms/about/bios/jinman/" target="_blank">Brian Muchmore</a></td>
+ <td style="text-align: center;">Chulalongkorn University Hospital, Bangok, Thailand</td>
+ <td style="text-align: center;">Installation of JCVI Prokaryotic Genome Annotation Pipeline.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.linkedin.com/in/dpreuss" target="_blank">Don Preuss</a></td>
+ <td style="text-align: center;">National Center for Biotechnology Information, NIH, MD, USA</td>
+ <td style="text-align: center;">1000 Human Genomes data deposited on Amazon, Cloud BIoLinux leveraged by NCBI to access and analyze the data.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.linkedin.com/pub/corban-rivera/11/447/153" target="_blank">Corban Rivera</a></td>
+ <td style="text-align: center;">Dupont Inc, DE, USA</td>
+ <td style="text-align: center;">Large-scale microbial data analysis using the VM's pre-installed tools, running VM on a in-house cluster and Amazon.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.linkedin.com/pub/alexander-richter/6/b81/848" target="_blank">Alexander Richter</a></td>
+ <td style="text-align: center;">J Craig Venter Institute, CA, USA</td>
+ <td style="text-align: center;">Working on adaptations to running on private clouds.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://in.linkedin.com/pub/duleep-samuel/13/224/280" target="_blank">Dullep Samuel</a></td>
+ <td style="text-align: center;">Institute of Horticulture Research, Bangalore, India</td>
+ <td style="text-align: center;">Assembly of Ion Torrent reads, Ralstonia and Xanthomonas species</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.linkedin.com/in/rsanka" target="_blank">Ravi Sanka</a></td>
+ <td style="text-align: center;">J Craig Venter Institute, MD, USA</td>
+ <td style="text-align: center;">Development and Galaxy-adaptation of Viral Assembly and Annotation tools. Development of documentation and main website.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://www.linkedin.com/in/andreyto" target="_blank">Andrey Tovchigrechko</a></td>
+ <td style="text-align: center;">J Craig Venter Institute, MD, USA</td>
+ <td style="text-align: center;">Created VICVB - a package for visualizing the annotations of multiple viral genomes inside Galaxy</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://scholar.google.co.uk/citations?user=fymuWrsAAAAJ&hl=en" target="_blank">Tony Travis</a></td>
+ <td style="text-align: center;">Institute of Biological and Environmental Sciences, University of Aberdeen, UK</td>
+ <td style="text-align: center;">Installation of the VM on a private cloud and use as basis to deploy data pipelines.</td>
+ </tr>
+ <tr>
+ <td style="text-align: center;"><a href="http://users.sdsc.edu/~jianwu/" target="_blank">Jianwu Wang</a></td>
+ <td style="text-align: center;">San Diego Supercomputing Center, UCSD, CA, USA</td>
+ <td style="text-align: center;">BioKepler project, large-scale data analysis workflows leveraging Cloud BioLinux as workflow component on private and public clouds.</td>
+ </tr>
+ </tbody></table>
+ <br />
+ </div>
+ </div>
+</html>
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127 new_gh_pages/default/index.html
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30 new_gh_pages/documentation.html
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
+
+ <div class="post">
+ <h1 class="title">Documentation</h1>
+ <div class="entry">
+ <ul>
+ <li><a href="http://biocloudcentral.org" target="_blank">BioCloudCentral</a>: Easily launch CloudBioLinux and CloudMan clusters </li>
+ <li><a href="http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html" target="_blank">Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy</a>: Detailed how-tos </li>
+ <li><a href="https://github.com/chapmanb/cloudbiolinux/blob/master/doc/intro/gettingStarted_CloudBioLinux.pdf?raw=true" target="_blank">Getting Started with CloudBioLinux</a>: a gentle guide for new users.</li>
+ <li>Accessing 1000 Human Genomes data using CloudBioLinux: <a href="http://youtu.be/A8JLh44L1Cw" target="_blank">Part 1: Starting</a>, <a href="http://youtu.be/BiPn3ezINYw" target="_blank">Part 2: Accessing data</a>. </li>
+ <li>Deploying production Galaxy instances using CloudBioLinux and CloudMan: <a href="http://bitly.com/prodcloudman" target="_blank">documentation</a>, <a href="http://bitly.com/prodcloudman-slides" target="_blank">slides</a> </li>
+ <li><a href="http://bcbio.wordpress.com/2011/11/29/making-next-generation-sequencing-analysis-pipelines-easier-with-biocloudcentral-and-galaxy-integration/" target="_blank">Building analysis pipelines with CloudBioLinux and CloudMan</a> </li>
+ <li><a href="http://bcbio.wordpress.com/2010/05/08/automated-build-environment-for-bioinformatics-cloud-images/" target="_blank">Build framework</a>: a high level overview of the automated build environment. </li>
+ <li><a href="https://github.com/chapmanb/cloudbiolinux#readme" target="_blank">Developer build documentation</a>: details on using and contributing to the framework.</li>
+ <li><a href="http://www.slideshare.net/agbiotec/ntino-cloud-biolinux-barcelona-spain-2012" target="_blank">Cloud BioLinux: Pre-configured Bioinformatics Computing for the Genomics Community by Ntino Krampis</a></li>
+ <li><a href="http://www.slideshare.net/agbiotec/cloud-biolinux-safrica" target="_blank">Cloud BioLinux: pre-configured and on-demand computing for genomics without institutional, geographic, or economic boundaries by Ntino Krampis</a></li>
+ <li><a href="http://www.slideshare.net/agbiotec/chi-next-genntinokrampis" target="_blank">Cloud BioLinux: Pre-Configured and On-Demand High Performance Computing for the Genomics Community by Ntino Krampis</a></li>
+ <li><a href="http://www.slideshare.net/chapmanb/big-cloud-2012" target="_blank">Amazon resources for bioinformatics by Brad Chapman</a></li>
+ <li><a href="http://www.slideshare.net/chapmanb/developing-distributed-analysis-pipelines-with-shared-community-resources-using-cloudbiolinux-and-cloudman" target="_blank">Developing distributed analysis pipelines with shared community resources using CloudBioLinux and CloudMan by Brad Chapman</a></li>
+ <li><a href="http://www.slideshare.net/chapmanb/biopython-at-bosc-2010" target="_blank">Biopython: challenges by Brad Chapman</a></li>
+ <li><a href="http://www.slideshare.net/chapmanb/chapman-opensource-cloud" target="_blank">Developing an open source community for cloud bioinformatics by Brad Chapman</a></li>
+ <li><a href="http://www.slideshare.net/chapmanb/nextgeneration-sequencing-request-management-system-in-galaxy" target="_blank">Next-generation sequencing request management system in Galaxy by Brad Chapman</a></li>
+ <li><a href="http://www.slideshare.net/chapmanb/biohackathon-2010-intro" target="_blank">BioHackathon 2010 Intro by Brad Chapman</a></li>
+ <li><a href="http://www.slideshare.net/chapmanb/lowering-barriers-to-publishing-biological-data-on-the-web" target="_blank">Lowering barriers to publishing biological data on the web by Brad Chapman</a></li>
+ <li><a href="http://www.slideshare.net/jandot/e-afgan-zero-to-a-bioinformatics-analysis-platform-in-four-minutes?from_search=2" target="_blank">Zero to a bioinformatics analysis platform in four minutes by Enis Afgan</a></li>
+ </ul>
+ </div>
+ </div>
+</html>
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55 new_gh_pages/index.html
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="content-type" content="application/xhtml+xml; charset=utf-8" />
+ <title>Welcome to CloudBioLinux</title>
+ <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
+ </head>
+ <body>
+ <div id="wrapper">
+ <div id="header-pic"> </div>
+ <div id="page">
+ <div id="content">
+ <iframe src="overview.html" name="iframe_panel" frameborder="0" height="1300px" width="100%"></iframe>
+ </div> <!-- End of content -->
+ <div id="sidebar">
+ <div id="sidebar-bgtop"></div>
+ <div id="sidebar-content">
+ <div id="sidebar-bgbtm">
+ <ul>
+ <li>
+ <h2>Site Navigation</h2>
+ <ul>
+ <li><a href="overview.html" target="iframe_panel">Overview</a></li>
+ <li><a href="applications.html" target="iframe_panel">Applications</a></li>
+ <li><a href="resources.html" target="iframe_panel">Resources</a></li>
+ <li><a href="documentation.html" target="iframe_panel">Documentation</a></li>
+ <li><a href="publications.html" target="iframe_panel">Publications</a></li>
+ <li><a href="cloudbiolinux_users.html" target="iframe_panel">CloudBioLinux Users</a></li>
+ </ul>
+ </li>
+ <h2>Organizations</h2>
+ <div style="text-align: center;">
+ <a href="http://www.jcvi.org/cms/research/projects/jcvi-cloud-biolinux/overview/" target="_blank"><img src="images/jcvi-logo.png" alt="JCVI logo" title="JCVI logo" /></a>
+ <br /><br />
+ <a href="http://nebc.nerc.ac.uk/nebc/tools/bio-linux" target="_blank"><img src="images/nebc-logo.gif" alt="NEBC logo" /></a>
+ <br /><br />
+ <a href="http://www.debian.org/devel/debian-med/" target="_blank"><img src="images/debian-logo.png" alt="Debian logo" style="width: 262px; height: 75px;" /></a>
+ <br /><br />
+ <a href="http://wiki.g2.bx.psu.edu/Admin/Cloud" target="_blank"><img src="images/galaxy-logo.png" alt="Galaxy logo" title="Galaxy logo" style="width: 210px; height: 58px;" /></a>
+ <br /><br />
+ <a href="http://www.hsph.harvard.edu/research/bioinfocore/" target="_blank"><img src="images/hsph-logo.jpg" alt="hsph logo" title="hsph logo" style="width: 272px; height: 67px;" /></a>
+ <br /><br />
+ <a href="http://www.irb.hr/eng" target="_blank"><img src="images/rbi-logo.png" alt="RBI logo" title="RBI logo" longdesc="http://www.irb.hr/eng" /></a>
+ <br /><br />
+ </div>
+ </ul>
+ </div>
+ </div>
+ </div> <!-- End of sidebar -->
+ </div> <!-- End of page -->
+ </div> <!-- End of wrapper -->
+ <div id="footer">
+ Web template design by <a href="http://www.freecsstemplates.org/" target="_blank">Free CSS Templates</a>.
+ </div>
+ </body>
+</html>
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33 new_gh_pages/overview.html
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
+
+ <div class="post">
+ <h1 class="title">Overview</h1>
+ <div class="entry">
+ <p><meta charset="utf-8" />
+ CloudBioLinux is a communtiy project that offers genome analysis resources for cloud computing
+ platforms such as Amazon EC2. We develop freely available, community maintained software images
+ and data repositories for biological analysis.
+ <br /><br />
+ Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly
+ provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms.
+ Users have instant access to a range of pre-configured command line and graphical software applications,
+ including <a href="http://galaxyproject.org/" target="_blank">Galaxy</a>, a full-featured desktop interface,
+ documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering,
+ assembly, display, editing, and phylogeny. Cloud BioLinux provides researchers with the ability to perform
+ computations using a virtualized compute grid of virtual machines with the
+ <a href="http://cloudman.irb.hr/" target="_blank">CloudMan</a> framework, on public and private clouds such as
+ <a href="http://aws.amazon.com/ec2/" target="_blank">Amazon EC2</a>,
+ <a href="http://www.openstack.org/" target="_blank">OpenStack</a>,
+ <a href="http://www.eucalyptus.com/" target="_blank">Eucalyptus</a>
+ or <a href="http://www.virtualbox.org/" target="_blank">VirtualBox</a>.
+ <br /><br />
+ CloudBioLinux is a community project and we welcome contributors and feedback. A fully automated infrsatructure
+ installs software and data, with packages specified in simple
+ <a href="http://github.com/chapmanb/cloudbiolinux/tree/master/config/#readme" target="_blank">configuration files</a>.
+ Please fork <a href="http://github.com/chapmanb/cloudbiolinux" target="_blank">our code on GitHub</a>
+ and suggest improvements and additions.
+ </p>
+ </div>
+ </div>
+</html>
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
+
+ <div class="post">
+ <h1 class="title">Publications</h1>
+ <div class="entry">
+ <ul>
+ <li><a href="http://www.ncbi.nlm.nih.gov/pubmed/23971032" target="_blank">Kajan L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angermuller C, Bohm A, Domke S, Ertl J, Mertes C, Reisinger E, Staniewski C, Rost B., "Cloud prediction of protein structure and function with PredictProtein for Debian.", BioMed Research International, 2013:398968, 2013</a></li>
+ <li><a href="http://www.ncbi.nlm.nih.gov/pubmed/22888776" target="_blank">Schonherr S, Forer L, WeiBensteiner H, Kronenberg F, Specht G, Kloss-Brandstatter A., "Cloudgene: a graphical execution platform for MapReduce programs on private and public clouds.", BMC Bioinformatics, 13:200, 2012 Aug 13</a></li>
+ <li><a href="http://www.ncbi.nlm.nih.gov/pubmed/22429538" target="_blank">Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE., "Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.", 13:42, 2012 Mar 19</a></li>
+ <li><a href="http://www.ncbi.nlm.nih.gov/pubmed/23181507" target="_blank">Afgan E, Chapman B, Taylor J., "CloudMan as a platform for tool, data, and analysis distribution.", 13:315, BMC Bioinformatics</a></li>
+ <li><a href="http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1109s38/full" target="_blank">Afgan E., Chapman B., Jadan M., Franke V., Taylor J., "UNIT 11.9 Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy", Current Protocols in Bioinformatics, Unit 11.9, 2012</a></li>
+ </ul>
+ </div>
+ </div>
+</html>
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <link rel="stylesheet" type="text/css" href="style.css" media="screen" />
+
+ <div class="post">
+ <h1 class="title">Resources</h1>
+ <div class="entry">
+ <ul><li><a href="http://groups.google.com/group/cloudbiolinux" target="_blank">Discussion List</a></li></ul>
+ <ul><li><a href="http://github.com/chapmanb/cloudbiolinux/tree/master/config/#readme" target="_blank">Included Software</a></li></ul>
+ <ul><li><a href="http://thecloudmarket.com/search?search_term=cloudbiolinux&amp;order=updated_at%20desc" target="_blank">Machine Images</a></li></ul>
+ <ul><li><a href="http://github.com/chapmanb/cloudbiolinux" target="_blank">Code Framework</a></li></ul>
+ <ul><li><a href="http://github.com/chapmanb/cloudbiolinux/tree/master/contributors.mkd" target="_blank">Contributors</a></li></ul>
+ <ul><li>Amazon EC2 (us-east-1): <i>ami-46d4792f</i> -- <a href="http://alestic.com" target="_blank">Ubuntu 12.04 64bit</a> (27 June 2012)</li>
+ <ul><li class="inner">These images work with micro instances, a cost effective way to explore Amazon resources.</li></ul>
+ <li>Cloud BioLinux can be executed on a desktop computer without the need for a cloud:</li>
+ <ul><li class="inner"> <a href="https://s3.amazonaws.com/cloudbiolinuxvms/Cloud+BioLinux+32bit.ova" target="_blank">Cloud BioLinux 32-bit VirtualBox appliance</a>
+ <br /> Information for end-users <a href="http://www.virtualbox.org/wiki/Downloads" target="_blank">for installing Virtualbox</a> and
+ <a href="http://www.virtualbox.org/manual/ch01.html#ovf" target="_blank">importing Cloud BioLinux images </a> for execution within Virtualbox.</li></ul>
+ <li> Cloud BioLinux images are available for execution on a private <a href="http://open.eucalyptus.com" target="_blank">Eucalyptus</a> cloud: </li><ul>
+ <li class="inner"> <a href="https://s3.amazonaws.com/cloudbiolinuxvms/CloudBioLinux-32bit.Eucalyptus.img" target="_blank">Cloud BioLinux 32-bit Eucalyptus .img</a> <br />
+ The .img file can be uploaded to your Eucalyptus cloud by
+ simply running "uec-publish-image file.img" from the <a href="http://packages.ubuntu.com/lucid/cloud-utils" target="_blank">Ubuntu cloud-utils</a> </li></ul>
+ <li>Indexed genome builds for aligners such as <a href="http://bowtie-bio.sourceforge.net/" target="_blank">Bowtie</a>,
+ <a href="http://bio-bwa.sourceforge.net/" target="_blank">BWA</a> and <a href="http://www.novocraft.com/" target="_blank">Novoalign</a> in the
+ <a href="http://s3.amazonaws.com/biodata" target="_blank">biodata S3 bucket</a>. An
+ <a href="https://github.com/chapmanb/cloudbiolinux/blob/master/data_fabfile.py" target="_blank">automated script</a> pulls the requested genomes and aligner indexes
+ to an Amazon machine or your local computer; integration with Galaxy is also provided.</li></ul>
+ </div>
+ </div>
+</html>
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+ margin: 0px;
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