Related CategoriesHuman Genome Browser ApplianceCentOS based appliance with MySQL, Apache, BioPerl, the Generic Genome Browser, and human genome data Description
This virtual appliance implements a standalone human genome browser. The main appliance components include the Generic Genome Browser from the GMOD project; the Apache web server; and a MySQL backend database. A sample database containing a limited set of human genome annotations is included. The appliance provides a convenient way of accessing genome annotation data when web access to the major online genome servers may not be available. Also the appliance may be used for managing custom annotation information. For instance, a scientist conducting a genetic study can dynamically load their own annotation data into the browser, and view that data alongside other genome information. In an academic or commercial setting, the appliance could be used for sharing large datasets from genetic studies in a convenient browsable and searchable format. Installation and configuration of the browser framework is a fairly complex process and requires a substantial amount of system and database administration experience, plus bioinformatics training. The availability of a preconfigured virtual machine vastly simplifies this process. To build the appliance, I started from a minimal install of the CentOS operating system. I then removed a number of packages that would not be required for this application, and installed a limited set of development tools required to build and install the BioPerl system. I installed Apache, MySQL, BioPerl, and the Generic Genome Browser components. Then I removed the development packages. Most of the configuration effort then went into setting up the annotation database and configuring the browser for a particular set of annotation tracks. The annotation data and browser configuration are on a separate virtual drive. I have installed a minimal set of annotations for demo purposes, obtained from the National Center for Biotechnology Information (NCBI) and the UC Santa Cruz Genome Center. The browser is configured for viewing this data. To use the appliance, start up the virtual machine with a VMWare tool such as VMplayer or VMware Workstation. After booting, the IP address of the virtual machine will appear on the console. On the host system open http://192.168.???.???/cgi-bin/gbrowse/ in a web browser. The top of that web page gives some examples of browser queries. The current VM is set up to use NAT networking but the server could be configured in bridged mode to enable access from other systems on the network. Documentation for the GMOD project and for the Generic Genome Browser is available from http://www.gmod.org. All components are open source and freely redistributable subject to their corresponding licenses. Last updated: 06/13/2006 Operating system: CentOS 4.3 Applications installed: VMware Tools installed: Yes
Size:
200 MB Primary account Submitted by: dhinds Download link provided by the submitter, not VMware. Report broken downloads here. « BACK... |