Computing Infrastructure

One of the foundations of Bioinformatics research and development is the availability of open source tools. Dissemination of knowledge and encouragement of collective development has been a tremendous benefit for the community. Installing and deploying those tools, however, are often non-trivial tasks for even the most seasoned bioinformatician. The major difficulty usually derives from technical dependencies of the tools on system and software libraries which may not be packaged with the distribution.

Today, with the wide use of Linux and Virtual Machine (VM) technologies, the possibility of distributing the tool as a VM, complete with all the necessary dependencies included in the OS, is possible.

Such an idea has been prototyped in the Bioinformatics Core at the UC Davis Genome Center to quickly building basic environments including Bioperl tools, Genome Browsers (gBrowse, UCSC browser), data analysis pipeline and customized LIMS system. There are great benefits to scientists packaging tools this way.

With VM’s available such as Biskit for structural biology (http://biskit.pasteur.fr/), snowflock for bioinformatics clustering (http://sysweb.cs.toronto.edu/snowflock), DNALinux for a suite of bioinformatics tools (http://www.vmware.com/appliances/directory/963), and even databases such as wormbase from CSHL (http://www.wormbase.org/wiki/index.php/Virtual_Machines), there has been direct experiences within the bionfo-core community with such systems. We provide services to build customized virtual machines, offering the promise of easy use for biologists to setup on their own desktops/servers.