Bioinformatics Live CDs

The concept of a live CD allows to create a CD or DVD that boots a computer, starts a defined set of application without a user's intervention and has all tools in place that suits a particular community. Such provide fully featured Linux workstations without additional installations of access to local disk space, alternatively booting via the network is supported by Debian, which particularly appeals to Blades or large clusters. The most successful such LiveCD is the Debian-derived Knoppix[13].

The descriptions below only summarise a few efforts but give insights into the vast realm of possibilities also for distributed computing. It should be pointed out that all Knoppix-derived[13] bioinformatics Live CDs may become members of the NorduGrid with the effort of Niels E. Larsen[15], who provides a respective script to create a LiveCD that lets one immediately join a grid with 4000+ CPUs[16].

The Quantian Scientific Computing Environment

Quantian is a remastering of a well established effort (Knoppix). Recent versions of Quantian [7] are based on ClusterKnoppix [25] and add support for OpenMosix [6], including remote booting of light clients in an openMosix terminal server context. Earlier releases are still available; see below for URLs for downloads as well as ordering information. More detailed information are available at the Quantian homepage.

The interesting part for biologists is that Quantian contains in addition all interesting packages of Debian-Med. The author Dirk Eddelbuettel, who is a Debian developer himself, just used the simply to install biological software feature we provide and thus made a great profit from Debian-Med.

Vigyaan - the biochemical software workbench

Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modelling software. VigyaanCD v0.1 is based on Knoppix v3.3.

Vigyann contains some programs which are not yet contained in Debian. It might be mutually beneficial to include these provided that the license fits the DFSG.


BioKnoppix is a customised distribution of Knoppix Linux Live CD. It is a very similar project to the previous which specialises Knoppix for computational biology and chemistry.

VLinux Bioinformatics Workbench

Also VLinux is at the time of writing a Live CD based on the same outdated Knoppix version 3.3 as Vigyann and includes a slightly changed software selection and surely a different background layout.

These are too many different initiatives that could all well do much more in order to share the burden of maintenance and updates. With Debian they have he right basic infrastructure. The time will show, whose packages will gain most momentum.

Andreas Tille 2005-05-13