What Bioinformatics and Computational Biology tools are available?

Solution 1:

I did some Googling on various Debian, RHEL and Virtal Machine based Operating Systems and Research tools for computational biology and bioinformatics. A few noteworthy are summarized below:

Debian Med: a Debian operating system that is particularly well fit for the requirements for medical practice and biomedical research.

DNALinux: is a Virtual Machine with bioinformatic software preinstalled.

Bioknoppix: is a customized distribution of Knoppix Linux Live CD. It comes with applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesn't touch the host computer (because it's a Live-CD), and is ideal for demonstrations, molecular biology students, workshops, etc.

Vigyaan: ("Vigyaan" means "Science" in hindi. But this isn't a me too Scientific Linux). 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 modeling software. VigyaanCD v1.0 is based on KNOPPIX v3.7.

VLinux: is a Linux distribution and appliance for students and researchers in Bioinformatics. It is based on OpenSUSE and is built using Novell's Suse Studio.

BioSLAX: is a new live CD/DVD suite of bioinformatics tools that has been released by the resource team of the BioInformatics Center (BIC), National University of Singapore (NUS). Bootable from any PC, this CD/DVD runs the compressed SLACKWARE flavour of the LINUX operating system also known as SLAX.

Bio-Linux 6.0: is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux 10.04 base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can also install Bio-Linux packages to handle new generation sequence data types.

My opinion as a bioinformatician is to download and run any Linux flavour that suits you. Almost all are free to download and use.In my research work, I use Ubuntu and CentOS. I will share my experience.

CentOS: If you install all libraries during setup, you will not encounter much problems later. I have used Molecular Dynamics package AMBER and Desmond on it. It runs generally without posing much problems.

Ubuntu: Since it does not come with many libraries pre-installed, you must know where to find information about running a software on it. However, since Ubuntu is very popular among researchers, I find no reason why you should not try it. If you encounter any difficulty installing or running a software, you can post questions on specific mailing lists related to that particular software. In Ubuntu software centre programs like Pymol, AutoDock, Unipro UGENE etc. are available. Gromacs was available earlier (I did not find it in 12.04).

I would strongly suggest you to take one time effort and install all your useful software on Ubuntu and then use Remastersys to make copies of your OS to put it on as many Desktops and Workstations you wish.

Personally, I see an immense scope in having a specialized Linux OS targeted for biology and chemistry research audience.

Hope it helps.

Solution 2:

Bio-Linux is a bioinformatics workstation on an Ubuntu base.

Beyond that there's a whole host of biology-oriented programs/tools for Ubuntu, enumerated and elaborated on here.

Solution 3:

There is not, as far as I know, a specialised distribution for this purpose.

(There exists a distribution called Scientific Linux, which is based on RedHat/Centos, but it is largely developed by and targets the needs of High Energy Physics (and does not have any general capabilities lacking in stock Ubuntu).)

There is a biology category (under science/engineering) with a collection of packages, although the number of specialised scientific applications packaged with ubuntu is relatively small (and I expect this would be also be the case for other distributions you might look at). Science+Engineering/Biology lists a few but doesn't appear to be up-to-date.

That said, many science tools, while not in the official respositories, provide ubuntu-compatible (.deb) packages you can download (eg libSBML), or generic linux binaries (eg Copasi), or are platform neutral (being written in java, python etc) and hence should run quite happily in Ubuntu (eg ImageJ).

I use Ubuntu for computational biology work, although this predominantly involves working with general purpose tools (eg R, python) rather than specialised applications.