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Today, I was asked to look for Scientific version(s) of Ubuntu. They actually are looking for tools to perform DNA sequence analysis, protein verification, estimations, and many biology related tasks.

First:

  1. Is there a scientific, bio-oriented version of Ubuntu

  2. Are there tools to do scientific analysis like the points mentioned above.

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I was about to post something on similar lines. Thanks for bringing this topic into light :) –  Chirag Aug 21 '12 at 23:26

4 Answers 4

up vote 14 down vote accepted

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.

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Well THIS is a very well researched answer. Thanks Chirag. Will take your advice into account. –  Luis Alvarado Aug 21 '12 at 23:13
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If community is serious about this. I can do more survey on the matter. I can generate online polls for computational chemists and biologists, regarding library support for scientific softwares. I am sure, Ubuntu can be made much more research friendly distro :) Many of my colleagues use ubuntu. I will have a word with them and let you know more. –  Chirag Aug 21 '12 at 23:19

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.

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Very nice analysis. Any thought of a Debian/Ubuntu based distro. –  Luis Alvarado Aug 20 '12 at 16:13
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Honest, I think there is little point in a specialised distribution. Certainly it would be useful if more specialist applications were packaged for debian/ubuntu, but it would seem much more appropriate to set up a PPA for those applications rather than go to the effort of maintaining an entire distribution - Ubuntu provides a perfectly good desktop, and it's not obvious to me that system-wide changes are needed for a good biology platform, just easily installable and tested tools for a general platform. That said, the uncertain licensing of much of this software could make it difficult. –  chronitis Aug 20 '12 at 19:14

I see there are several Ubuntu Science remixes available, but they all seem to have died. This seems to be the way with a lot of Ubuntu remixes, because many times they just don't offer a whole lot besides for just automatically installing some applications, so they don't get the critical mass needed for the developers to keep them up.

My suggestion would be to use a solid science-based distro, like Scientific Linux, which is what is used (and developed by) by Fermilab, CERN, etc. This is a distro that isn't going anywhere anytime soon, and has great support from the scientific community. Unfortunately, it is based on Red Hat, so it may not fit your needs perfectly.

If you need to use Ubuntu, there are several scientific applications available in the repos, just fire up Ubuntu Software Center and browse "Science & Engineering" -> Biology. I am not certain of the usefulness of these programs, as it is out of my expertise. If they were sufficient, you could set up a quick bash script that installed them all when you set up a new machine.

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+1 For the good information –  Luis Alvarado Aug 20 '12 at 16:13

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.

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If you can add the following: distro.ibiblio.org/bio-linux/iso I found it holds the latest and up to date version for it. I thought it was 2 years old but there I can see it keeps updating. –  Luis Alvarado Aug 20 '12 at 16:11
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It appears that Bio-Linux is still in active development. It is based on the LTSs. According to this bugs.launchpad.net/bio-linux/+bug/998144, version 7, based on Ubuntu 12.04 should be out some time in October. The current version (6), is based on 10.04. –  reverendj1 Aug 20 '12 at 16:21

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