The Kaptain on … stuff

28 Mar, 2009

BioLinux – Ubuntu with a focus

Posted by: TheKaptain In: Cool Toys

I work for a company that develops bioinformatics solutions, so when I came across BioLinux I just had to check it out. An Ubuntu 8.0.4 distro loaded with more than 500 tools for analysis, including sample data and comprehensive documentation to get you started.
There was an available virtual machine image at the bagvapp virtual appliance repository, thank you very much, so I installed in VMWare and was off to the races. Alternatively you can download an install image, order a live CD or install on a memory stick.

I saw a lot of familiar software, things like the CLC Workbench and BioJava and a multitude of single purpose apps to facilitate research and analaysis for proteomics, genomics and other disciplines.  The majority of the applications have been built and accumulated over the course of years, mostly on linux and all either open source or just plain free.  They’re pretty rough around the edges – not a lot of flashy GUI’s here, mostly command line interfaces and simple single window apps. Reminds me of why there’s a need for software like I write – to provide a workbench for managing the multitude of different activities scientists do on a day to day basis, and to help organize the giga-bytes of experimental data that gets created along the way.

This particular distro was pretty impressive, had everything installed that I would expect(and a bunch of things that I had no clue about – no biology PhD here I’m afraid). And fresh – all of the installed software was up to date, which I have yet to see on a downloaded VM image.

A big thank you to NEBC for putting out this well thought out – and visually beautiful – distribution, and to VMWare for making virtualization such a piece of cake.

[nggallery id=1]

Reblog this post [with Zemanta]

3 Responses to "BioLinux – Ubuntu with a focus"

1 | Deepak

June 24th, 2009 at 12:39 pm


Hi TheKaptain,
I need to use Biolinux on MAC. I am having difficulty in installing it. Can you help me in getting it set up?

2 | TheKaptain

June 29th, 2009 at 5:34 pm


Sure I can help. First off you need to grab a copy of VMWare Fusion – you can download a free trial to evaluate it for now, although you will have to supply your email.

Next you need to download the virtual machine image for BioLinux 5.0 (available at the bagvapp link above).

Installing the vmware image with Fusion is basically following the install wizard and selecting the downloaded filed. You might want to think about how large you want the image to be, although you can resize it later if needed. I went with 8GB.

When you’re done you should have a working linux virtual machine. If you need anymore help, feel free to ask!

3 | Bill Markey

August 26th, 2010 at 6:21 am


The live DVD’s for both BioLinux 5 and BioLinux 6 will boot on an Intel Mac just fine–you put the DVD in, reboot the mac, and hold the C key to make the computer boot from the DVD.
Once you are in the linux environment, it has an icon for your hard drive so you can save your work.

Comment Form