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View Full Version : HOW TO: Set up Ubuntu as a bioinformatics workstation



Daz
March 1st, 2005, 11:24 AM
Wrote a short guide for my web-site...

Can be accessed from here: link (http://hocuspokus.net/2008/03/bio-linux-bioinformatics-tools-for-linux/)

Also, if you want packages for distributed/grid computing, there is an excellent repository from VDT (Virtual Data Toolkit) (http://www.cs.wisc.edu/vdt/index.html), that sets up very easily.

I have to say that I am loving Ubuntu! :razz:

EDIT (27-Dec-2010): Updated the link as was asked to...

can8dnSix
March 1st, 2005, 01:09 PM
Wrote a short guide for my web-site...

Can be accessed from here: link (http://www.bioinformaticsonline.co.uk/linux_biolinux.html)

Also, if you want packages for distributed/grid computing, there is an excellent repository from VDT (Virtual Data Toolkit) (http://www.cs.wisc.edu/vdt/index.html), that sets up very easily.

I have to say that I am loving Ubuntu! :razz:

Can this also be done using 'sudo' I know there are some people who would rather not enable or log into their root account for security reasons.

can8dnSix

Daz
March 1st, 2005, 01:28 PM
Yep, can all be done using sudo. :D

I just put that there for those who are not familiar with sudo, (majority of the users on that site have not yet tried the delights of ubuntu...)

Cheers,

Daz

kOoLiNuS
December 10th, 2007, 11:58 AM
Wrote a short guide for my web-site...

Can be accessed from here: link (http://oakley.bioinformaticsonline.co.uk/?q=node/14)

Hi !
i've just found this thread via Google searches .... unfortunately the link proposed isn't showing up the article any more.

Do you have a copy or an equivalent link ?

djv0022
March 28th, 2010, 09:30 PM
Hi I found a new link

http://hocuspokus.net/2008/03/bio-linux-bioinformatics-tools-for-linux#more-120

tyoli
July 23rd, 2010, 10:22 AM
Hi I found a new link

http://hocuspokus.net/2008/03/bio-linux-bioinformatics-tools-for-linux#more-120

hi, this link is for ubuntu 7.10
any one know alink for ubuntu server 9.10?
thanks.

Philoo
August 3rd, 2010, 09:33 PM
the packages in the repo are dubbed "unstable" anyway, following the same instruction set for karmic or lucid will do. There is a couple of ubuntu specific packages in subdirectories for newer versions of ubuntu.

Bioinformatics is quite vast, one should also bear in mind that ncbi balst and blast2 as well as mummer are already in the std repositories and can be installed with a simple sudo apt-get install

I did not see them in the app stor... sorry software center ;)

mummer's doc is in a separate package

jasmine25
September 23rd, 2010, 03:53 AM
Just curious if anyone has come across any good tools for manipulating DNA sequence data . During my Windows daze I used Bioedit extensively, and although it works fairly well with WINE I'd like to find a native application. Any ideas?

bio seo informatics (http://www.genebyte.firm.in/)