Biomedical Informatics » Tip

Installing Ensembl Human Database for Bioconductor exonmap Package

utah_guy — Tue, 01 Apr 2008 20:41:21 +0000

There is a page that explains how to do this, so I won’t repeat it, but here is a link: http://oct2007.archive.ensembl.org/info/software/website/installation/ensembl-data.html

Evaluating a p-value Using Simulation

utah_guy — Wed, 05 Mar 2008 18:43:45 +0000

You get your test statistic on the observed data; then you randomize the data (multiple times) and get your test statistic on the randomized data. Then you see how many times your randomized test statistic is greater/less (depends) than your observed test statistic = x. Then you divide x by the number of simulations/randomizations and assess its significance.

Educational Programs in Biomedical Informatics

utah_guy — Fri, 02 Nov 2007 20:20:07 +0000

When I decided to leave my job and pursue a graduate degree in informatics, I explored various programs. Below is a list of a few US universities that offer advanced degrees in informatics (in alphabetical order).

The following map (borrowed from http://www.nlm.nih.gov/ep/GrantTrainInstitute.html) shows the locations that have training grants from the National Library of Medicine.

Publicly available genome-wide association data for breast/prostate cancer

utah_guy — Mon, 10 Sep 2007 21:09:08 +0000

Interesting resource I had not previously encountered. It’s great to see data sharing.

https://caintegrator.nci.nih.gov/cgems/aboutSetup.do

Testing an Oracle tnsnames.ora Entry

utah_guy — Mon, 27 Aug 2007 18:31:43 +0000

I have been using Oracle lately, so I’m going to try to write a few tips about working with it.

The first is an easy way to test an entry in your tnsnames.ora file. The tnsnames.ora file contains connection information for Oracle servers to which you want to connect. Once you have an entry, you can test it by using a command-line utility called tnsping. If you have Oracle (client or server) installed locally, you should be able to just go to the command-line and type tnsping , replacing with the actual name of the tns entry, and hit Enter.

Running Ubuntu Linux on Windows

utah_guy — Wed, 22 Aug 2007 02:25:05 +0000

For the last year my friend Ryan has been trying to get me to install Ubuntu on my system. But I was nervous about messing up my computer and couldn’t think of a good justification to invest the time. Now that I’m getting into bioinformatics (and planning to do more development in Java, Perl, and Ruby), I felt like it was a good time to take the leap.

I learned about VirtualBox, which allows you to run other operating systems virtually within another operating system (similar to other virtualization solutions but open source). I have Windows XP running and want to keep it. I installed VirtualBox so I could run Ubuntu from within Windows (it runs fully functionally in a window within Windows). You don’t even have to create a CD–you can just install it via the ISO file. One cool thing is that it allows you to share files and the clipboard between operating systems.

So far, Ubuntu has lived up to the hype for me. It’s easy. Having brushed up recently on Linux basics has helped me do more advanced work, but I was able to install it without that. It comes with Firefox and OpenOffice installed along with other basics.

This tutorial took me through the installation steps.

To install the Guest Additions, I had to open a Terminal window (accessible via Applications -> Accesories) and type the following two commands (more details here):

sudo aptitude install build-essential kernel-header-`uname -r`
sudo sh /media/cdrom0/VBoxLinuxAdditions.run all

I know this isn’t a comprehensive tutorial, so please let me know if you run into any problems, and I will post corrections. I just wanted to show how easy it is.