What I’m reading: Drinking from the Fire Hose — Statistical Issues in Genome-wide Association Studies

Another article that talks about issues related to genome-wide association studies. Also emphasizes the value of sharing data publicly.

http://content.nejm.org/cgi/content/full/357/5/436

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

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

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

What I’m reading: Genome-wide association studies for common diseases and complex traits

Well-written article that describes the challenges and potential of genome-wide association studies as of 2005. It’s 12 dense pages but worth the time to read.

http://www.nature.com/nrg/journal/v6/n2/full/nrg1521.html

Sequencing Entire Genomes

In 2001, two groups published a version of the human genome. Each was a conglomeration of the DNA of multiple people. Recently, the entire genome of both Craig Venter and James Watson have been recorded. Venter’s genome has now been published.

This is significant because it means we are getting closer to having the entire genome for groups of people, which can help research efforts. Currently researchers and clinicians can only work with a snapshot of a person’s DNA. The intermediate goal, which is motivated financially by a a $10,000,000 reward by the X-Prize Foundation, is for a person’s genome to be sequenced for $10,000 or less in a reasonable amount of time. The ultimate goal is for clinicians to use a patient’s genome as a personalized guide in treating disease. (There are legal and ethical considerations with this, but it’s the ideal.)

What Is Needed for Biomedical Researchers to Collaborate?

A recent article on CNN states that big drug companies are starting to collaborate more in an effort to combine resources and mitigate risks. It sounds like these collaborations are for very specific purposes rather than wholesale sharing of resources (including data and tools).

One of the goals of translational informatics is to help disparate groups come together and share resources for a greater benefit. This article doesn’t mention any informatics methods drug makers are using. If they are not already using them, they could likely benefit from such methods.

Sharing resources between institutions is a big focus lately in academic research where competition is also fierce. The National Cancer Institute is sponsoring the caBIG(TM) project, which is one example of funders encouraging groups to collaborate and providing a framework that makes it easier. i2b2 is another data sharing initiative.

An ideal goal would be for public and private institutions to work together rather than in their own silos. However, this will only be possible as the rewards of success and the penalties of failure are shared (at least somewhat fairly) between participants. As the article suggests, this type of arrangement can open the door for fierce competitors to cooperate in ways that benefit both parties–and hopefully also consumers.

Testing an Oracle tnsnames.ora Entry

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 <tnsentry>, replacing <tnsentry> with the actual name of the tns entry, and hit Enter.

Linux Tutorial Links

In the process of learning to use Linux, I have come across a few Web sites that have been helpful. Below are a few that helped me get started.

• Linux Command Quick Reference
• File Permission
• Writing Robust Bash Shell Scripts
• How to Use the vi Editor
• Configuring and Administering
• vim Quick Reference Card

This is by no means a comprehensive list. Please let me know if you have any other suggestions for Linux tutorial sites.

Running Ubuntu Linux on Windows

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.

Clinical Practice Guideline Search Tool

Last year I had some spare time in between homework assignments, so I threw together a little program to prototype a better way to search through clinical practice guidelines such as those provided via http://www.guideline.gov. I presented this program at the 2007 AMIA Spring Congress on May 22-24 in Orlando, FL.

It was a fun little project, and I think there is merit to clinicians using this type of user-friendly program as opposed to searching via the Web site. However, since it’s not related to my current PhD research, I probably won’t pursue it further unless someone expresses interest in continuing it.

This file is a copy of the poster.

What Is a Gene?

I came across an article published by researchers at Yale University who are involved in the ENCODE Project. I love the article because it gives a nice history of how our understanding of genes has evolved over the past 150 years. It was also intriguing because it explains how the ENCODE research may contribute to a drastically revised understanding of what a gene is and how it functions.

I recommend this article if anything as a means to understand the history of genes.