After doing a fresh install of OSX Leopard on my Mac and having to re-familiarize with some of my Biostatistics/Microarray education background it was time do a fresh install of R on my machine.
R is a freely available statistical programming language modeled after S programming language. Matthew Keller, a founder of the Richmond R group describes some of R’s advantages over other statistical packages as the following:
- Its fast and free
- State of the art: Researchers provide their methods as R packages
- Its second only to MATLAB for graphics
Some points that I would like to add to the list are:
- Its graphs and tables can be used with the ever popular LaTeX
- Its programming/scripting like interface makes it rather extensible
- Its a great starting point for people interested in Biostatistics and Microarrays
- The BioConductor project is primarily based on R
- Did I mention that its free?
R is a rather powerful tool and I consider it to be a must have for any Biostatistician or Bioinformatician’s toolset. So check it out, and let me know what you think.
Other Important R Links:
- CRAN, the Comprehensive R Archive Network (similar to perl’s CPAN)
- The R Help Mailing List a good place for getting answers to R related questions
- R Seek, a useful tool as google isn’t designed to just search for “R”
This is my third MIA post and I’d like to think that taking time to finish my Master of Bioinformatics degree, get a job, move, and get engaged would be suitable excuses for my lack of posting. But who knows, maybe I’m just not cut out to be a blogger. But as with all good/bad trilogies, things must come to an end so expect this to be my last MIA post.
Currently on the queue of posts that I have begun to write about are the following:
The R Programming Language- Links for free Bioinformatics and Biology classes
- Consed’s .ace file format
- NCBI’s OMIM
If there is anything else that anyone is interested in, leave the topic ideas in the responses.
I’m in the process of developing an application that utilizes information from protein-protein interaction databases. One specific database I am working with is BIND, the Biomolecular Interaction Network Database. As my application will be looking at a large number of genes I had to figure out how to write an application that interacted with the database.
The solution I found was BIND SOAP, an API designed to help developers interface with BIND using either C, Perl, Java, or VB .NET. SOAP or the Simple Object Access Protocol provides a basic messaging framework which allows for communication between applications across the interenet.
After some research I decided that Perl was the best way to go as there was already a Perl module available for use with SOAP, conveninetly named SOAP::Lite. If you have the CPAN module installed on your system the best way to get the SOAP::Lite module on Linux systems is to start the CPAN shell:
[root]# perl -MCPAN -e shell
Once the shell is started, run:
cpan> install SOAP::Lite
If you are having problems installing the module or installing from another system you can go here [soaplite.com] for additional instructions.
Continue reading ‘BIND and SOAP’
As I mentioned in a previous post, I’m currently working on a new look for the site. This entire week I was constantly changing the design. Realizing that I may be causing some inconvenience to my readers, I decided to go “old school” and set up a local LAMP (Linux, Apache, MySQL, Perl or PHP) server that ran Wordpress.
I just happened to have an old Dell Dimension L400c laying around so I went ahead and did a FC6 (Fedora Core 6) LAMP install as covered at howtoforge.com. The install was pretty straight forward and I ended up skipping steps 8 (Chrooted DNS Server) and 10 (Postfixas) as I felt I had no need for those options as the machine is just for testing purposes.
The WordPress Install was even simpler taking only about four commands and the modification of only one file. More information can be found at linuxjournal.com and wordpress.org. Now I have a reliable system to test the design of my page without wasting too much bandwidth. Sorry if I caused an inconvenience to anyone. If you have questions about the install feel free to contact me.
biowhat.com is officially validated!
This all started with me trying fix my sidebar for IE browsers <= 6.0. For some reason the sidebar drops to the bottom of the page after all the content. While searching for a solution, I ran into a site that inspects the code of your site to ensure that it meets the standards as published by World Wide Web Consortium (W3C). After a troubleshooting about 260 errors biowhat.com was finally validated. The largest issue I ran into was for the flash plug-in I used in one of my previous posts.
Using a plug-in from slide.com I was presenting a slideshow from my “scalping” experience. The problem was, it was using an <embed> tag that was not part of XHTML specifications. After some help from alistapart.com and wimpyplayer.com I was able to fix the problem. I had to get rid of the <embed> tag and use the XHTML compliant <object> and <param> tags instead. For more information follow the previously mentioned links
Non compliant XHTML code:
<div style="visibility:visible;">
<embed src=”http://widget-0d.slide.com/widgets/slideticker.swf”
type=”application/x-shockwave-flash” quality=”high” scale=”noscale”
salign=”l” wmode=”transparent”
flashvars=”cy=ms&il=1&channel=288230376157364493&site=
widget-0d.slide.com” width=”426″ height=”320″ name=”flashticker”
align=”middle”/>
<div style=”width:426px;text-align:left;”>
<a href=”http://www.slide.com/pivot?ad=0&tt=17&sk=0&cy=
ms&th=0&id=288230376157364493&map=1″ target=”_blank”>
<img src=”http://widget-0d.slide.com/p1/288230376157364493/
ms_t017_v000_a000_f00/images/xslide1.gif” border=”0″
ismap=”ismap” /></a>
<a href=”http://www.slide.com/pivot?ad=0&tt=17&sk=0&cy=
ms&th=0&id=288230376157364493&map=2″ target=”_blank”>
<img src=”http://widget-0d.slide.com/p2/288230376157364493/
ms_t017_v000_a000_f00/images/xslide2.gif” border=”0″
ismap=”ismap” /></a>
</div>
</div>
Compliant XHTML code without the slide image links included at the bottom of the flash player:
<div style="visibility:visible;">
<object type="application/x-shockwave-flash" data="http://widget-0d.slide.com/widgets/slideticker.swf" width="426" height="320" align="middle">
<param name="flashticker" value="http://widget-0d.slide.com/widgets/slideticker.swf"/>
<param name="quality" value="high" />
<param name="scale" value="noscale" />
<param name="salign" value="l" />
<param name="wmode" value="transparent" />
<param name="flashvars" value="cy=ms&il=1&channel=
288230376157364493&site=widget-0d.slide.com” />
</object>
</div>
While the validation process has ensured that my content will work consistently among the major browsers, my sidebar issue is still not fixed. I will be troubleshooting this issue over the next couple of days and further customizing the look of the site. Feel free to drop any suggestions or praises of the changes in my comments section. Constructive criticism is always welcome.
Last week, I attended the Systems Biology Summit in Richmond, Virginia. The opening session in the Summit was entitled “the Systems Biology Challenge in 21st Century Biomedical Research”. It consisted of speakers from the Research Institute, the National Institute of Health, Academia, and the Pharmaceutical industry providing their various viewpoints of Systems Biology.
Dr. Leroy Hood began the session with his keynote lecture on systems approaches in Biology and Medicine. The following is Dr. Hood’s thoughts on where we are in systems biology:
The information we are finding represents the “parts” of the system, when we move into the realm of establishing functionality of the system we are determining the blueprints for these parts.
A later speaker, Dr. Keith Elliston of Genstruct, expanded the discussion with his research on biological causal networks and their use for diagnostic reasoning or predictive inference. The following was his entertaining quote on networks and pathways that was repeated throughout the weekend:
System biology is not pathways but networks…stupid. A pathways is a specific path through the network.
Another entertaining quote was from Dr. Burt Adelman, representing Industry’s perspective and their thoughts on the transition of animal research to human treatments.
We treat humans. They’re very complex not inbred… mostly. We have to find what aspects of human biology are animal research reproducing.
The session ended with a panel discussion on systems biology. The most intriguing of the topics covered was the current problems in systems biology:
- The peer review system for grant applications in the United States.
- Researchers fear of failure.
- Lack of effective collaborations.
- The lack of tools for non-elite scientists.
- The need of better leadership in the scientific community.
Overall I thought the summit was a great experience and I would go again if another opportunity arose. I got to network with different people and learned some new things that I will discuss on this blog in the next couple of weeks. My biggest gripe with the summit was that it was 90% presentations and 10% workshop. As a programmer coming into biology I know I should not expect anything like the WWDC, but if we are to build better collaborations and novel tools I just think the summit could have spent more time with people working together rather than gathering in a room and listening to one person talk. It would be interesting to put something like that together one day, what does everyone think?
As covered by Nature magazine a couple weeks ago, the full genome of James D Watson, one of the fathers of DNA, has been sequenced. The article also describes how Watson’s DNA sequence revealed his predisposition to cancer. This revelation brings on several important questions. Will people come forward to see what diseases they are prone to have? More importantly how can future employers, health providers or insurance companies use this information to genetically discriminate against you?
As covered by Slashdot a month ago there is a bill currently waiting the approval of one senator to getting passed that addresses genetic discrimination. This bill will make it illegal US citizens to be denied jobs or insurance because of an implication of a disease provided by their genetic code.
I just hope this bill passes soon as it is essential to the use of novel Bioinformatic practices in the medical field.
Sorry to be MIA once again. I got busy with wrapping up my course work, fending off hackers from this site and attending last week’s Systems Biology Summit (more on this in a follow up post). But besides that, I was privileged enough to be asked to contribute some thoughts on working in Bioinformatics with regards to Academia at Bioinformatics Zen for their 11th Bio:blogs. You should check out the article, there is a various assortment of information provided by some of the more prominent bloggers in the Bioinformatics community.
The biologists in my lab study the effects of ethanol (alcohol) on the brain. To do this they have to come up with animal based experiments to model various alcohol based conditions. One of these models is known as the alcohol deprivation effect (ADE). What it models is the possible increase in alcohol craving or consumption after a period of withdrawal (deprivation).
One such experiment may expose mice to a volunteer intake of ethanol. Then after a measured amount of time (i.e. two weeks) the ethanol is taken away (i.e. another two weeks); this is known as the deprivation period. Once the deprivation period is over the mouse is reintroduced to choice bottle drinking of ethanol versus a plain solution. This gives the researcher a variety of things to study (i.e. average amount of ethanol consumed, ratio of ethanol versus plain solution consumed, etc).
This past weekend I said goodbye to all my hair to support kids with Cancer. I was fortunate enough to exceed my goal of $500 (donations are still welcome and appreciated)! By bundling my hair I also I got to donate to Locks of Love.
As someone who is in academics and benefits from funds raised by this type of event, I felt it was necessary to participate. Not only did I have the opportunity to give back but it also helped to remember why we do the research we do; why we participate in science. I came back to school so I could pursue a career that benefited other people’s well being. Prior to that I was just twiddling my fingers away working for a credit card company. I enjoyed this event very much and encourage anyone else who has the opportunity to participate in various things outside of the lab to remember why we do what we do.
For everyone who donated:
THANK YOU!
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