MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'biowhat.com' source. Thu, 27 Nov 2008 22:40:13 +0100 http://biowhat.com/2008/11/11/whats-going-on-with-biowhat/ What’s been going on here you may be asking. Well I’ve been pretty much swamped with my job at INCOGEN. I have every intention to keep this site going but it just has not been a huge priority. What we may have going on here, though is the addition of a new writer. Hopefully he’ll start posting soon. A goal of mine is also to revamp the look of this site as well as the writing style. So if you still have us in your reader, please stay tuned. I apologize for the lack of content and as always feedback/questions are always welcome. (Source: biowhat.com) biowhat.com blogs http://www.medworm.com/rss/comments.php?id=1951979 Tue, 11 Nov 2008 16:17:22 +0100 1951979 http://biowhat.com/2007/12/17/rrrrrrrr/ 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 Biostat... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=1100162 Mon, 17 Dec 2007 21:58:18 +0100 1100162 http://biowhat.com/2007/12/11/mia-the-trilogy/ 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 and Biostatistics 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. (Source: biowhat.com) biowhat.com blogs http://www.medworm.com/rss/comments.php?id=1087619 Tue, 11 Dec 2007 23:34:45 +0100 1087619 http://biowhat.com/2007/06/21/bind-and-soap/ 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:... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=687732 Thu, 21 Jun 2007 17:47:09 +0100 687732 http://biowhat.com/2007/06/17/lamp-and-wordpress/ 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 f... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=683271 Mon, 18 Jun 2007 01:27:10 +0100 683271 http://biowhat.com/2007/06/15/a-validated-biowhatcom/ 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 wa... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=676153 Fri, 15 Jun 2007 16:08:30 +0100 676153 http://biowhat.com/2007/06/12/2007-systems-biology-summit/ 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 ... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=676154 Wed, 13 Jun 2007 03:11:22 +0100 676154 http://biowhat.com/2007/06/11/genetic-discrimination/ 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... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=676155 Mon, 11 Jun 2007 18:01:03 +0100 676155 http://biowhat.com/2007/06/10/mia-once-again/ 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. (Source: biowhat.com) biowhat.com blogs http://www.medworm.com/rss/comments.php?id=676156 Sun, 10 Jun 2007 13:58:50 +0100 676156 http://biowhat.com/2007/04/11/bridging-the-gap-alcohol-deprivation-effect/ 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 c... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=537185 Wed, 11 Apr 2007 15:32:02 +0100 537185 http://biowhat.com/2007/03/26/st-baldricks-day/ 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... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=502968 Tue, 27 Mar 2007 00:58:34 +0100 502968 http://biowhat.com/2007/03/20/bridging-the-gap-stem-cells/ My “bridging the gap” posts were intended to help teach other computer scientists biology jargon. If you’ve been here for a while you know I haven’t really been followed through (only two posts) with this concept, but starting today I’ll to give it another run. Today I attended a seminar and found myself looking up various terms related to stem cell research. I’m sure you all have heard all the buzz going on about stem cell research the past couple of years. But I’m sure you didn’t know that there were two kinds branches of stem cells. More specifically there if a cell can differentiate into a mutre type then it is classified as either a pluripotent stem cells and multipotent stem cells [Stem Cell Research Foundation]. As I have very little k... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487095 Tue, 20 Mar 2007 19:12:53 +0100 487095 http://biowhat.com/2007/03/20/looking-up-genes/ I attended a seminar today where the speaker mentioned a gene whose name or function I’ve never heard of before. I used to use Wikipedia to look up a gene but that source is frowned upon by the scientific communtiy due to its unreliability. Now I use NCBI’s Online Mendelian Inheritance in Man (OMIM) which gives a nice condense summary of common knowledge on a gene. Another one of the graduate students in my lab suggested iHOP that not only has a cool looking monkey on the front page but is also presents a page describing a gene that is loaded with links to various abstracts contained within PubMed. What tools does everyone else out there use? (Source: biowhat.com) biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487096 Tue, 20 Mar 2007 17:45:03 +0100 487096 http://biowhat.com/2007/03/16/vertical-text-selection/ Want to select that list of genes without the pain of closing and reopening the file in Excel? Diana Higgins at Windows Fanatics reminds us to do this using most text editors (it can also be done in Word). Simply hold down the Alt key (or the option key in Macs) when making a selection. Unfortunately this little trick doesn’t work in Microsoft’s notepad and I wasn’t able to find such a key in Gnome for Linux either. Does anyone else out there know? (Source: biowhat.com) biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487097 Fri, 16 Mar 2007 17:53:10 +0100 487097 http://biowhat.com/2007/03/16/go-rams/ Sorry that this wonders off the purpose of the blog but I feel its necessary. Congratulations Rams! (Source: biowhat.com) biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487098 Fri, 16 Mar 2007 15:58:28 +0100 487098 http://biowhat.com/2007/03/15/eye-color/ I found an interesting post on today explaining the genetic properties of eye color. The article describes how eye color is a polygenetic trait (i.e. more than one gene involved) and of the genes involved one particular gene, OCA2, has more of an influence than the rest. Its a brief article but I thought it would be useful as it has some jargon that is commonly used in biology and bioinformatics. Key Terms: single nucleotide polymorphisms (SNPs), gene expression [Wikipedia] (Source: biowhat.com) biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487099 Thu, 15 Mar 2007 15:36:03 +0100 487099 http://biowhat.com/2007/03/14/the-iguana/ This actually happened about three months ago but I never got time to share. Since I came into my lab two years ago I have become involved in an age long battle between biologists and computer scientists (when I say age long I really mean never existing). The biologists and technicians called me “Neo”, asked me regularly if I was hacking into the FBI’s website, and complained when they couldn’t use my computer (I’m running Fedora Core 6). I called their bench work fancy biological hand waving. An exceptionally good prank of theirs was wrapping my computer, mouse, monitor and keyboard all unplugged in bubble wrap. I actually thought we were moving labs. Pure comedy. I got the tech back by remotely logging into his Mac and having it sing a little tune for him. I... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487100 Thu, 15 Mar 2007 03:49:28 +0100 487100 http://biowhat.com/2007/03/14/hello-me/ It seems like my public ramblings are not a waste. Not only am I talking to myself and former classmates but people from other blogs as well. Even Google’s first search result for “bioinformatics blogs”, nodalpoint, references this site. Although I don’t like the heading “perl hacking”, I shouldn’t complain for being acknowledged by my own peers. Plus its my fault that I don’t post more often. Who knows maybe this recognition we inspire me to post more when Spring Break ends. You’ll just have to tune in and see =). (Source: biowhat.com) biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487101 Wed, 14 Mar 2007 22:53:15 +0100 487101 http://biowhat.com/2007/03/13/network-theory/ This network made digg about a month ago. I thought it was interesting because I actually saw it a year ago. You’ll find that network/graph theory is a big topic in Bioinformatics. I personally find its use in Bioinformatics to be a little bit of a double edge sword. Their importance has emerged as these networks are used to present a systematic overview of various biological processes (i.e. all the gene interactions at a given time in the cell). Which is one of the overall goals of Systems Biology as I briefly touched on in my previous post. But at the same time their novelty has also caused their misuse in biological community. You may find biologists who want to include these networks in there study but have no knowledge of how they are constructed. One of the Ph.D. students in m... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487102 Wed, 14 Mar 2007 02:13:12 +0100 487102 http://biowhat.com/2007/03/13/systems-biology/ Here is an interesting quote form my school’s site that a professor recently pointed out in class: … systems are more than a sum of the parts, and that nonlinear interactions of components and processes result in emergent properties that can not be predicted from knowledge of the individual components and their behavioral processes. In lamen’s terms, the study of entire biological systems (i.e. looking at all the genes of a cell at once) provides more insight to properties of the system that could not be seen or identified with the old biological dogma of single gene studies. This is what Bioinformatics has done to the study of Biology. It has transcended the study from a micro exploration of individual gene function to the macro examination of the system as a whole by ob... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487103 Tue, 13 Mar 2007 18:12:46 +0100 487103 http://biowhat.com/2007/03/13/begginers-guide-to-bioinformatics/ As a computer scientist coming into Bioinformatics I was faced with the heavy task of catching up on my Biology and Chemistry (I was a Physics minor in undergrad but that wasn’t applicable to my Bioinformatics catch up). This meant two semesters of General Chemistry, a semester of Organic Chemistry and a semester of Cell Biology. Though all this course work was very educational and useful for my degree I don’t think its all that necessary for a someone who may be interested in fooling around with Bioinformatics problems on the side. Here is a very general overview of cell biology for Non-Biologists wanting to get involved in Bioinformatics: Proteins are the essential part of all living organisms. Proteins have a variety of functions and are involved in every process within our... biowhat.com blogs http://www.medworm.com/rss/comments.php?id=487104 Tue, 13 Mar 2007 17:49:30 +0100 487104