Finally this paper in Cancer Informatics is indexed by PubMed. This paper describes the early "model formulation" phase of my PhD work. As I approach the end, and obtain more shareable results, I will include more Biomedical Informatics resources on this website.
More information about the paper:
- Title: A Novel Information Retrieval Model for High-Throughput Molecular Medicine Modalities
- Authors: Firas H. Wehbe, Steven H. Brown, Pierre P. Massion, Cynthia S. Gadd, and Constantin F. Aliferis
- Journal: Cancer Informatics
- Keywords: clinical bioinformatics, information retrieval, molecular medicine, predictive models
- Links: PubMed, PubMed Central, Journal Link, PDF File, Export to bibliography
- Licence: Creative Commons Attribution By License
Abstract:
Significant research has been devoted to predicting diagnosis, prognosis, and response to treatment using high-throughput assays. Rapid translation into clinical results hinges upon efficient access to up-to-date and high-quality molecular medicine modalities.We first explain why this goal is inadequately supported by existing databases and portals and then introduce a novel semantic indexing and information retrieval model for clinical bioinformatics. The formalism provides the means for indexing a variety of relevant objects (e.g. papers, algorithms, signatures, datasets) and includes a model of the research processes that creates and validates these objects in order to support their systematic presentation once retrieved.We test the applicability of the model by constructing proof-of-concept encodings and visual presentations of evidence and modalities in molecular profiling and prognosis of: (a) diffuse large B-cell lymphoma (DLBCL) and (b) breast cancer.
Labels: biomedical informatics, clinical bioinformatics, gradschool, information retrieval, phd, research, science
I am very inspired by Tyler's online pledge to lose 100 pounds. Visit his website and help him meet his goal. I wish I was brave enough to document my training/weight-loss goal.
Magnetic Movie from Semiconductor on Vimeo.
The secret lives of invisible magnetic fields are revealed as chaotic ever-changing geometries . All action takes place around NASA's Space Sciences Laboratories, UC Berkeley, to recordings of space scientists describing their discoveries . Actual VLF audio recordings control the evolution of the fields as they delve into our inaudible surroundings, revealing recurrent ‘whistlers' produced by fleeting electrons . Are we observing a series of scientific experiments, the universe in flux, or a documentary of a fictional world?
More info here www.semiconductorfilms.com/root/Magnetic_Movie/Magnetic.htm
An Animate Projects commission for Channel 4 in association with Arts Council England.
Labels: science
If I am to say one thing this month on my blog, I would praise the CakePHP Framework. I love it. The documentation leaves a lot to be desired, but for me the fun of coding in CakePHP is looking at the code and figuring out how well everything is put together and how intuitive the framework is.
Labels: cakephp, coding, technology
I'm going out of town for two weeks tomorrow morning, and I'm running late on my packing. I also haven't blogged in a long while. Then, why am I taking the time out to write this? It's because I can't look at my open luggage bag without remembering the events of this afternoon and I have to get this off my chest. I even went to the gym specifically to "work it out," but my blood still boils when I remember this, so maybe venting about it publicly will help me rid myself of this negativity.
I, a graduate student, have a very small number of long button-down shirts that are good enough to be worn for family events, specifically my girlfriend's family with whom I will be spending the holidays and for whom I need to appear well dressed and having more than one nice shirt. Two-thirds (i.e. two) of said shirts are currently at Village Cleaners. I was stupid enough not to pick them up until today and not to check what time they closed. I realized very late that they close at 4pm on Saturdays instead of 6pm. So I hopped in my car and got there as fast as (safely) possible. I pulled up at 3:59 (according to my iPhone) in front of the shop. The lights were still on, another car was pulling out and another client was loading his clothes into his car. I got out of the car to find that the door was locked. The employee behind the glass made a sign that they were closed. I smiled and made a begging gesture hoping to change her mind, but she SHOOK HER HEAD. I tried, in mime, to explain that I was leaving town tomorrow morning (including emulating plane wings with my hands). She saw that, but shook her head more, TURNED OFF THE LIGHT AND WALKED AWAY. How mean is that?!?!?! I gathered what little dignity I had left, got in my car and called Maggie (I wanted to time-stamp the moment in my next cell-phone bill just to make sure I'm not crazy! Maggie said her Sprint phone got my call at 4:00).
I'm not saying that they wronged me. They don't have to open past their closing time for anyone. I did, after all, show up late. If fault is to be assigned for me not having my shirts (and for me to buy new ones so that I can wear something for the holiday dinners) then I should take the blame for not getting there earlier. I also know that businesses have to enforce business hours, and that employees have to go home to their own families on time and that books and registers need to be closed. I know all that, and again, I'm not saying they faulted me, but REALLY? Did she REALLY have to treat me that way??
I have been a patron of Village Cleaners for more than 7 years! It's a good mom-and-pop business. The employees know me and I've had nothing but good experiences with them, until know. One person who works there, Jerry, doesn't even ask me for my name anymore! He writes down my weird foreign name on the ticket with no spelling errors. How awesome is that? One time I pointed out that the buttons on the cuffs of one of my shirts were melting. The next time I brought that same shirt, and without saying anything, THEY CHANGED THE BUTTONS. Again how awesome is that? That's why I loved that place and kept coming back. That's also why I felt so upset this afternoon. It's like a good friend suddenly turning mean on you. Did you really HAVE TO turn down a desperate-looking client acting like a mime-clown behind the glass on 4pm on a Saturday night in the holiday season?? Really?? I'm not complaining that they did anything wrong per se, but this is a sure way to alienate a loyal client and to squander YEARS of mutual good will. In an age where rich powerful corporations in Detroit and Wall Street are being hung to dry for incompetence and bad products, small businesses need to capitalize on their charms and personal relationships to hold on to consumers not lose them. Now if you'll excuse me, I will be using the money I saved on this trip from cheaper gas to buy me some shirts for the holidays.
My name is Firas Wehbe, their name is Village Cleaners, and they are located at 2010 Acklen Ave Nashville TN 37212 by the post office. I hope every search engine on the internet indexes this post and I approve this rant.
I am now re-reading Isaac Asimov's The Gods Themselves published in 1972. The events in the book take place in 2100 AD. A maverick scientist is warning a resistant establishment about his discovery of the dangers of Inter-Universe Electron Pumping, a new found supply of abundant free and clean energy that had revolutionized humanity. He wanted it abandoned. This is his exchange with a senator in the International Congress.
"It is a mistake," [the senator] said, "to suppose that the public wants the environment protected or their lives saved and that they will be grateful to any idealist who will fight for such ends. What the public wants is their own individual comfort. We know that well enough from our experience with in the environmental crisis of the twentieth century. Once it was known that cigarettes increased the incidence of lung cancer, the obvious remedy was to stop smoking, but the desired remedy was a cigarette that did not encourage cancer. When it became clear that the internal combustion engine was polluting the atmosphere dangerously, the obvious remedy was to abandon such engines, and the desired remedy was to develop non-polluting engines."
Inter-Universe Electron Pumping is not a danger to humanity as MANBEARPIG is though :).
Labels: isaac asimov, science, scifi
I was introduced by my brother to Stephen Fry, an English humorist, actor, novelist and filmmaker. He presents a show on the BBC called Q.I. (Quite Interesting). Allan Davies, the "permanently installed guest", is one of the funniest comedians I've ever seen. Fry is featured in a short film that celebrates the 25th anniversary of the GNU operating system and talks about free software. Free as in "free speech", not "free beer". See link for video and more information.
Labels: technology
I took dozens of pictures at the Smithsonian National Museums (Air and Space, and Natural History) this summer when my parents were visiting. I enjoyed it so much that I nearly declared taking photographs in science museums an official hobby. I love taking my time at museums. Having a camera in my hand establishes that and gives me an excuse to linger and wander around. I came across this article about photographing the science museum (via Boing Boing) that gave me a lot of validation. I promise to put more pictures up from previous and (hopefully) future trips. Here's a link to the set.
Labels: personal, photography, science
Labels: nashville, photography
I will be running in the Komen Race for the Cure with the Juggling for Jugs team. Please join us or support this very good cause by donating here.
Labels: nashville
Labels: gradschool
Blog + Flickr + Delicious