Obtained: Gallant surcoat+1.

The title of the post pretty much says it all. I’ve finally been able to obtain this piece of artifact armor+1 after searching for the last item I needed for about five months.

November 25, 2006

New heading and other stuff

As you can see I have a new heading, courtesy of Melissa, featuring Saber from Fate/stay Night. Aside that, updates on this blog will continue to be slow for a little while, as I will try to rush and finish S.T.E.A.L. at last this Sunday.

November 25, 2006

A simple annotator

In the past two days I’ve written a simple annotator program, that given an input list of RefSeq genes, automatically determines the relevant Entrez Gene IDs and annotates them using the flat files provided by the NCBI. A direct conversion was not possible due to limitations in Biopython’s parsers, but I managed to use the GenBank parser to identify and extract the references to the Gene IDs (and putting them in a list).

November 17, 2006

Random photos

Since recently (thanks to my brother) I got a new cellular phone with better capabilities, photo-wise, I decided to take a few photos of my workplace. I changed office a while ago, now I’m located on the first floor of the building, sharing the office with 5 other people: Raoul, Michele, Giorgio, Roberta and Alessandro. This photo shows my current computer setup: 429 Quant was running a screensaver when I took this photo: the mouse pad and that other black thing next to the keyboard are gel pads to help me with my tendinitis.

November 15, 2006

More studying

EURASIP Journal on Bioinformatics and Systems Biology is having a special issue on text mining for biology. My boss wants to publish something there, and asked if I and a colleague could work on that. I’ll probably focus on evaluation methods, since I’m not an expert in text mining or language processing. And that’s where the problem comes in: I know almost nothing on text mining. Which means this will add up to the ever growing pile of papers and books I have to study, including but not limited to Python programming, microarray analysis and XML…

November 10, 2006

The joy of meta-analysis

Recently, I’ve been in need to retrieve some records regarding renal cell carcinoma referenced in papers by Zhao et al. and Higgins et al. The records of the former were hosted on NCBI’s Gene Expression Omnibus, while the latter records were uploaded to EBI’s ArrayExpress database. Getting data from others and using it for your own analysis is called meta-analysis, and it’s often used to validate methods and algorithms with different data sets.

November 7, 2006

PhD students

After discussing my second PhD year today, and after noticing that not even a single professor from the commitee was there (save my boss and a person that joined later on), I realized that the situation for students like me isn’t really the best. A PhD program is supposed (at least here) to be a cross between a research job and a student’s position, since you should study but at the same time conduct research and (if you’re lucky) also get paid for it.

November 3, 2006

New computer

Wednesday I got around to assemble a replacement for largo, what used to be my old “main” desktop. I also got a new case and power supply for leon, the other desktop I own, but I need to switch things around from the “old” largo to leon and I didn’t have the time yet. Without any more delay, here are the specifications: Pentium Core 2 Duo 6600 NVIDIA GeForce 7950GT

November 2, 2006

Software and biology

I’ve noticed that the journal Science code for Biology and Medicine has finally launched. While some said that would be a journal if someone is desperate for a publication, I think it fills in a gap that’s very felt in bioinformatics: the availability of source code.

October 28, 2006

ToAU Mission 22

Last Tuesday I assembled a group and we took on the (only) battle present in the new Treasures of Aht Urhgan update. I had to look for members, but since Besieged was going on I lost a lot of time shouting for members. In the end I managed to get a red mage and a ninja along people I had arranged to meet with.