Thursday, August 26, 2004

I'm a Master! Woohoo!

Late update again!

Been busy with the administrative side of finishing a master's thesis... Which means I'm a master in Bioinformatics, no less! It's been a pain tough...They made me come back 3 (!!) times for missing documents (from one of my evaluator), punctuation on the front page (capital E or É? Does it really makes a difference?) and for the best one...

"Sorry, we can`t allow you to do your final deposit right now, we did not sent you the invitation to do so, please come back tomorrow".

Grrrr... this University been like that since the beginning. What could I do? Dump it on the desk? Yes! That's exactly what I did... with a smile of course ;) It`s over now...well, if we don't consider doctorate admission and funding requests (CIHR, among others)...

On the upside, now I get to be called Master, which is nice ;) On the downside, the $%?$%? PCR machine broke AGAIN (3rd time in 4 years, new machine, different problem each time). For you information, it's a TECHNE... is it standard for PCR machines to break that often? I guess my construction of a new virus of DOOM (don't worry too much ;)) will have to wait! There's a drink at stakes... I must hurry!

Meeting early tomorrow (with doughnuts!) so I guess I'll get some sleep...

Oh almost forgot! Blogger removed adsense and let us put it back for our own profit... which is nice! I was thinking to move the blog elsewhere... but this is cool! I moved the ad somewhere less intrusive and more visible at the same time... Very cool targeting I must add! Google is definitively a company with enormous potential ;)

Thursday, August 12, 2004

I'm alive!

Sorry for not posting for so long... been very busy (doing minor corrections on my master's thesis... final deposit tomorrow! freedom!) AND been very sick at the same time... Fate has a twisted sense of humor it seems. Ok... being on the highway in the pouring rain for 2 hours probably didn't help :) So... here's today article for my (2) recurrent, non-comment posting readers :P

Open access to scientific litterature is getting hot... very hot. Think open source science, free access to all. See BioMed Central for a good primer on this. Predictably, it's publishers vs pro-open access people (basically, everyone else... researchers, students, etc). The restricted access model is not only very costly, it's very frustrating. We have to pay BOTH for submitting papers and to have access to the journal. Many universities (like mine) can't pay for internet acces to all the journals, especially the most interesting (Nature, Cell) which are very costly, even for an institution subscription. So you have to order the articles which interest you, a process that can take from 1 to 2 weeks (and cost a pretty penny, too). It's just restricting science, slowing the process for... no good reason, except the bottom line of the publishers we don't even need. Sure, they provide the peer reviewing platform. And open access platform can do the same... I'd be more inclined to pay ONLY for submitting papers.

Anyway, I don't think they'll resist for long. The internet is too powerfull... and shouldn't be limited in any way.

Sunday, August 01, 2004

I'm back!

Back from my 2 days vacation! It was a pretty cool trip, except for the mosquitoes part (I must be tasty, I got eaten alive while my friend was barely getting any attention from them!) and the 'Oh no I don't have a lift to get back in town so let's hope someone will take me on the highway while it's RAINING' part :) Took 4 hours instead of 2... even with these inconvenient, it was totally worth it. Wolves howling at night… can we ask for something more?

Let’s get back on topic. Today’s rant is about GenBank (well, the protein and nucleotide sections of Entrez). Right now, this database is growing exponentially, which is a good thing. Except for the “our search engine isn’t worth squat” thing. Try to search for the most common thing, let’s say GFP. First result?

PREDICTED: Gallus gallus similar to ataxin-1 ubiquitin-like interacting protein (LOC426353), mRNA

Hmmm... not very relevant. Out of the 2990 results, the true GFP is at position 2348. I’m not joking… and it’s basically the same story for every search, especially on HIV-1 clones (let’s say NL4.3). No options to sort by relevance. It’s a big, exponentially expanding mess. Couldn’t they sort with a Google like algorithm, with the most linked entry being to most important? I hope that they’ll fix it pretty soon, because it’s really a pain to use…