Monday, July 26, 2004

Vacation time!

Oh well, I think that summer time isn't that great to start a blog about a (student) scientist's job... people come back next week! Things should get more interesting by then. In the meantime, I'm getting vacations of my own! Camping in a national park with a friend... only for 2 days, but that's better than nothing!

Before I go... some thoughts about the bioinformatics field that might be of some interests. It's still in it's infancy; a boon and a bane. Comparing to other fields of informatics, it's 10, maybe 20 years late. Ugly, non functional command line interfaces are predominant (think GCG); some are just being replaced by uncute, non functional graphical interfaces.

UNIX seems like the OS of choice, for the only reason than it's been like this in this field since the beginning; I can't honestly think of a real advantage to use this over a more accessible Windows platform. Newer programs compatible with Windows are more often than not written in Java, with it's trademark, ugly interface. I know it's more portable to multiple platforms.

Web interfaces, while very nice for big portals (Ensembl, Pubmed, etc...), are just not suited to programs made by some guy in his spare time. Links go dead, server go down... just release the binary (or better yet, open source!) and be done with it! Most applications in bioinformatics don't require much CPU power by today's standard anyway....

Most programs are buggy, amateurish AND/OR very costly. Example : The demo for a 3000$ microarray analysis program, which I won't name, managed to crash my WHOLE machine (not just the OS) reproducibly. When it kinda worked, it refused to recognize Affymetrix data (a standard in the field). Features advertised on the website we're non-existent. Algorithms used were not defined anywhere in the (ridiculous) documentation. The best part? Incompetent tech support. They have their answer list for a list of possible problems, and that's it. They don't have a clue about their own software, the way it works (if it works at all, that is) or the nature of the data it's supposed to analyze. I won't get in the 'they're Indian, im from Quebec' understanding each other problem... I guess this company is just another example of people going into the field because it's "hot"; a major problem in my view. Informatics suffered a lot from that; think dot-com. I'll talk about it in another post for sure.

For now, I'll go. Back in two days. Oh, and if someone knows how to mutate the GPI-anchor cleavage site of the mouse's Heat Stable Antigen (HSA) in order to inhibit the GPI-anchoring but preserve the membrane localization, I would be thankfull! And if anybody have a spare gmail account to give, show some love!

Monday, July 19, 2004


I have finished! My master's thesis that is ;) I am now waiting for comments from the evaluators... let's hope that they'll be nice ;) Everyone's in vacation this week in the lab... I have the feeling that the end of July will pass sloooooowly... :| Hopefully the (lucky) girls that were at the AIDS 2004 conference in Bangkok will be back this week with lots of interesting stories... At least I have work to do : write my (top secret!) doctorate project, which i'll propose soon to my director! Exciting stuff, I swear ;)

Just to show some art I've done recently (text is in French... and no, I'm not sorry!). Comments appreciated ;) Posted it using BloggerBot ... very usefull stuff for picture hosting!

Monday, July 12, 2004

Almost done!

Oh my god... i'm almost done! Two of my colleagues finished reading it today and provided me with some advice, which I appreciate a lot. Writing is weird (especially in French); you can reread you a million time without spotting errors or confusing paragraphs. External advice before terminal evaluation is therefore always nice to have ;)

Too bad this site doesn't offer pictures hosting, I managed to create some very nice pictures of HIV-1 depicting structure of the virus... all in French, obviously ;) It's sad but good art in science is very rare; everything seems to be done with circles and boxes in MS paint. And the concept of scale is everything but implemented, which can often lead to misinterpretation. Photoshop courses should be the norm in science! :)

Now let's get this finished, once and for all...

Sunday, July 11, 2004

I always feel extremely tired on weekends. Must be cause I wake up at 1:00 pm to recover from lost sleep during the week. Can't be good for circadian rythms ;) On this subject, very interesting research is done via microarrays on drosophilia... check it out on pubmed! Very elegant stuff (life never cease to amaze me!) See : DNA microarray analyses of circadian timing: the genomic basis of biological time by Duffield GE for a good review.

Watched the world chess championship match today (finals between Adams and Kasim). It was a very intense match! And Adams won, so there's a final match tomorrow (and rapid blitz in case of a draw). The winner get to play Kasparov... can't wait to see that ;)

Now let's get some work done... cmon, just 2 graphs to do...

First Post!

Let me introduce myself.

I'm a scientist working on AIDS. Well, technically, i'm still a student, but in academics, we're stuck this way for a loooooong time. And i'm only 24 ;) I'm specializing in two (currently) very hot areas of science - bioinformatics and HIV. Let's just hope that bioinformatics ain't just a trend like the .com bubble :) At least HIV ain't going anywhere soon. Doing research on HIV-1 is both exciting and challenging; no surprise that no permanent cure / vaccine is not yet available! Trust me, this bug is a tough one!

More later, it's midnight here and I have work to finish (Master thesis! Hopefully done this week...)