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!

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