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Biohackathon
wjv writes: "Open source Bioinformatics hackers from around the world are meeting in the
first ever Biohackathon to hack, eat, hack, sleep, hack... The South African
Business Day has the scoop, or see our weblog. The
event is co-sponsored by my employer
and O'Reilly. I'm typing this from the
hackathon, and you wouldn't believe the buzz... or the scenic venue!"
For what it's worth, I've been to South Africa and met lots of nice people there :-)
Paranoia isn't an infectious condition, it's a way of life
Uh, excuse me but they're making it sound like
these twenty year olds are THE EXPERTS in
bioinformatics. This is overly pretentious to
say the least. I have worked for a bioinformatics
company for the last 10 years and would not say
that the world's top bioinformatics programmers
would actually be there.
This meeting is nothing but hype and crap!
They would not say that they are the creme de la creme - they would say that they are actually coding, and that they are willing to share. Unfortunately, many of us bioinformaticians are stuck working for some company that looks for competitive advantage and won't allow sharing of pre-competitive code. These guys are not so un-encumbered (sometimes at personal cost - how much are you making?) and they choose to contribute to this cause.
As to being 'hype', would you prefer I3C?
Real artists ship.
http://bio.perl.org
'nuff said
I think the exerpt was saying that it's hard to tempt programmers making from 50-80k into being somebody's post-doc researcher, making maybe $20k a year, or less.
If you work professionally in bioinformatics, you will do much better, probably on par with being a programmer professionally. This guy was just pointing out that its much harder to convince bright and well trained people to slave for nothing in the academic world, since their skills are still rare and in high demand. Since everyone's working for private corporations, nothing gets published, so the body of open research in bioinformatics increases only very slowly.
You can find a list of bioinformatics programs here: http://www.ib3.gmu.edu/courses/bioinfogradprgm.htm l
Doing my part to piss off the religious right.
Altough I agree that having a "wet" lab experience will have an impact on your computational research, i also think that having biology knowledge isn't required. Projects are usually narrow enough that all you need to understand is your local view of the problem.
I'm a computer science student, and i am enrolled in a coop program. Having basically no knowledge in biology, I have been able, within 3 months of work, to learn everything i needed and to produce enough results/data to create 3+ M.Sc./Ph.D wet lab projects.
as i said, it depends on what you want to do and what you want to get out of it. anyone with a narrow view and some programming abilities can generate data. it's the interpretation of the data that gets the discoveries...
I'm a computer science student, and i am enrolled in a coop program. Having basically no knowledge in biology, I have been able, within 3 months of work, to learn everything i needed and to produce enough results/data to create 3+ M.Sc./Ph.D wet lab projects.
good for you (i really mean that!). but can you analyze the data you generated and make useful conclusions that further the understanding of that particular project/field?
what you describe falls into the type 1 category i mentioned...and don't get me wrong--it's a very important category. it's just not what excites me...i'm more about having a relevant biological question (what is the function of gene x? is gene y involved in disease z? etc.) and then figuring out what tools i need (and create them if they're not already extant) and what data sources i need to mine. i can pump out gigs of data, but, in my mind, it's all about what useful information one can glean from it, not about how much you can produce. (and i'm not saying that that is what you were saying)
the more projects you become involved in, the more your knowledge base grows...be sure to have the scientists you're working with explain the _entire_ project to you so that you can see the bigger picture of what they are trying to accomplish...and maybe you'll be able to bring a different way of thinking to the project...it's not all about 1's and 0's.
james
As a student persuing Bioinformatics at UCLA, I must agree with a previous reply saying that your statement is a bit too narrow. However, I'll go so far as to say that we need to do both at the same time. I believe it was either Dr. Fox or Dr Eisenberg who said that no one can know every part of the problem at the same time. One *MAJOR* problem I've run into is that Biologist don't state many of their assumptions about a biological system when speaking to a non-biologist; while mathematicians and CS people don't know enough about biology to understand that any solution to a bioinformatics problem needs to have "biological relevance." From what I can see, this means it needs to conform to all the unspoken presuppositions that biologists and biochemist take for granted. This is not insignificant.
As my boss Parag Mallick pointed out, either we (math/CS people) come up with a solution that's formally correct but takes longer than the biologist's hacks that aproximate the system; or we find the solution to a problem that no one cares about.
Another major barrier is the vocabulary. There's a reason that mathematicians and chemists are often at eachothers' throats. The math they use is the same, but the vocabulary and notations are very different, so it's like working in a foreign language. Take this to the nth degree when you're a mathematician listening to a biologist give a presentation. The breadth of knowledge is huge, even though the depth to any one part of biology can be rather shallow (relative).
By comparison, it's brutal to watch the biologist tack a probability/statistics class. Don't even bother with a topology/measure theory class. The breadth of knowledge isn't that big, but the depth of the theorems is massive. I've noticed that this leads to a "if it doesn't look like a tool I already know, then I'm not going to use it" attitude among many biologists. After remembering my boughts with algebraic topology, combinatorics, and advanced linear algebra (and listening to myself when I try and explain my Newest Idea(tm)), I can't blame them.
So we need education in both directions. The problem is way too big to be tackled by any one mindset.
Just my 2 pessos.
"One man can change the world with a bullet in the right place."
- Mick Travis, "If..."