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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!"
If they were serious they would have biohacked some cyborgs to do all the future biohacking for them. Then they could just sleep, eat, sleep, eat, etc.
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Technically it's the second part of a two-part hackathon. The first part was held (as you rightly mention) in Tucson, Arizona. Following that, everyone was given the chance to go home and catch their breath, and now it's on to the part two.
The original intention was (I believe) that part one would be "talking" and part two "hacking". But as it happens, a lot more got done in Tucson than most attendees anticipated.
Interesting venue to hold a Biologicaly minded event. Many Capetonians will not go to the Oudekraal hotel, when the hotel was developed about 3 years ago there were large protests against developing on that part of the mountain due to ecological sensetivity, the fact that it is one of the last stretches of the coastline that isn't developed and its proximity to a kramat (burial place of a muslim Holy man). They also demolished a historic homestead to build the thing...
The Biomedical Information Science and Technology Initiative, for the National Institutes of Health, says: Today the disciplines of computer science and biology are often too far apart to help one another. A computer-science student often stops studying other sciences after freshman biology or chemistry; a biology student, even one knowledgeable about computers, may not ever have had formal computer-science classes. Biomedical computing needs a better -- and more attractive -- meld of those disciplines. Today computer-science students have little incentive to learn about biomedicine. The barrier is not just the rigorous demands of computer science, it is also the relative rewards: The $50,000 to $80,000 a year that professional programmers earn makes the compensation associated with many research positions in biology laughable. This situation is even more risible when one includes the reality that staff positions on NIH research grants are guaranteed for no longer than the grant award.
This is a problem in every field of scientific computing but it is particularly acute in biology because of the bizarre and heterogeneous data set. Ultimately, the question is whether it is more efficient to teach a computer science student biology or teach programming to a biology student.
People who go into computer science typically do so because of fascination with the tools and techniques, not because they are interested so much in the data. The scientific mindset of the biologist might transfer to computer science much easier than the mindset of the programmer transfer to biology.
The computer has the same fundamental status in biology as the microscope. Computer science in the form of bioinformatics should perhaps be as basic to the study of biology as organic chemistry.
I am the director of a core molecular biology laboratory with a focus on agricultural genotyping at a major midwestern university. I am happy to see that there is an interest in providing better downstream tools for data analysis.
My main area of concern however is the lack of good tools to take the raw data from sequencing machines and produce genotypes. Most software available is vendor specific, closed source, not very robust and extremely expensive. The closed source vendor specific solutions which are available lock up the data in proprietary databases, making it difficult to migrate to equipment from other vendors in the future and to get the data organized for many projects. All the software (including the few open source projects that exist) that I have evaluated has the same basic flaw, it starts with the premise that the lab will use them to screen against an existing database of genotypes (for disease or pedigree). These are fine medical applications (for which they were developed) but does not address the needs of the basic research laboratory which is working to discover the genotypes to begin with.
I would like to build an open source application that gives the user the freedom to choose the data collection platform, the freedom to move the data from one application to another and the freedom to improve and expand the application itself. I face two challenges: 1) Administration that says "open source, why would we want to use shareware". This one I'm addressing by building the information infrastructure using Linux. 2) Finding qualified programers that would like to work on the project. (I'm a pretty good admin, but am not a programmer).
The need for this work is great. In talking with other people in my field, I've found that the key thing they want to know is what software are you using to do the raw analysis. No one is satisfied with the current situation, but most of these are old school and don't know anything about opensource software. I've showed them that we can use existing open source software to run the lab. I'd like to show them that we can develop our own software to do some of the basic work. Any volunteers?
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
http://www.extremeprogramming.org
You wouldn't believe the lack of anarchy among these people. They sound young, but there is a lot of personal discipline in that room.
The best product is the one that is tested and evolves with that experience - and this is working code, used in anger by the human genome project.
Hey, check out http://www.ensembl.org and see what you think.
No way! I bet it's a BLAST!
*groan*