Open Source And Genetics

UnanimousCoward writes "SFGate has an article about some researchers pushing for the open sourcing of genetic research software. Of course, the pros and cons are debated." It's the age-old debate; what follows the heart of the scientific method more? Peer review, or getting the information out as fast as possible?

Comments

Redundancy...

[metlin]

Despite all the arguments favouring IP rights et al, I'd say that most of the research has to be open-sourced, so to speak.

There is no point in re-inventing the wheel. It becomes ridiculous when 10 different companies engage in enormous investments independently on 10 different projects, when they could have all done 10 different projects to begin with.

IP has it's own say, no doubt, but over doing it leads to commercialization of science, and defeats it's very purpose. Engaged in silly patent and copyright wars, we have no doubt postponed many a useful invention by at least a few decades, IMHO.

Re:Redundancy...

[caesar-auf-nihil]

Good research is best accomplished by having all access to all information, so that you don't have to re-invent the wheel or relearn the experiments.

So why do some companies reproduce research that 10 other groups/companies are doing?
1. To see if the work can actually be reproduced. Patents are notoriously unreliable for their reproduciblity in the chemical sector.
2. To learn more about the technology, to either improve it or use it for another project. By doing the experiments yourself, you get a lot of knowledge that is never written down on paper.
3. Having a completely different group of scientists working on a research project can lead to a completely different way of interpreting the results. Therefore, the conclusions and applications of the research are different. (Diversity of thought!)
4. The idiots forgot to do a literature search before starting their project. This unfortunately happens more often than it should.

It does look like at first glance that reproducing other previously done work is a waste of time. However, given the advantages of the first 3 points, it will continue to occur this way, and for the benefit of science, it probably should.

open source of university researchers' code!

[phranking]

Be more clear in the writeup: the subject of the article is a petition to open-source any code that results from federal grant money from reseachers in a university setting. It is *not* about open sourcing all bioinformatic software, everywhere. In other words, code developed in a private setting, independant of university grant money - who cares? (at least in this case). Alternatively, grad students who strike it rich on code they wrote while on the government dole? Open source *their* work, since it was already paid for by the taxpayers. I don't see anything wrong with this particular distinction.

Re:Redundant?

[Heem]

nono. Not essentially. its the same article. word for word.
However, I'm glad it got posted again, for I missed the first posting of it, and I work for a biotech company. I don't know how the programmers in my company feel about this, but I tend to agree with Brenner in that it should be kept open-source. Of course, the size of my paycheck may depend on it costing an arm and a leg.

Advantages of open source scientific software.

[rice_burners_suck]

*O*H***W*E*L*L*

Software for research in genetics, biology, fluid dynamics, astronomy and any other subject that requires such colossal amounts of computations should, in my opinion, be open sourced. This way, several things can take place:

• While some folks are using the software, others can optimize it for increased speed. One of the things that bothers me when I read about some great new supercomputer is wondering how many of those bajillion cycles per second goes to waste because of nonoptimal computation loops. A small change here will make a large difference in the amount of time it take to achieve results.
• The software can by analysed and broken up into distributed programs which can be run on millions of computers worldwide, a la SETI@home.
• Distributed programs can be analysed and combined into one monolithic program that runs on a supercomputer.
• Scientists (or programmers) can add features to these programs, making them perform multiple similar purposes. Or, scientists can pick out a specific computation that they need done on huge amounts of data, and save countless hours, days, or even months that would have been spent computing unnecessary data.

Well, you get the picture. All of this becomes incredibly expensive with closed source software. Of course, nobody said it has to be free software. Obtaining the source code could very well require an NDA, if that's what will float the developer's boat.

*O*H***W*E*L*L*

But science is open-source

[DaoudaW]

Unlike scientists who keep research secret until it is published in a peer-review journal, some software developers -- who get little credit when their code leads to a genetic breakthrough -- want to share their work as soon as it leaves their keyboards.

It's an old debate in the world of computing -- and a new culture clash in bioinformatics...

It seems like there is some confusion here. Sure there is some time-lag between the research and its publication, but peer-reviewed journals are in fact similar to bugzilla.

The problem being addressed by the petition isn't what is published in peer-reviewed journals, its what isn't being published. Making scientific techniques proprietary not only slows the advance of science, but takes technology which could benefit the public and allows a few people to benefit disproportionate to their contribution.

The software that is used, not the data

[atheist666]

What should be open source and free beer free is the specialized software used by many researchers for processing DNA and Protein sequence information. For instance, take the very nice software package Vector NTI. Does many things researchers want. Also costs $5000. Instead of NIH (government science funding agency) money being spent many times (once per funded lab), what they should do is earmark some money to get programmers to write for free usage software like Vector NTI. It would cut down on the redundant purchase of software by many government-funded laboratories. Don't even get me started on how much research money is being spent on Windows, Word, Excel, PowerPoint, and Adobe Acrobat...