Open-Source Biology

nicholast writes with this "article describing the growing use of open-source collaboration methods in biology. The subtitle and main question is: Can a band of biologists who share data freely out-innovate the corporate researchers who hoard it?"

Comments

Open Source Biology isn't limited to biogenetics

[jfrumkin]

For instance, we're doing an open source phylogenetic project called The Tree of Life, which promotes both the open access to phylogenetic information, and open source software through the code itself. Many biologists are using open source software to further their research - case in point in O'Reilly's recent Bioinformatics conference.

Answer

[NiftyNews]

"The subtitle and main question is: Can a band of biologists who share data freely out-innovate the corporate researchers who hoard it?"

Answer: No, certainly not. That will never work. Why do you ask such silly questions?

Sincerely,
NiftyNews
Automated Response Unit for Data-Hoarding Corporate Researchers, Inc.

an example, and some experiences.

[mkoz]

As a scientist involved in a largescale database (www.pbdb.org) that is trying to build a large collaborative project I can say a couple of things about my experience.

1. Working in groups can be very difficult... i.e., when people don't share the same priorities, or see the same sources of bias as important.

2. It can be very helpful... often times getting other people's perspective is very informative. Generally in science we get feedback at the end (publication review), but here it happens at all stages, including data collection. This is really good.

3. People tend to start off thinking that they need to protect and hide data, but once they start to share data they tend to become big fans of sharing data.

4. Data transparency is essential to good science, these type of projects make that more and more possible. It does not take people long to realize how useful it is to have open and easily excessible data.

5. It is very important to open code used in analyses. I am in the process of working on a couple of papers where we have written some code to perform some fairly complex calculations. While I would like to say I am a great programmer, reality has a way of intruding. Collaboration has vastly improved the code, and I fully intend to post the code when I am finished with it. (for fear of being slashdoted I will not post the URL here).

Pretty ignorant article

[Otter]

Two points:

1) The idea of sharing information within and beyond the scientific community is hardly a new one. On the contrary, if anything secrecy has increased in recent decades, partly because of industrial applications but mostly becuase science is much bigger and more cutthroat than when it was a wealthy gentleman's pursuit.

The sort of collaboration described here is new and is driven by the Internet and by the large data sets in current biology. But to say that scientists got the idea to share information from Linus Torvalds is idiotic. That's not even where computer scientists got the idea.

2) Claiming that patents encourage "hoarding" of information is the sort of thing you expect to see in +1 Slashdot comments. The whole point of patents is to _encourage_ the sharing of information instead of relying on secrecy. Inventors trade disclosure for a temporary monopoly.

Again, there's a germ of truth here that companies after a patentable discovery need to be closed-mouthed about their progress, but that's probably given the author too much credit.