Open-Source Biology 122
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?"
an example, and some experiences. (Score:5, Informative)
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).
Re:Open Source Biology isn't limited to biogenetic (Score:3, Informative)
At least some of bioinformatics stuff (eg bioperl) includes some phylogeny stuff. Or, so I was told by someone on #bioinformatics on OPN.
Re:Scientific Journals Obsolete (Score:2, Informative)
There is also OVID, which is an online database of journals available at most universities. Not completely opensource, but for all practical purposes (at least from the perspective of the scientist), it is "open source" "policy of scientific journals to not publish that has been "published" previously"
Science literally changes hourly. There are things I thought were true on Monday, that I know are patently untrue today (seriously, specific things). There's no point in writing them down until you reach a reasonable degree of certainty. Publication is the last step before it leaves your hands entirely, it finalizes what you have say.
Presentation at conferences, retreats and workshops; poster sessions, informal review (passing your manuscript around to all of your buddies before publication), and the all important coffee room are what comprise the "open source" community of science for works in progress. Sharing prior to publication is like sharing prior to ever trying to compile your code. You'd look like an idiot.
Open source bioinformatics tools (Score:2, Informative)
bioinformatics.org [bioinformatics.org]
bioperl.org [bioperl.org]
biojava.org [biojava.org]
and even www.cvbig.org [cvbig.org] for a talk on bioinformatics with PHP/Ming
Re:Free Flow of information? (Score:3, Informative)
Incidentally, I can't recommend Ensembl [ensembl.org] highly enough. Not only have I been able to significantly further my research with their tools, but they have open-sourced the entire code behind their site! And the documentation is even in Wiki [wiki.org]! I really think what they have done is incredible and should be one of the first projects anyone mentions when expounding the virtues of open-source software as well as sharing information in the field of Biology.
-Ryan