Open Source/Open Science

Stephen Adler (the guy who always does really cool write-ups of various events) writes "A one day conference titled Open Source/Open Science will be held at Brookhaven National Laboratory on October 2nd, which will focus on the use of Open Source in science. This is a pre-announcement so that the organizing committee may be able to better gauge community interest in attending. The full text can be found on the conference web page. "

Comments

It's vice versa

[stonehenge]

It has been pointed out correctly by ESR and others before that the principles that make the open source movement nowadays so successful, are the same that made modern science so successfull for the last hundred or so years.

BNL truly a leader in open source / open science

[ubiquitin]

I'm not affiliated with BNL, but merely someone who has been to Brookhaven National Lab with the past few months and seen some of the open source apps they have on the synchrotron floor. I highly recommend attendance of this one. Can't wait for Oct. 2. The macromolecular guys and many others at the NSLS have Linux boxes all over the place, folks, doing anything you can imagine. Can't wait to see an organized display of the OSOS stuff being worked on.

Gotta get front-row tickets for this event. Any scientists from the Boston area want to carpool down to BNL via the Long Island Ferry? It's on a Saturday but I can't think of a better reason to play hookie, personally. email me at: ubiquitin@crystallography.net

an "open lab"

[Bizzaro]

We all know that the open-source development model has been extended to several areas beyond computer programming. But have you heard of it being extended into the realm of scientific research?

"Bioinformatics" is branch of biology that is completely computer-based, and typically involves the analysis of data stored in public databases on the Internet. This is my field of study.

As you may know, scientists in all areas tend to work secretively on projects for many years before publication, often limiting access to discoveries and innovations to those who work in the very same room! And that is something that has always bothered me about science. It seems we are to share our ideas with humanity (which we often do, if and when we publish in a refereed journal), yet the priority is really to protect one's self from being "scooped". It appears to me that we (scientists) care more about getting credit for the discovery than the discovery itself. Does this remind anyone of the mindset of the proprietary software developer?

A thought I had was that bioinformatics, being computer-based research, may present an opportunity to make an "open laboratory" or "collaboratory". Following the model for open-source software development, an open lab would place on the Internet all of the work in progress for a particular research subject (analyses and/or new techniques). Communication between collaborators, which would include anyone who comes along and decides it is an interesting project, can take place via mailing lists, and so on.

The only worry, even still for me, is that someone can come along and swipe the whole project and take credit for it. But of course anyone who gives away software code would have the same concern. It really comes down to human nature: Just how much are we willing to share with others, at the risk that someone may take it all away?

But I think even temporary measures to prevent yourself from being scooped are restrictive and contrary to the scientific ideal. Why? Because these measures very much squelch free thought and exploration, what science is supposed to be all about.

The one thing I particularly enjoy about free software development is the ability to brainstorm with anyone anywhere over a new project, without fear of idea-theft. To me free software is not just about seeing the code or downloading free binaries--something even a closed organization can accommodate. What I like about GNU- or Linux-style development is the open exchange of ideas--the "bazaar" model Eric Raymond refers to.

My whole point is that it's something VERY MUCH MISSING in all research projects prior to publication--when the scientist feels there is nothing to lose and nothing left to be gained. I just want to see that change.

So I started The Open Lab, or "The Open Collaboratory of Molecular Bioinformatics," a non-profit organization established to promote open collaborations for research and free software development in the field of molecular bioinformatics.

http://theopenlab.uml.edu/

The Lab supports Internet-based collaborations that will advance knowledge in this scientific field. This means not only GNU-licensed software development but pre-publication research projects that are completely open for the public to view and contribute to.

Jeff

This sort of thing has cropped up before. And it has always been due to human error.