Sunday, December 23, 2012

My year in open science

Reinventing Discovery
In 2011 I dipped my toe in the open access waters and in 2012 I dived in head first.  I come from the GAMESS group, which has always made the source code freely accessible (though under a license) and when it came time to releasing the first standalone software package from my own lab (PROPKA) in 2005 this was done under an open source license. (This year we finally moved all group software to Github.)

So when I came across +Michael Nielsen's Reinventing Discovery in late 2011 I could nod along when I read many of the chapters, but far from all of them.  However, the book makes a very compelling case for the idea that secrecy and greed is retarding the progress of science.  Shortly after I read the book Elsevier gave a very blatant demonstration of the latter.

The Elsevier Boycott
Sometime in January I became aware of the Research Works Act, which was an outrageous piece of proposed US legislation designed by publishers to squeeze the last few cents out of scientific publishing by making it illegal for papers describing publicly funded research to be made freely accessible online. This lead to a call for boycotting Elsevier, which I signed early on, but it also got me interested in open access publishing (see next section).

I should mention that I have broken the boycott twice already.  I agreed to do a review without checking the publisher first and I submitted a paper to an Elsevier journal at the request of a coauthor.

Publishing in the open access journal PLoS ONE
So after some soul-searching on my part we took the plunge an submitted a paper to PLoS ONE.  This went alright and 2012 resulted in four PLoS ONE papers and a fifth one submitted.  Though PLoS ONE does not count impact as a review criterion I have found the reviews every bit as thorough as for any other journal I have experience with, but you can judge for yourself as I have started posting my reviews on this blog.

arXiv is for research and journals are for CVs plus my own little boycott
Perhaps the most important "open access thing" I did this year is posting preprints on arXiv when we submit to a journal.   Just like an open access journal it makes the information freely available, but it does so right away (and discoverable on Google Scholar within a week of deposition) rather than many months later after the review process. If every scientist did this it would be a giant leap for open science and, yes, arXiv does accept manuscripts outside of physics.

In fact I think deposition on arXiv is so important that I have started boycotting journals that don't accept manuscripts that have been deposited on arXiv.

Computational Chemistry Highlights
This year I also initiated the overlay journal Computational Chemistry Highlights.  The idea grew from the ensuing on line-discussion of the role publishers and publishing alternatives on Gowers's blog and elsewhere following the Elsevier boycott.  I realized, as have many others, that there are two main reasons people publish in conventional journals: dissemination of results and prestige.  Dissemination is now a comparatively trivial contribution in the age of the internet and prestige is conferred by the scientific community, not by publishers.  CCH is an attempt at generating a platform for conferring prestige on papers that is independent of how its disseminated, using freely available tools like It will take a while to generate "prestige" for CCH but in the meantime is still provides a useful service to the scientific community by highlighting interesting papers.

Signing reviews
I have started signing my manuscript and proposal reviews. I am not sure what scientific impact this will have but at least it makes science a tiny bit less secretive.  On a more practical note I find that I do think a little bit harder about what I write in the review and I am much more careful about doing the review on time.

Posting funded proposals
I made all my funded proposals available online.  Unfortunately I was not able to add to this collection in 2012.

Open Notebook Science
I don't practice Open Notebook Science in the traditional sense of "making the entire primary record of a research project publicly available online as it is recorded."  But that is because of the sad fact that I don't personally produce any research data (running calculations) anymore.  However, I do try to publicly share my meager contributions the scientific process here and on Molecular Modeling Basics and, increasingly, Google+.

I can't really emphasize the utility of summarizing your thoughts on a topic via a blogpost enough.  If you have clearly thought the issue through it takes no time to write and if not, it helps you to think it through and is well worth the time it takes.  I also find it strangely liberating to write knowing that the comment section is there: if I skip something I think is trivial or well known I know the reader can easily ask for clarification.

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 Unported License.