Proteins and Wave Functions: My year in open science

"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... Sometime in January I became aware of the Research Works Act ... 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.  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... Perhaps the most important "open access thing" I did this year is posting preprints on arXiv when we submit to a journal... 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 ... 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... 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 Blogger.com. 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...  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...  I made all my funded proposals available online.  Unfortunately I was not able to add to this collection in 2012...