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Reflections on 2011: Open Source, Open Science and Open Chemistry

It has been so long since I uttered a word here, 2011 was certainly a busy year for me and I hope to ensure I dedicate more time telling people about what I am up to in 2012. In preparation for that I have spent some time moving my blog to some new hardware, in the cloud. I also got to the bottom of the poor performance of page loads, and things should be much snappier now. After all that I figured it was time for a cosmetic refresh, so after upgrading the Serendipity I selected a new and hopefully cleaner theme.

As an extra special treat I updated the photo to something a little more recent to - me emerging from my TARDIS with a mug of espresso in hand! Kitware grew a lot last year, so much so that we had to take space in a new building across the road. It was decided that our scientific computing team would move, along with the communications team. In the move I got my own office, with a view of the old office across the street.

VTK was accepted as a mentoring organization in the Google Summer of Code program. We were lucky enough to get two very talented and tenacious students who produced some great work over the summer. We also continued improving and extending Gerrit, and thanks to the Google Summer of Code I had the opportunity to attend both the Mentor Summit and the Git Together (held the day after). Not satisfied with two meetings in one trip I also attended a small portion of the Open Science Summit, and hope to be able to attend the whole thing if it happens again in 2012.

Speaking of Open Science, 2011 was a big year for the area both on a personal level and in the wider community. I talked about our work in open science at several conferences, and more specifically the work we have been doing in Open Chemistry. I wrote a Source article introducing the work that we have done in Open Chemistry since I joined Kitware, and we recently acquired the domain and have begun populating it. We were also awarded a Phase II SBIR which gives us two years of funding to develop many of the applications and libraries that I mentioned in the article.

The Science Code Manifesto was conceived in 2011, and Michael Nielsen released his new book Reinventing Discovery. There was also Open Access Week which highlighted the need for open access to scientific journals and data. I was very pleased to be a coauthor on two open access articles in 2011, the Quixote project and the Blue Obelisk five years on. I was also honored to receive my own Blue Obelisk award in 2011 from Peter Murrary-Rust!

There is so much else, but I am out of time for now and this post is already very long. Google+ was released to the masses, you can see a little more of me there, and I have created an Open Chemistry page that I will try to keep updated over the coming year. I was invited to a workshop on Semantic Physical Science in Cambridge, England and so I will be starting my traveling very much earlier than usual - leaving next Thursday. Here is to a great new year, one in which I hope we as a community can make significant progress in opening science for the world, and creating a truly shared set of tools for all!

I hope that 2012 is the year more of us start sharing in meaningful ways.


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Luca Beltrame on :

Luca BeltrameOn the topic of Open Science, I think some community guidelines for software are sorely needed (kind of like the MGED did with the MIAME standards for DNA microarrays): there are a lot of papers out there (at least in bioinformatics, my own field) where the software advertised isn't even working. Clear guidelines (and journals abiding by those) would IMO help the production of software that satisfies a (scientific) need, rather just the need of getting a paper out.

Pascal Pieters on :

Pascal PietersYour VTK link is broken. It points to instead of

Marcus D. Hanwell on :

Marcus D. HanwellLuca, I could not agree more and this is one thing we have been working on at Kitware too. The Insight Journal is one place where we are already working on establishing best practices, but we certainly need to do better. I think that the paper really shouldn't be the only unit of measurement in science, I felt tremendous frustration at the low priority of software development and good practices. Hopefully with enough of us working on this things will improve.

Thanks Pascal - fixed the link.

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