Saturday, December 16, 2017

The National Plan Open Science Estafette: my own first Open Science steps

Noot: als je liever Nederlands leest, lees dan het origineel.
Earlier this year Delft hosted a meeting for Dutch scholars aimed at hearing and learning about, and to give feedback on the National Plan Open Science (doi:10.2777/061652). I'm very happy I have been able to contribute to this effort, because more and better access to knowledge is very dear to me. During lunch time everyone could demonstrate their own Open Science. From this the idea evolved to have a relay race ("estafette"). In each part of the relay someone will tell about their Open Science story. This post is te start: every next runner tells their story on what role Open Science has in their research. And it does not matter if the focus is on Open Data, Open Access, or Open Source, because the diversity in the Dutch Open Science community is just very high.

My Open Science story goes back to the time that I was studying chemistry at what is now called the Radboud Universiteit. Chemistry students could get access to the internet in 1994 and this opened a world of Open knowledge to me! Our library was well stocked, but I still had to visit research department to read certain journals. Always uncomfortable as a young student to walk into a coffee room with senior researchers.

I learned HTML and later Java. Java, with their applets, brought the internet to life. It could visualize 3D models of chemical structures. A paper journal cannot do that. Twenty years later journals still don't have this functionality, but that's not the point. In those three, four years I got introduced to three projects, each Open Source, Jmol (now JSmol), JChemPaint, and the file format "Chemical Markup Language" (CML). The first was to visualize 3D structures on the internet and the second was to visualize 2D chemical diagrams. CML was a format that could store 2D and 3D coordinates for me. But the problem was that neither Jmol nor JChemPaint could read CML.

But that's where Open Science comes in. After all, I could download the Jmol and JChemPaint source code, change it, and share that with others. That was brilliant! And I dived in. Of course, I could have just used my changes myself, but because I realized it could benefit others too, I sent my changes ("patches") to the authors of Jmol and JChemPaint. Extremely happy and proud I was when the two researchers from Germany and the U.S.A. included those patches in their version!

And in the end it was not in vain. In the final year of my chemistry study I submitted an abstract to an international conference. It got accepted! But now I had to go to Washington (Georgetown, to be precise), to talk about my work. On top of that, we agreed to meet the authors of Jmol and JChemPaint in South Bend, where we laid the foundation of a new Open Science project, the Chemistry Development Kit (CDK). Expensive trip, but fortunately I got a bursary from a Dutch company. A peculiar trip it was. We used an Amtrak sleeping train and had dinner with a soldier who served during D-Day. In New York I stepped off the sidewalk onto the street to evade a group of scary heavy boys (which turned out to be a popular boys band), and we stood in the WTC (a year before 9/11) to hear two tourists ask at the musical ticket sale desk "what broadway was?".

I am proud that I have been able to contribute to these Open Science projects and that I co-founded the CDK. The Open nature of these projects have had a significant impact and, after twenty years, still do. Sure, it's not the same is discovering a new protein or metabolite, but these projects definitely not only benefited my research. Of course, also with a huge thanks to Hens Borkent, Dick Wife, Dan Gezelter, Christoph Steinbeck, and Peter Murray-Rust.

BTW, thinking about this relay race, Open Science itself is also a relay race: you take the token of the people before you, adopt the token, and pass on the token to the next scientist. And every day the token gets brighter!

This Nationaal Plan Open Science Estafette also continues. I am delighted to pass my token to Rosanne Hertzberger. Read her story here (in Dutch).

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