Some two months ago we decided to go back to the Netherlands, after having lived for more than three years here in Sweden. We have had a great time in our three houses, but feel a need to settle down, closer to family.

A week later I was contacted by Chris Evelo contacted me for a position to work on Open PHACTS. Chris and I only met for the first time in March, when I visited the group when I had a conference in Maastricht. His bioinformatics group is very much into Open Science and with a good track record in metabolism and transcriptomics analyses (something we do here at KI too), and Open PHACTS is an interesting EU project into the application of semantic web technologies to the life sciences, something I have worked a lot on in the past two years.

In the next two months here at KI, I'll be working hard on finishing my work for the other great EU project, ToxBank, on which I am working now. I personally see clearly how these projects complement each other, but no clue if such can be given shape at a EU level, where there is intention and consortium agreements :)

And, of course, I got a bit of funding rewarded here at KI, that I will use next year for two or three visits back to Stockholm, because there is some low-hanging fruit that remains to be picked.

All in all, I am very much looking forward to my next post-doc position and definitely my last. What's after that, I won't have to care about in at least the next two years :)

The Oscar4 paper (CC-BY, just like the screenshots of the paper below) was out already some days now, but the formatting has finished:



I spotted a rogue 'http://' in the code example b) in Appendix B:


I'll see what I can do about that, but the API might evolve a bit anyway.

That leaves me to mention that Bioclipse has an Oscar extension (Bioclipse has a lot of functionality nowadays, in fact), and that I blogged several times on Oscar4 when I was working with the other authors on the refactoring last year.

I guess reader of my blog already heard about it via other channels (e.g. via Noel's blog post), but our second Blue Obelisk paper is out. In the past five-ish years since Peter instantiated this initiative, it has created a solid set of shoulder on which to developed Open Source-based cheminformatics solutions. I created the following diagram for the paper, showing how various Blue Obelisk projects interoperate (image is CC-BY, from the paper):


It shows a number of Open Standards (diamonds), one Open Data set (rectangles), and Open Source projects (ovals). What does diagram is not showing, is the huge amount of further Open Source cheminformatics projects around, that use one or more of the components listed here, but which do not link themselves to the Blue Obelisk directly. And there are many indeed, both proprietary and Open.

I am proud of this diagram: it really shows that the interoperability we set out in the first paper worked out very well! This makes the Blue Obelisk an excellent set of shoulders to do translational cheminformatics.

Translational cheminformatics?? Well, I have been looking for a while for a good term for my research regarding all that hacking on the CDK, Bioclipse, etc. Now, that's the translation of my core molecular chemometrics research to other scientific fields, like metabolomics, toxicology, etc.

Guha, R., Howard, M., Hutchison, G., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J., & Willighagen, E. (2006). The Blue Obelisk - Interoperability in Chemical Informatics Journal of Chemical Information and Modeling, 46 (3), 991-998 DOI: 10.1021/ci050400b

O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR, James CA, Jeliazkova N, Lang AS, Langner KM, Lonie DC, Lowe DM, Pansanel J, Pavlov D, Spjuth O, Steinbeck C, Tenderholt AL, Theisen KJ, & Murray-Rust P (2011). Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal of cheminformatics, 3 (1), 37 PMID: 21999342 DOI: 10.1186/1758-2946-3-37