Archive for the ‘Open Source’ Category

Internship in Bioinformatics/Cheminformatics

We are looking for a candidate for an internship/trainee position in bioinformatics/cheminformatics at the European Bioinformatics Institute (EMBL-EBI) to work on a high-performance generator for chemical structures. This position requires strong programming skills in Java, a reasonable working knowledge in chemical structures and graph theory as well as an interest in learning about Apache Hadoop […]

DIY Bookscanner Kit arrived

I love books. Real books, made of paper, ideally hard cover and properly bound with needle and thread. And I have assembled a nice library over time. On the other hand, due to peculiar choices of where to live and where to work, and due to the nature of my job, I essentially live on […]

CDK-Taverna paper published

We are glad to announce that our article about CDK-Taverna, an open workflow solution for cheminformatics, is now online on BMC Bioinformatics. CDK-Taverna, which lives at, features more than 160 workers for various tasks in molecular informatics. The workflow paradigm allows scientists to flexibly create generic workflows using different kinds of data sources, filters […]

What do we expect from a chemical structure editor applet?

My team at the EBI maintains a couple of databases [1,2,3] dealing with various aspects of (bio-) organic chemistry. All of them need chemical structure editor applets where users can specify queries for substructure searches and which are used by our curators for data entry.The development of these databases is funded by the European Union […]

NMRShiftDB now with more than 12.000 proton spectra

The number of structures and spectra in NMRShiftDB now exceeds 31.000 and 35.000, respectively. The number of proton spectra alone is now 12.934. This is due to NMRShiftDB developer Stefan Kuhn in my group importing a recent donation from our collaborators Reinhard Dunkel and Heinz Kolshorn. Thanks to Heinz and Reinhard for their generosity.

ChEBI release 56, now with SD file

We are pleased to announce release 56 of our database of Chemical Entities of Biological Interest (ChEBI). SDF files are now available with ChEBI Release 56. They can be exported via the Downloads section or the search results page. We also have automatically generated links from IntEnz ( and Rhea ( This release contains 17842 […]

CDK Workshop 2009 Wrap-up

The CDK workshop 2009 is over and what is left is a bad cold. But I’ll get over it. The workshop itself was phantastic – we had 40 participants with well balanced contributions from industry and academia. The first half day was dedicated to tutorials on various aspects of CDK, basic installation, our CDK and […]

CDK Workshop 2009 kick-off talk

I’m collecting some thoughts for my CDK workshop kick-off talk on Monday and I guess I’ll go for the boring regular version, with an introduction to CDK history, followed by some statistical figures and ending with an explanation of the format for the developers workshop on Tuesday afternoon. As anyone can read on our CDK […]

Open Access Journal of Cheminformatics now live!

I’m delighted to announce that the first open access journal of our field, the Journal of Cheminformatics, is now live and has published its first articles.  Journal of Cheminformatics is a new open access journal from Chemistry Central publishing peer-reviewed research in all aspects of cheminformatics and molecular modelling.  It is run by Editors-in-Chief David […]