German Conference on Chemoinformatics 2006: Day 1 and 2

The 2nd German Conference on Chemoinformatics started yesterday, with two chemoinformatics tutorials: one on industrial chemoinformatics (I saw this presentation before… not sure when), with a good overview on integrating different information sources; the second one was about opensource chemoinformatics by Christoph Steinbeck (being involved in opensource chemoinformatics for almost 10 years now!), which included a Bioclipse demo (by me) and a demo by Thomas Kuhn on the CDK based chemoinformatics plugin to Taverna. Other opensource projects of the Blue Obelisk movement were mentioned and a few outside it too. 2 minute read

Organic chemists can now tune properties without changing the molecular structure??

Paul Bracher and Joshua Finkelstein pointed my attention to a nice discussion in Nature on the future of chemistry, in What Chemists Want to Know, by Philip Ball. Paul and Joshua already reviewed it thoroughly, but I could not resist commenting in it too. Having chosen chemistry as specialization when I went to university, and with a minor in supramolecular chemistry, this is a something I do relate to. 2 minute read

When is open source chemoinformatics successful?

Open source chemoinformatics has become a common phenomenon, though many projects are small in nature: source code is developed by only few developers, or even in a closed manner and released when considered done. Within open source software there is room for distinguishing a subset of open development chemoinformatics, that is, Bazar-like, instead of Cathedral-like (see ESR famous writing). 1 minute read

Chemical Blogspace updates

Chemical Blogspace is up and running fine for some time now. Since the start the number of aggregated blogs increased from 19 to 64 now, of which a number are situated at ChemBlogs which is a site where you can run a blog. Meanwhile, the number of cited papers went up to 186! The JACS is most popular so far, followed by the Angewandte Chemie Int. Ed. less than 1 minute read

Bioclipse Workshop: short but productive

The Bioclipse Workshop has ended and, for just three days, turned out quite productive. We have first bits of scripting support for JavaScript using Rhino. At this moment the scripting plugin needs to explicit depend on plugins to be able to access their classpath, but we plan to solve that. An example script: 1 minute read

The Bioclipse Workshop is in progress

The Bioclipse Workshop is in progress, and Ola is now leading a discussion about future releases and functionality. Proceedings are live updated, and presentation sheets will be available shortly. less than 1 minute read

Opensource Chemistry and Opensource Chemoinformatics

The Blue Obelisk mailing list has seen an interesting discussion on ambiguity in the term ‘open source’, triggered by a study by Beth Ritter Guth. For example, Jean-Claude Bradley performs ‘open source’ science (see his Useful Chemistry blog) who is not opposed to using closed source software, while the Blue Obelisk is about ‘open source’ software. It seemed that this was contradicting, and Peter Murray-Rust [wp:en] wrote up a lengthy overview of the use of the term ‘open’. 2 minute read