With some help, I got the kfile stream analyzer for Strigi working. This means that Strigi will now index the meta data fields defined by the kfile-chemical plugins. The problem why it was not working earlier, was that it segfaulted on every creation of KDE classes. That’s something I really hate about C/C++: the lack of stack traces, though valgrind was helpful. It turned out that adding the below line fixed all.

Desktop searching has become a hot topic (some earlier blogs ), now that years of data accumulated on ones hard disk: PDFs, OpenOffice.org documents, Latex manuscripts, old Java source code, digitized music, and a lot of chemical files. Well, on my hard disk that is. Unlike piles of paper, a computer could search this data, but due to the size an index is required. What’s KDE4 going to offer?

Just wanted to make sure this news made it to the Blue Obelisk Planet too: David Strumfels reported that he extended MS-Excel with CDK functionality . I wonder how difficult it would be to do this with Kspread or Gnumeric?

Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics (green OA) discusses (reasonably) recent additions to the CDK. It appeared in issue 17 of this years Current Pharmaceutical Design volume, after being too long in the queue after being accepted; but I am happy that it is out now.

Together with Christoph, Christian and Jerome, I will be representing the Blue Obelisk movement on the first First Workshop on Chemoinformatics in Europe with the topic Research and Teaching . Though I wonder what this theme excludes? Development? Can’t imagine that commercials companies will not be represented as usual. Moreover, it will likely include some bioinformatics too, unless you consider that to deal with sequences only.

Geoff Hutchinson blogged about his OS/X ChemSpotLight, an indexing tool for chemistry documents. It’s like, but more advanced than, the kfile_chemical and Kat I have been working on (with others) for the KDE desktop (see earlier blog items). ChemSpotLight currently does more than the KDE tools: it adds Spotlight comments. I assume these are like the Linux extended attributes, used for example by Beagle.

Yesterday I installed the Eclipse Web Tools Platform again, and now succesfully, using the Eclipse update mechanism, on my Kubuntu dapper eclipse install. Because it has a validating XML editor, the one last thing I still needed jEdit for. (I do miss the vertical selection feature of jEdit, though.) It signals me of errors, and allows autocompletion.

November last year, I reported my plans to develop a live CD with all our favorite chemo- and bioinformatics software. Bioclipse requires Java5 and sort of still depends on the Sun JVM (I will experiment with classpath-generics later), but is now distributable with operating systems.

Classpath 0.91 is released with 1.45 million lines of code and with 98.96% coverage of Java 1.4.2, and 99.82% of java.swing. Or, as Dave calls it: 0.91 rocks! JChemPaint runs again (they fixed the XML parsing problem), and Jmol still runs <i class=”fa-solid fa-recycle fa-xs”, but slow. I also tested Taverna which now also starts up, but has an XML parsing error too: Exception occured whilst loading RDFS!

BioMed Central is setting up a new peer-reviewed, open access journal Source Code for Biology and Medicine. It will “encompass all aspects of workflow for information systems, decision support systems, client user networks, database management, and data mining” . Basically, anything that fits into chem-bla-ics. (Thanx to Werner, for pointing me to the website!) The ‘source code’ aspect is the interesting thing of this new journal.

Timo Hannay blogged in Nature’s Nascent blog about the Open Text Mining Interface (OTMI), which is “a suggestion from Nature about how we might achieve text-mining and indexing purposes”. The idea is that each article has a link pointing to a machine readable file containing raw data about (and from?) the article.