Bling! Bling!. Mark Wielaard announced the GNU Classpath 0.92 release, with the following changes: an alternative awt peer implementation based on Escher that uses the X protocol directly. Various ImageIO providers for png, gif and bmp images. Support for reading and writing midi files and reading .au and .wav files have been added. Various tools and support classes have been added for jar, native2ascii, serialver, keytool, jarsigner.
Mix one of the oldest and one of the latest computer technologies, and you get FoX (BSD license), a Fortran library for reading and writing Chemical Markup Language, and thus XML.
Something I have not completely comfortable with about the CDK in the past, is the way Atom’s are constructed: IAtom carbon = new Atom("C"); Not that it is horrible code, but the CDK has an Element too. Why not reuse that?
Technorati is nice in several ways, one being the feature to set up a watchlist. I have set watches on chemoinformatics, Jmol, Bioclipse and a few more. This allows me see the latest blog items on these topics. Often, the point to Asian blogs, mostly Chinese and Japanese, which I mostly find hard to read.
Recently, a second beta of Java 6 was released, which triggered a patch for the Debian java-package package. It was a Bioclipse bug report today, however, which made me patch my java-package setup and install the beta. So, next thing was to try to get the CDK compile with the Java 6 beta.
The Eclipse Rich Client Platform (RCP) is very powerfull, and takes a lot of architectural things of your hand when developing a bio- and chemoinformatics GUIs. Bioclipse is based on it. One thing the RCP offers is a Help View which works with plain (X)HTML files, and one neat feature is the context help. It is help shown in the Help View when one focused on a specific GUI element.
With chemometrics in mind (QSAR, data mining, …), I have started working on matrix support in Bioclipse, because the matrix is the important step between (bio-)molecular content and statistical analysis. I implemented this such that the actual matrix implementation can be freely chosen, that is, bc_statistical provides a IMatrixImplementation extension point.
David Strumfels posted news about the Useful Chemistry CMLRSS feed . He explains how this feed can be accessed using Jmol and Bioclipse. The latter are accompanied by two AVI movies: one about creating a new OPML file, and one about accessing the CMLRSS file from the OPML.
I started a spin-off blog earlier this week: kemistry desktop environment. It will deal with integration of chemistry on opensource desktops, with KDE as one of them. Today, it features an overview of earlier blogs on the subject in this new blog.
In reply to interesting comments to my previous blog on Strigi and xAttr support in KDE4, I would like to suggest the following mockups, which I would find very useful. The deal with the ability to store keywords, for example, not but necessarily using xAttr. I have no idea on how to implement these mockups, so any help or pointers are appreciated.