Bioclipse uses a custom target-platform... but since I am using the Eclipse 3.5 from Ubuntu now, extra features I download (GEF, BIRT, EMF, ...) end up in $HOME... so, I need to add a folder to the target-platform.target file... but I cannot find the variable for $HOME/.eclipse/org.eclipse.platform_3_foo_bar/plugins, such the files has things like @{eclipse_home}/plugins too... Right now I have the below, but that clearly is not the solution:

Dear all, while it is still very much in progress, I have made good progress with writing a new BSD-licensed replacement for Sun's DocCheck utility for testing the library's JavaDoc quality. The DocCheck's never really satisfied me, and the most recent version is ancient. Because it is closed source , no one can continue on those efforts. DocCheck is MIA. PMD is given nice, simple overviews instead.

We recently submitted a second paper on Bioclipse, and have worked hard in the past two weeks on addressing the reviewers' questions (and we love these feature requests! See also these two blogs). One reviewer seemed very interested in seeing docking available in Bioclipse.

One thing that has been on my wishlist is to be able to run the unit tests we have for Bioclipse from inside a running Bioclipse instance. That is, we have a Bioclipse Test Suite features on the update site, matching the functional features we have there. Each such test suite would run all JUnit tests we have for that feature.

Dear Planet Eclipse readers, please take notice of my problem with adding an Import-Package to the MANIFEST.MF using the Plug-in Wizard templating mechanism. Any suggestions and pointers very much appreciated! I'd really like to remove step 7 from the following tutorial: Last Friday, the Bioclipse 2.1 development series moved to Eclipse 3.5, so I had to update the Bioclipse SDK too, which we developed earlier.

Quick and short reminder about my Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source and Open Standards talk on Monday.

Last week, there was a very interesting thread on the DBPedia mailing list, on using Java for doing remote SPARQL queries. This was one of the features still missing in bioclipse.rdf. Richard Cyganiak replied pointing the code in Jena which conveniently does this and which bioclipse.rdf is already using anyway.

Today, Jonathan, Carl, Arvid and I made writing managers for Bioclipse a bit easier. Plug-in development Eclipse in itself is already tricky to learn, and the use of Spring by the Bioclipse managers is not helping. And because very soon two new people will be starting with writing a new manager rather soon, we thought it was time to lower the activation barrier a bit.

For the application note which we are about to submit, I was working on improving the PubChem Bioclipse API a bit, resulting in new download methods: The search allows using PubChem Filters which provides many simple means to restrict the search results.

Sometimes you can feel so stupid. For example, when the answer is right on front of you, but only after many hours you realize the right question belonging to that answer. For example, take this answer:add the line: -Dorg.eclipse.swt.browser.XULRunnerPath=/usr/lib/xulrunner This is the problem I was trying to solve: I'm running 64bit Ubuntu Jaunty with Eclipse 3.4.2 for Bioclipse development. The answer above is the correct answer.

The Uppsala and EBI CDK-teams have been working hard on finishing the rewrite of JChemPaint I started with Niels earlier. While the EBI-team focused on the applet (and Swing application), the Uppsala team, obviously, focused on the SWT side, for integration into Bioclipse.