I decided to concentrate my blogs and have categories for specialist blogs like this one. You can continue about my

 chemical RCP adventure

here.

This blog is continued elsewhere

Dear Eclipse Community,    I know there is a tremendous amount of information online, and StackOverflow full of Eclipse-RCP questions already. But the downside of that is that there is a lot of noise. Would it be an idea to set up a StackExchange dedicated to development of Eclipse RCP-based applications? If you like the idea, please contribute to the Definition process.

A StackExchange about developing Eclipse RCP applications?

Triggered by posts in the past three days, I though about writing up a short tutorial on how to perform code review for existing code on GitHub. Therefore, this applied to CDK and Bioclipse source code, many but will work for any project hosted in GitHub. Even if it is not, you could consider putting up a copy there yourself.

How to use GitHub for [CDK|Bioclipse] code review

As you know from my blog, one of the things I am working on is to push RDF functionality in Bioclipse, as I believe it to be the missing link between molecular chemometrics and literature, databases, and other non-numerical information sources.

RDF-powered QSAR wizard: SPARQL end points providing wizard content

I just added an entry to the Google Summer of Code 2010 Ideas wiki page:

 Resource Description Framework (RDF) is ~10 year old W3C standard. Uptake is taking off now, and it would be nice to see a Eclipse project like the Web Tools Package to provide basic RDF related functionality.

A GSoC project idea around the Resource Description Framework

When Bioclipse reads filed its workspace, it used

 IFile.getContentDescription()

in version 2.0 and 2.2. However, I now note that unit tests that use this method fail where they used to work in earlier versions.

IFile.getContentDescription() returns null on files from the workbench. Advice?

Jonathan worked this week on new features for the Bioclipse RDF editor (see these two earlier items). This version still does not edit, but only display using Zest. Jonathan created for me an extension point so that anyone can make the editor aware of domain objects, by simply registering the extension implementation along with the

 rdf:Class

URI of the

 rdf:type

of an object.

RDF, Jena, Bioclipse, Eclipse, Zest #2: icons and an extension point

Quite a while a go, I blogged about Zest in Bioclipse showing a bit of ONS Solubility data. I could not follow up on that until now, as I had yet to do a lot of RDF work in Bioclipse, so the screenshot back then was kind of a mockup.

RDF, Jena, Bioclipse, Eclipse, Zest: Mashups

Ola is releasing Bioclipse 2.2.0 today, and asked me to show case the semantic web functionality in Bioclipse. I realized that I do not have a nice page showing the semantic web overview.

Semantic Web features in Bioclipse 2.2

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

Reminder: my talk in Frankfurt on Monday; Want to meet up?

Bioclipse 2.0 introduced a new, powerful molecular table support, and we have been eager to test that on large SD files. A recent ChEBI SD file failed to open, and eyes were immediately at the CDK, which is the cheminformatics library used in Bioclipse. After careful investigations, it turned out that the ChEBI file contained a few entries which were not MDL molfiles, but queries for the ISISBase system.

Validating MDL SD files and Symyx molfiles with the CDK

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:

Target Platform to have $HOME/.eclipse/$ECLIPSE/plugins ??

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.

Call for Collaboration: JavaDoc validation with OpenJavaDocCheck

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.

New Bioclipse Features: Kabsch Alignment, RMSD Distance and Tanimoto Simarlity Matrices

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.

Extension point for running JUnit tests in a RCP Application instance?

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.

New Plug-in Wizard template: Can I add Import-Package programmatically?

And I just got around to grasping some more of the details of handling dependencies with plugins. Bioclipse has a product file, which uses features to run it. That works fine. It also uses Spring (version 1.0.2 in our case) in a set up where we use custom managers to do stuff, like run things from a JavaScript environment (e.g. this), but use the same methods to be run from Bioclipse GUI elements, like buttons, menus and wizards.

Eclipse-Spring Export problem: uses conflict for spring aop

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.

Bioclipse and SPARQL end points

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.

Making Bioclipse Development easier: the New Manager Wizard

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.

Searching PubChem from within Bioclipse

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.

Running Bioclipse Plugin Unit tests: solving the XPCOM error

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.

Chemistry in Eclipse: Bioclipse-JChemPaint

Dear lazyweb! I have been trying to figure out which Eclipse 3.4 feature I must install from the update site to get the org.eclipse.zest plugin in my environment. I installed the Zest feature (which I am going to use to visualize an RDF network), but my workspace still complained that I did not have the plugin.

Which feature must I install for org.eclipse.zest?

Yes, yet another blog by me. This one is special, being the first where I just copy/paste blog items from other blog I do. Just, so that people only interested in RCP related stuff, can tune in here. If only I knew how to do categories on blogger.com.

A RCP dedicated blog

In preparation of the CDK workshop next week, here is a small Bioclipse2 script to calculate the XLogP value for a given SMILES, using the a CDK-based XMPP service:   Earlier in this series:Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in JmolBioclipse2 Scripting #2: searching PubChem

Bioclipse2 Scripting #3: XLogP calculatation using a XMPP CDK cloud service

Bioclipse is an environment for handling and processing life sciences data. This data is present in files with a wide variety of formats, each of which can contain a particular data type. For example, a we can have a single molecule in MDL molfile and in CML.

Multiple inheritence for content types?

While Bioclipse is much more, it could be an interesting alternative to the Jmol application.

Bioclipse: a powerful Jmol application

I ran into an Eclipse Grep Console plugin (EPL license) today that takes regular expression to color output in the Console.

Highlighting Console output in Eclipse with Grep Console

RDF is swiftly becoming the lingua franca of life sciences (see for example [1,2]). Bioclipse is an excellent platform to visualize results from analysis of the network, both for graph visualization (see [3]), as well of visualization of domain specific data types (e.g. sequences, molecules, ...).  Yesterday I uploaded a Bioclipse feature that adds a rdf manager to handle RDF content, which includes SPARQL support.

Solubility Data in Bioclipse #2: handling RDF

As you might have read, Bioclipse has scripting support (see for example, Scripting JChemPaint), and that we have been collection them on Gist and indexing them on Delicious with the tags bioclipse and gist. This provides a nice overview of what you can do with the current SVN version of Bioclipse2. And, hopefully, when released, allow users to quickly learn about Bioclipse features, allow people to share scripts etc.

Bioclipse and Gist integration

One advantage of using XML is that one can rely on good support in libraries for functionality. When parsing XML, one does not have to take care of the syntax, and focus on the data and its semantics. This comes at the expense of verbosity, though, but having the ability to express semantics explicitly is a huge benefit for flexibility.

Editing and Validation of CML documents in Bioclipse

Stefan, Gilleain, Arvid and I had a JChemPaint Developers Workshop in Uppsala, to sprint the development of JChemPaint3, for which Niels layed out the foundation already a long time ago. Gilleain and Arvid merged their branches into a single code base, while Stefan worked on the Swing application and applet. The Bioclipse SWT-based widget is being developed for Bioclipse2.

A Chemical RCP Adventure

Scripting JChemPaint

A RCP dedicated blog