Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in Jmol

After some difficulties this week with making an export of CDK plugins in the Bioclipse2 Cheminformatics feature of with the cdk-eclipse software, I got the following cute Bioclipse2 script up and running:

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Git-Eclipse integration

Recently, I have been blogging about Git:

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Bugzilla Eclipse IDE integration: Mylyn

A new environment means new tools. Bioclipse is Eclipse RCP-based, so colleagues work with Eclipse and are much more into Eclipse too. For example, into Mylyn. Mylyn is a tool to track tasks and assign context to them. The tasks I am interested in (for this blog item), is fixing bug reports. Mylyn is rather suited for this, as it allows linking Java source files to bug reports. With a growing list of projects in my navigator, browsing them becomes difficult because the list is way too long. Mylyn allows me to only show those source files which are actually related to the bug I am fixing. Cool!

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GitToDo support for Freemind: graphical mapping of important things on my schedule

About a week ago, I hooked up my GitToDo software with Freemind. This allows me to organize the projects I am working on, without having to code this in GitToDo directly. I also immediately take advantage of visualization, for example, adding an icon for projects with one or more TODO items marked TODAY or URGENT:

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Chemical Editing...

As you might have seen, we, Uppala and the EBI, are working on the next generation JChemPaint. JChemPaint is an editor, and therefore, consists of a model (IChemModel), a view (IRenderer) and a controller (IController). See the many posts in Gilleain’s blog.

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Chem-bla-ics turns 3!

Five days ago, my chem-bla-ics blog turned 3. Here’s the first post. It defined:

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Chemoinformatics p0wned by cheminformatics... #2

Some time ago Noel ran a poll on chemoinformatics and cheminformatics, so I set up a poll too in part #1 of this series. The outcome is clear:

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