plug-in for Taverna

August 29, 2008

I have just installed the plug-in for Taverna and I am really excited about its possibility.
You can view, search, download and run all the workflows which are published within myexperiment. That’s really cool.
Here a screenshot:

CDK-Taverna at

August 29, 2008 is an open platform which allows users to share their workflows.
Today I started to upload workflows to that platform.
In the next couple of weeks I will upload many more. So if you need examples check out the cdk-taverna group at

The first workflow I have uploaded loads molecules using an iterative file reader from a MDL SD-file. Each molecule gets stored within a Postgres SQL database which uses the Pgchem::Tigress extension.

Here is an screenshot of the first workflow:

CDK-Taverna mentioned within an publication

August 28, 2008

Egon found a publication some time ago which mentioned the CDK-Taverna plug-in.

see Egon’s post: here

This is the paper:
Peter Li, Tom Oinn, Stian Soiland, Douglas B. Kell, Automated manipulation of systems biology models using libSBML within Taverna workflows, Bioinformatics 2008 24(2):287-289, doi: 10.1093/bioinformatics/btm578

CDK-Taverna Version 0.5.1 released

August 28, 2008

I am happy to announce the release of CDK-Taverna version 0.5.1. This is more or less a bug fix release but it includes also some new worker.

The mayor work on the last couple of weeks was related to the ART2A algorithm. There I removed some bugs and added some worker which allows a better analysis of the results.

There are also two new worker which uses the Weka library. They allow a simple KMeans and an EM clustering. The “old” other Weka worker will be removed or replaced for the next release because they are no longer maintainable.

JChempaint was also removed for this release. That’s because the current cdk version from trunk does not support JCP anymore. (It will be rewritten.)

This release is usable with the Taveran version and you can install it from within the Taverna Plug-in Manager. There you have to add the following plug-in site

The documentation for this release will follow.