Time evaluation for calculating molecular descriptors using the cdk

To estimate the time needed to calculate molecular descriptors for many molecule (more than 200000) I created a workflow which measured the time needed to calculate each molecular descriptor. This workflow can be found here.

The time needed to calculate different molecular descriptors for 1000 molecules:

Atom typing on natural products with the cdk

During some work on natrual products I analysed a proprietary database with over 180000 molecules with the help of cdk-taverna. The aim of the work will be a diversity analysis of natural products. Therefore I have to calculate some molecular descriptors from the cdk. But before I could calculate the descriptors I have to check whether the cdk could handle these molecules or not. Therefore I develope workflow to test how the cdk performs with natural products, especially how many wrong or missing atom types will be detected within this public database.
Therefore I developed the following workflow:

This workflow can be found here on myExperiment.org

For the proprietary database of natural products which contains over 180000 molecules the cdk had only problems with 1350 molecules. Which is less than 0.8 % of the molecules. These molecules has 1854 wrong or failing atom types.

The large number of wrong nitrogens is mainly caused by five bonded nitrogens for which the cdk currently has no atom type defined.

myexperiment.org plug-in for Taverna

I have just installed the myexperiment.org 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 www.myexperiment.org

www.myexperiment.org 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 myexperiment.org

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

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

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 1.7.1.0 and you can install it from within the Taverna Plug-in Manager. There you have to add the following plug-in site http://cdk-taverna.de/plugin/

The documentation for this release will follow.

CDK-Taverna blog

This blog will provide information about the CDK-Taverna plug-in for Taverna. It will show example, announce new versions and or show other stuff releated to this topc.

CDK-Taverna Version 0.5.0 released

I am happy to announce the release of the CDK-Taverna plug-in version 0.5.0. This is a plug-in for Taverna which is a free open-source workflow enviroment. The CDK-Taverna extension will provide chemoinformatics functionality to this workflow solution.

This release is usable with the Taveran version 1.7.1.0 and you can install it from within the Taverna Plug-in Manager. There you have to add the following plug-in site http://cdk-taverna.de/plugin/

The documentation for this release will follow on the next couple of days here.

I hope you have fun with the new version and I looking forward to your bug reports.