Friday, July 01, 2011

Running 2.6 GB of ChEMBL data through the CDK Atom typer with CDK-Taverna


CDK-Taverna 2.0 with Taverna 2.0 can in fact do this. Major technological improvement! Also, you get visual feedback on how far it has progressed. It still is rather unpolished, but I am happy to see progress!

Posted via email from Egon's posterous


  1. I'm quite interested in learning to use CDK-Taverna and thought that repeating your ChEMBL data check might be a good place to start.

    However, the experience of actually setting up CDK-taverna is a nightmare. Is there any place where I can give feedback on this?

    Is a 'just about' functional set of instructions which gives the new user no idea why they are doing any of the operations. I'd even be willing to contribute some time to re-vamping this page.

  2. Hi Dave,

    I assume that your problem was that it is unclear from the CDK-Taverna instructions that you are done after step 6 of
    "How to install the CDK-Taverna 2.0 plugin in Taverna".
    There is no need for Joe User to go on with the rest of the page. In so far, I understand you criticism.
    Would you say that even those 6 basic steps are a nightmare? In any case, we'd be happy to work in you suggestions about how to make this page better. What we are going to do in any case is move the rest of the section on this page to separate pages and make clear that the first section is all you need in order to get a working version of CDK-Taverna.
    Cheers, Chris

  3. Hi Dave, I have forwarded your reply to the developers.

  4. @Christoph Hmm, so you are saying that the 4-5 h that I've spent today installing Maven, Tortoise SVN, Eclipse and trying to get Maven to build the CDK-taverna plugins (then puzzling why 88 of the tests failed) was not necessary?

    [cue several deep breaths]

    Everything up to Step 7 (Finally the plugin should be available in the service panel.) in the first section was clear. Though I'd note that saying that a plugin is in a service panel is not as clear as: " Now you are ready to start using the CDK-Taverna plugin, see: {relevant URL} on how to start exploring the functionality."

    The rest of the section probably still needs some work when it is separated off into another page.

    But thanks for the response and thanks Egon for forwarding on my query.