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Saturday, February 21, 2009

Bioclipse2 Scripting #2: searching PubChem

This week I have been porting the PubChem plugin for Bioclipse 1.2 to the new manager-based architecture. While still working on the Wizards, you can run the following JavaScript in Bioclipse2 from SVN and from the next beta (*):

*) There was some confusion on the two beta Bioclipse2 releases so far. Some people expected a release without any bugs left. That release is what we planned to call a Release Candidate. We agree that the first two betas at least turned out to be more alpha than we actually hoped, and we thank everyone who has given these releases a go. Those who tried several development releases of Bioclipse2 saw a lot of ongoing development, and we are fixing any bug reported on these releases. So, do not hesitate in reporting bugs!

Earlier in this series:

6 comments:

  1. So what does it use underneath for the actual communications with PubChem servers? Just curious...

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  2. The Entrez Eutils. I ported the old Bioclipse1 code, which was written prior to the PUG.

    See:
    NewFromPubChemWizard.java

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  3. Hi Egon,
    This is a nice one. I usually have a whole list of names I need to find and wanted to create something like this in taverna but this seems much easier.

    Cheers,

    Peter

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  4. Peter, we can even create a SD file from it right now, and I should make an example script for that too...

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  5. Hi Egon,

    Just wondering where to get the pubchem manager from. It does not seem to be in the latest bioclipse release (2 beta 5)

    Cheers,

    Peter

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  6. We did not set up an update site for beta5... I'm starting to get convinced we should have.

    I also realize that we need good webpages to describe what is found in what feature...

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