Sunday, July 02, 2006

CML In RSS Feeds

As an addition to my 6/30 post, the RSS feeds for usefulchem-molecules and malaria37 contain CML which can be processed by molecular display software such as Jmol and Bioclipse. To load these feeds in Jmol, select "Open URL" from the File menu, and enter the feed address in the input box. Processing with Bioclipse is a little more complicated. First you must create an OPML file (File/New... -> CMLRSS -> New OPML Resource), and edit it to contain the following (if you are processing usefulchem-molecules):

<opml version="1.0">
<head>
<text>Useful Chemistry Molecules</text>
<outline text="Useful Chemistry Molecules">
<outline title="Useful Chemistry Molecules"
xmlurl="RSS feed URL">
description="Useful Chemistry Molecules" />
</outline>
</opml>


RSS feed URL should be set to the address of the usefulchem-molecules feed, in this case
http://showme.physics.drexel.edu/usefulchem/Software/MoleculeBlogInfo/usefulchem-molecules/usefulchem-molecules.rss. You can, of course, simply copy/paste the above code into the working directory (e.g., as C:\bioclipse\workspace\UsefulChem-Molecules.opml) of your Bioclipse installation (remember to enter the feed address!); alternatively, simply download the entire file from here. The Bioclipse Wiki site has a screen shot of this feature of Bioclipse. A Flash screencast of creating an OPML file can be found here, and another on how to use an OPML file to load CML resources from an RSS feed can be found here.

2 Comments:

At 4:02 AM, Blogger Egon Willighagen said...

Hi David,

on the Bioclipse mailing list Rich Apodaca requested today to make the movies more prominently available, e.g. on YouTube:

"I thought I remember reading a few months ago that two movies documenting Bioclipse were made. Unfortunately, as I remember it, the server on which they were hosted was so slow that I gave up trying to download them. So I never saw them.

Assuming these movies have been made and are still available somewhere, how about putting them on YouTube and placing a prominent link on the Bioclipse site - like on the front page?"

(The full email should be in archives).

Any chance on that?

 
At 3:20 PM, Blogger Jean-Claude Bradley said...

The youtube display was not clear enough so I created the Flash versions and replaced the AVIs.

 

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