[Accessibility-handlers] SBML and CML

Neil Soiffer Neils at dessci.com
Mon Jan 19 11:45:21 PST 2009


Systems Biology Markup Language (SBML) <http://sbml.org/> is a mixed bag as
an example for a handler.  On the one hand, it appears to be very rich and
capable of describing models that are way too complex to be desribed via a
program.  On the other, sometimes it describe chemical reactions or process
that have relatively succinct notational descriptions that could be coverted
to words.  Eg, see
 http://sbml.org/Image:Sbml-simple-reaction-example.jpg

I don't know enough about biology or SBML to say whether this is normal or
an exceptional case.  There seem to be quite a number of piecies of software
that make use of it.



Chemical Markup Language <http://cml.sourceforge.net/main.html> (CML) looks
very promising as an example handler.  There is at least one applet viewer
for web pages (which has no keyboard navigation I could find.  It is called
JChemPaint and here's a page on embedding it in a web page (mostly just how
to embed an applet):
http://apps.sourceforge.net/mediawiki/cdk/index.php?title=JChemPaint_Inside_Webpages

Here's a demo page which kind of shows the navigation/interaction
possibilities (but isn't accessible as far as I can tell).
http://cdk.sourceforge.net/jcpapplet/ViewerApplet.html
Also, I think that JCehmPaint can read several formats besides CML, and in
the above example, it appears to be reading a .mol file which is not part of
CML AFAIK.

    Neil
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