[gmx-developers] XML

Erik Lindahl lindahl at csb.stanford.edu
Wed Oct 15 18:17:02 CEST 2003

Hi Michael,

That's great news - give them my and/or David's email and we'll do 
something about it.

The nice thing with XML is that it isn't critical to use exactly the 
same format (it would be convenient, but I can imagine all parts would 
diverge pretty soon :-), since you can write XSLT stylesheets for very 
fast transforms between them.

> There are standard formats for binary data as well - NetCDF seems to 
> be the
> format of choice - one can imagine that an output file would be some 
> mix of
> XML and binary data.
> One possiblity for input files, of course, is that either people could 
> write
> them by hand, or there could be a simple interpreting program -- 
> either a gui
> or a parser, that could hand-hold those that didn't want to / feel 
> comfortable
> writing the XML.  There are a wide variety of XML parsers already 
> available
> for various code bases.

That's trivial - since we use C we can simply call the free libxml2 
directly - we're already using it :-)

> Anyway, a working group will be forming to address the issue of 
> standards for
> macromolecular modeling, so let me know if you're interested, and I 
> can pass
> your information along to the organizers.

Is Michael at Scripps? Perhaps we should go down and have a meeting 
with David & Charlie about it...



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