[gmx-developers] Re: markup for macromolecules in biology

Erik Lindahl lindahl at csb.stanford.edu
Wed Oct 15 10:35:36 CEST 2003

Hi Marc,

This is very useful feedback - one of the main reasons why we hesitate 
about XML for "everything" was that we expected users to choke on it, 
but your points make sense :-)



On Tuesday, October 14, 2003, at 11:36 PM, Marc Baaden wrote:

> Hi,
> just a quick comment,
>>>> Michael Banck said:
>>> IMHO XML is not really useful as an input file format, at least not 
>>> in
>>> general (there might be nice XML editors and emacs-modes, but that 
>>> would
>>> cut off general easy editing). It's really good for data files 
>>> though.
> I don't totally agree. I can see that it is more tedious to edit an 
> XML input
> file (except eg with emacs :))) ), but there is one big advantage: due 
> to the
> strict XML structure you have a very good chance that this input file 
> can still
> be read by a future program version (eg in 10 years or so). This is 
> often quite
> important in the context of a lab where people change frequently and 
> you might
> want/need to work with their data a couple of years after they have 
> left.
> Furthermore, once you have a "standard" input file, you will only need 
> to
> change small bits of it from time to time. You usually don't have to 
> re-create
> it from scratch every day. So if Gromacs already came with a simple 
> useful
> example, people could restrain to modify that, which even or should I 
> say
> in pareticular in XML is an easy task.
> Also, XML provides tools to check your document for validity. So you 
> can
> eliminate a large number of input file format/syntax problems before 
> even
> starting up Gromacs.
> And then also XML is - because of its verbosity - very human readable.
> As an example: for entries like T-coupling or P-coupling where there
> can be several groups, it is not obvious in an mdp file how you need
> to format/seperate them (except by reading the doc or having an 
> example).
> XML would make that clear from its very structure (DTD) which good 
> editors
> (yes they exist !) do parse and can even suggest you which tags you are
> allowed at a given position in the file.
> Hope that makes my point.
> Cheers,
> Marc
> -- 
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
>  FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217
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