[Pipet Devel] XML and Pise

[J.W. Bizzaro]

Raynald wrote:
> However, it seems that the Piper XML is not yet completely defined.

Here are some of the DTD's made by Brad:

https://alpha.bioinformatics.org/cgi-bin/cvsweb.cgi/piper/dtd/

It is a work-in-progress, since Piper is so complex and we are just now
trying to glue some very big pieces together.

> In two words, this is an interface builder. It makes HTML pages and CGI
> scripts for unix programmes related with Biology. My point is it uses XML
to
> describe the program to be interfaced. This program is under GPL and well
> documented. I think it would be great if Piper and Pise could share the
same
> DTD...
>
> Pise DTD
> http://www-alt.pasteur.fr/~letondal/XML/pise.dtd

It would be great, but I think Piper's DTD for wrapping command-line
programs will be rather unique, based on the connection of Overflow nodes.

Also, Piper is meant to be general-purpose, not biology-related (/Loci/ was
originally supposed to be biology-related).  I see some Pise tags like
"Sequence", which we wouldn't want to use.

I think Pise's DTD will be helpful to study, but without a lot of
modification (which you said is not acceptable), we couldn't make direct use
of it.

I'd like to hear Brad's and Jean-Marc's opinions as well.

It's good hearing from you again, Raynald :-)

Cheers.
Jeff