[Psidev-ms-dev] Fwd: Invitation to review the PSI-document TraML: Transitions Markup Language

[Matthew C. <mat...@gm...>]

Here is Brendan MacLean's review of TraML. It looks like we have some work to do with regard to 
well-defined use cases and richer example documents (I guess that just confirms what we already knew).

-Matt


-------- Original Message --------
Subject: 	Fwd: Invitation to review the PSI-document TraML: Transitions Markup Language
Date: 	Fri, 18 Mar 2011 06:53:30 -0700
From: 	Brendan MacLean <bre...@pr...>
To: 	Matt Chambers <mat...@gm...>



Hi Matt,
Here is my response to the request for review feedback.

Summary:

     * The original TraML vision is unrealistic and outdated.
     * I would be open to working with you and Eric on a TraML standard version that allows a full
       round-trip from a Skyline document to TraML and back.
     * I am also open to Skyline supporting something closer to the existing TraML spec in order to
       enable a compelling use case, though a few issues like requiring a Unimod ID as the only valid
       way to represent a modification might be tricky.

How is it going?

--Brendan

---------- Forwarded message ----------
From: *Brendan MacLean* <bre...@pr... <mailto:bre...@pr...>>
Date: Wed, Aug 25, 2010 at 2:32 AM
Subject: Re: Invitation to review the PSI-document TraML: Transitions Markup Language
To: Christian Stephan <chr...@ru... <mailto:chr...@ru...>>


Hi Christian,
My apologies for running a bit over on the 4 weeks I promised.  My review is attached.  Hope this
helps at least in planning for a TraML 2.0, if you decide to move forward with the current
limitations in a TraML 1.0 specification.

Thanks again for the opportunity.

--Brendan

On Thu, Jul 22, 2010 at 3:08 AM, Christian Stephan <chr...@ru...
<mailto:chr...@ru...>> wrote:

     Dear Brendan MacLean,
     given your expertise in this area, I would appreciate your comments on the
     above mentioned paper work on “TraML: Transitions Markup Language".

     The documents are found here:
     http://www.psidev.info/index.php?q=node/449

     As PSI-Editor I would like to invite you to review this article.

     Please let me know within next 48 hours if you could review the
     article and the attached instance/comments within the next 4 weeks.


     Best regards,


     Christian

     --
     Dr. Christian Stephan
     Head of Bioinformatics
     Medizinisches Proteom-Center
     Zentrum Klinische Forschung (ZKF E.141) Ruhr-Universität-Bochum 44870
     Bochum
     Phone: +49 234 32 29 288
     Fax:   +49 234 32 14 554
     http://www.medizinisches-proteom-center.de