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* The original TraML vision is unrealistic and outdated.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
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