Dear All
The issue of how a CellML model should handle time delays has been
discussed previously by the Auckland CellML group, and at the time there
was a tracker item filed on this subject:
https://tracker.physiomeproject.org/show_bug.cgi?id=70
The topic has been recently raised again (see the email discussion
below), and it was discussed at today's CellML meeting (13th Feb, 2008).
We'd like to open up this discussion to the CellML community to see if
anyone has any thoughts, ideas, or preferences as to how time delays
should be a) expressed in a CellML model and b) handled by the software
tools.
Thank you in advance for your feedback.
Best wishes
Catherine
Hi Rui,
If you are already familiar with Virtual Cell, I'd stick to that. The
initial version of SBML was largely based on the internal VCML used by
the Virtual Cell, and I suspect the VCell developers remain involved
in recent developments within the SBML community.
In the past, VCell was capable of importing CellML models but I seem
to recall that there might be issues with that in recent versions. If
it is still possible, you should be able to import the CellML version
of the model and then touch it up from there (add in the time delay).
You should then be able to export the SBML version for use in other
tools if required.
CellML2SBML is a collection of XSL stylesheets which are capable of
processing most models from the repository. As Catherine mentioned,
you'll lose the metadata from the CellML model in the resulting SBML
model, but the math should largely be intact. From my understanding,
the CellML2SBML stylesheets are mainly targeted at CellML models which
use the now deprecated reaction element, so if the model you are
interested in uses reactions then you'll get the best SBML version.
Otherwise I suspect you'll end up with a generic SBML encoding of the
mathematics.
Oh, and I'm pretty sure VCell will allow you to specify time delays
although I can't remember the specific syntax or interface options and
you can see https://tracker.physiomeproject.org/show_bug.cgi?id=70 for
a bit of discussion on this issue within CellML - feel free to add to
that discussion!
Not sure if I can offer much more help than that but let me know if
you have any more questions...
David.
Catherine Lloyd wrote:
Dear Rui
You are welcome!
Hmmm, much as I would hate to lose a potential CellML user to SBML, I
can see the advantage for you if indeed, SBML can handle time delays.
Although I'm not familiar with the structure of SBML, my understanding
is that the cellml2sbml converter is not perfect - if nothing else, it
strips all the metadata out of a CellML model. But you might be able to
use it as a foundation which you can then edit by hand.
I have cc'd David Nickerson in on this email - if anyone deserves the
title of CellML expert it is David!... David do you have any idea
which SBML tool might be best to use in this case?
I've also cc'd Poul Nielsen and Peter Hunter who lead the CellML
project. I'm sure they will be interested in this case and they may
have an idea how long it might take to develop the CellML tools such
that they are capable of handling time delays.
I'm sorry I can't help you more myself, but I imagine we can work
together to get this up and running for you.
Best wishes
Catherine
Rui Zhu wrote:
Dear Catherine,
Thank you so much for your reply! It is very helpful! Learning CellML
modeling from an expert is a really delightful experience.
I am having another thought. I searched online, and it says SBML
level2 can deal with the time delay term, and there is a software
(cellml2sbml) to convert CellML to SBML. Do you think it is a good
idea to use SBML to solve the problem? And from SBML website, there
are a lot of tools that can run SBML model, like virtual cell. I am
wondering if you have any idea which tool can handle the time delay
term. Thanks!
Your suggestion will be appreaciated!
Many thanks,
Rui ZHU
- Original Message -
From: Catherine Lloyd [EMAIL PROTECTED]
Date: Sunday, February 10, 2008 11:19 am
Subject: Re: time delay term in CellML model
To: Rui Zhu [EMAIL PROTECTED]
Cc: Poul Nielsen [EMAIL PROTECTED], Peter Hunter
[EMAIL PROTECTED]
Dear Rui
Thank you for your interest in CellML. I am familiar with the model
you
are interested in, and I know the original model author (Michael
Zagar)helped me to translate this model into CellML. I'm sorry if our
curation status confused you - it does indeed state that the CellML
model recreates the results of the published model - but it should
statethat the models almost match - with the exception of the time
delay(I'll change the text now).
Unfortunately this is a current limitation of CellML. While it is
possible to express a time delay in the CellML language, the tools
whichrun CellML models (PCEnv and COR) are unable to handle time
delays at
present. This is something
