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Hi all

This is a copy of a comment I just posted on the Tracker Item:

We discussed time delays in more detail after the CellML meeting today.
Andrew agrees with me that the specification for this needs to be resolved
before it can be incorporated into PCEnv, since it would be implemented in
the API, which needs to be consistent with the specification. We also agree
that it would be suited to a secondary specification (see CellML 1.2
proposal for secondary specs).

I proposed, however, that we could implement this on a branch, before the
appropriate specification was finalised.

Andrew also pointed out that there are further factors to be catered for:
1) Initial values (i.e. if y is delayed, its values before the initial time
need to be specified, either as an explicit function, or as Andrew said when
we discussed this a few months ago, via FieldML).
2) In general, delays would not fall on time points corresponding to
previous integration steps. Interpolation would be required, and the choice
of interpolant may need to be specified.
3) Lag may vary with time.

I suggested that some sweeping simplifying assumptions could be made, e.g.
delayed variable is assumed to have a constant value for all time points
before the time range of integration; always use linear interpolation; only
allow non-variable lags.

However, we will try and look at some of the models that require delays to
see if these simplifications would be applicable anywhere.


Regards,
Randall

> -----Original Message-----
> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
> bounces at cellml.org] On Behalf Of Catherine Lloyd
> Sent: Wednesday, 13 February 2008 12:08 p.m.
> To: cellml-discussion at cellml.org
> Cc: Rui Zhu
> Subject: [cellml-discussion] Time delays in CellML models
>
> 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 <c.lloyd at auckland.ac.nz>
> >> Date: Sunday, February 10, 2008 11:19 am
> >> Subject: Re: time delay term in CellML model
> >> To: Rui Zhu <rzhu at usc.edu>
> >> Cc: Poul Nielsen <p.nielsen at auckland.ac.nz>, Peter Hunter
> >> <p.hunter at auckland.ac.nz>
> >>
> >>
> >>> 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 which we expect to be a feature in
> future
> >>> releases of the software.
> >>>
> >>> Please let me know if you have any further questions and I will try
> to
> >>> answer them for you.
> >>>
> >>> Best wishes
> >>> Catherine
> >>>
> >>>
> >>>
> >>> Rui Zhu wrote:
> >>>
> >>>> Dear Catherine,
> >>>>
> >>>> This is Rui ZHU, a Biomedical Engineering Ph.D student in
> >>> University of Southern California. I am very interested in using
> >>> CellML to do modeling. Recently, I saw the CellML model you made
> >>> based on the paper "A Delayed Nonlinear PBPK Model for Genistein
> >>> Dosimetry in Rats" on the CellML website.
> >>> http://www.cellml.org/models/zager_schlosser_tran_2007_version03
> >>>> And I tried to use that model to do simulation using PCEnv to re-
> >>>>
> >>> generate the results in the original paper. However, I found the
> >>> result was different from the one the in original paper, and the
> >>> reason it that, in the original paper, there is a time delay term
> in
> >>> the differential equation d( Acon_b )/d(time) = kbile * H_Ccon_l
> >>> * Ccon_l ( t - d(t, C_gen_l) ) * Vl, but in the CellML model the
> >>> differential equation is without the time delay term d( Acon_b
> >>> )/d(time) = kbile * H_Ccon_l * Ccon_l * Vl. I was trying to
> >>> add a time delay term in the CellML model, but I don't know how. If
> >>> you have any idea of how to do it, would you please let me know.
> >>> Thank you!
> >>>> Your kind help is really appreciated! Look forward to your reply!
> >>>>
> >>>> Rui ZHU
> >>>>
> >>>>
> >>>
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion

---

• [cellml-discussion] Time delays in CellML models, Catherine Lloyd, 02/13/2008
  • [cellml-discussion] Time delays in CellML models, Matt, 02/13/2008
  • [cellml-discussion] Time delays in CellML models, Andrew Miller, 02/13/2008
    • [cellml-discussion] Time delays in CellML models, Rui Zhu, 02/13/2008
    • [cellml-discussion] Time delays in CellML models, Michael Hucka, 02/13/2008
    • [cellml-discussion] Time delays in CellML models, Nicolas Le novère, 02/18/2008
  • [cellml-discussion] Time delays in CellML models, Randall Britten, 02/13/2008

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