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My guess is to keep it simple:

1) don't prescribe how simulation software is to calculate this -
i.e. don't prescribe a particular mathematical formulation for
representing time delays
2) calculate the variable(s) representing the output of delayed
function separately - e.g. in a separate component or math element -
i.e. don't promote variables to being able to be functions also

I think it is necessarily going to require:

1) math elements that point to user defined code
e.g. in the simplest case the code will buffer of a particular
variable and perhaps create a local approximation curve around the
time required and return a result.

2) referencing math elements from other components
e.g. to calculate f(y-T) you need to at least have a reference to the
math of y in the case that someone has an analytical method to apply
instead of some algorithm over a history of values



On 13/02/2008, at 12:08 PM, Catherine Lloyd wrote:

> 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
>>>>>
>>>>>
>>>>
>
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> cellml-discussion mailing list
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---

• [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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