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[cellml-discussion] Time delays in CellML models


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  • From: rzhu at usc.edu (Rui Zhu)
  • Subject: [cellml-discussion] Time delays in CellML models
  • Date: Tue, 12 Feb 2008 21:11:40 -0800
Hi Andrew,

I attached here the specification of SBML level2, which I downloaded from
this web page http://sourceforge.net/project/showfiles.php?group_id=71971

In section 7.9, it gives an example of a simple model involving a delay
function. Hope this helps!

BTW, can we use something similar in CellML to express a delay functon?

Thanks,

Rui ZHU


----- Original Message -----
From: Andrew Miller <ak.miller at auckland.ac.nz>
Date: Tuesday, February 12, 2008 7:12 pm
Subject: Re: [cellml-discussion] Time delays in CellML models
To: CellML Discussion List <cellml-discussion at cellml.org>, rzhu at usc.edu

>
> >> 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,
> Hi Rui,
>
> I have been looking into ways in which time delays could be
> represented
> in CellML, and supported by CellML tools. I have been unable to
> find any
> way of using delayed variables in SBML (although I am aware that
> SBML
> Level 2 does define support for events which happen with a time
> delay, a
> rather different concept). I suspect that you may have come across
> some
> extension to SBML, which I would be interested in taking a look at.
> Would it be possible for you to point me to the information you
> found
> which describes how to use delayed variables in SBML?
>
> Best regards,
> Andrew
>
> >>> 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
> >
>
>
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