Chronological Thread 

< Chronological >      < Thread >

---

>> 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
>

---

• [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

---

Archive powered by MHonArc 2.6.18.