[cellml-discussion] Time delays in CellML models

[Rui Zhu]

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
> >   
> 
> 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: sbml-level-2-version-3-rel-2.pdf
Type: application/pdf
Size: 2439587 bytes
Desc: not available
Url : http://www.cellml.org/pipermail/cellml-discussion/attachments/20080212/b5c6ef07/attachment-0001.pdf