>> 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 <[EMAIL PROTECTED]> >>> Date: Sunday, February 10, 2008 11:19 am >>> Subject: Re: time delay term in CellML model >>> To: Rui Zhu <[EMAIL PROTECTED]> >>> Cc: Poul Nielsen <[EMAIL PROTECTED]>, Peter Hunter >>> <[EMAIL PROTECTED]> >>> >>> >>> >>>> 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 > [email protected] > http://www.cellml.org/mailman/listinfo/cellml-discussion > _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
