Dear Chaitanya Thank you for your email. It depends on what you mean by multiscale models. CellML can currently represent lumped parameter models (i.e. algebraic and ordinary differential equations). Such models can represent multiscale processes so long as the equations do not include partial differentials. The import mechanism of CellML 1.1 is useful to gather lower-level models in to a new larger scale model. Some examples of this feature are available on the CellML website at <http://www.cellml.org/tutorial/cellml_1.1>. More generally, multiscale processes are often represented by distributed parameter models (i.e. ones that include partial differential equations). Such models are currently beyond the scope of CellML as they require some notion of continuously varying quantities such as scalar, vector, or tensor fields. Work is currently underway to define a flexible field specification format <http://www.physiome.org.nz/xml_languages/ fieldml> but there is still much work to be done on this project. However, there are examples of coupling CellML models into distributed parameter models using CMISS <http://www.cmiss.org/>, an open source research tool for solving finite element and boundary element problems.
In your case it appears that you may be able to describe your problem as a series of interacting cells, where each cell is a lumped parameter model of biochemical networks. Such networks of cells, where interactions are described by direct connections rather than via fields, can also be described as a large scale lumped parameter model. If the cell models are identical (or have a good deal of similarity) they may be best represented by a single model (or a small number of similar models) which can then be imported multiple times into a large scale model that represents the collection of interacting cells. Let me know if you would like some help with this. Best wishes Poul On 2007 Nov 10, at 00:51, Chaitanya Athale wrote: > Hi all, > > I am a complete newbie to CellML and have occasionally used SBML > for biochemical models. Can somebody please point me to documents > (if they exist) on the possibility of using CellML to represent > multi-scale models? Is there any example around? > > I want to try and use this, if it does work on a model we had > worked on earlier which has cells with interactions modelled with > some individual rules. The cells themselves are governed by > biochemical networks that provide "state-inputs" to the cell for > determining its behaviour (J Theor Biol. 2005 Apr 21;233(4):469-81.). > > Cheers, > Chaitanya Athale. > > > > [EMAIL PROTECTED] wrote: >> >> Send cellml-discussion mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> or, via email, send a message with subject or body 'help' to >> [EMAIL PROTECTED] >> >> You can reach the person managing the list at >> [EMAIL PROTECTED] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of cellml-discussion digest..." >> >> >> Today's Topics: >> >> 1. cellml in synthetic biology (James Lawson) >> >> >> --------------------------------------------------------------------- >> - >> >> Message: 1 >> Date: Mon, 29 Oct 2007 17:18:31 +1300 >> From: James Lawson <[EMAIL PROTECTED]> >> Subject: [cellml-discussion] cellml in synthetic biology >> To: CellML Discussion List <[email protected]> >> Message-ID: <[EMAIL PROTECTED]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Here's a really interesting project (IMO) that seems to be pretty >> keen >> on using Cellml. >> >> http://openwetware.org/wiki/ >> Talk:Registry_of_Standard_Biological_Models >> http://openwetware.org/wiki/Registry_of_Standard_Biological_Models/ >> Registry_organization >> >> Openwetware is a big MIT based initiative to create a forum for and >> standardise synthetic biology. >> >> Seems to me they need some info on CellML... and some support. The >> first >> link talks about SBML (Mike Hucka is quoted,) but also mentions that >> multiscale modelling will be essential, which isn't something that >> SBML >> could call its forte. We, however, can. >> >> So don't mind if I do... ;) >> >> James >> >> >> >> ------------------------------ >> >> _______________________________________________ >> cellml-discussion mailing list >> [email protected] >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> >> >> End of cellml-discussion Digest, Vol 39, Issue 12 >> ************************************************* >> >> >> > > > -- > Chaitanya Athale, > Postdoc, > Karsenti Lab, > Cell Biology and Biophysics, > EMBL Heidelberg. > http://www.embl.de/~athale > _______________________________________________ > 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
