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- From: r.britten at auckland.ac.nz (Randall Britten)
- Subject: [cellml-dev] Pluggable solver for CellML
- Date: Wed, 16 Apr 2008 07:56:32 +1200
Another option is to use COR, which can generate Java code for the model.
There is a good possibility that PCEnv will have this feature too, in the
near future.
> -----Original Message-----
> From: cellml-tools-developers-bounces at cellml.org [mailto:cellml-tools-
> developers-bounces at cellml.org] On Behalf Of Andrew
> Sent: Tuesday, 15 April 2008 11:26 p.m.
> To: Michael Cooling
> Cc: cellml-tools-developers at cellml.org
> Subject: Re: [cellml-dev] Pluggable solver for CellML
>
> Michael Cooling wrote:
> > Hi
> >
> > Some collaborators in Newcastle want to run integrators over CellML
> > model programmatically. What hooks do PCEnv or COR have to do this?
> Do
> > they have a Java-accessible bridge/api or similar to enable
> > integration of the solvers with other code?
> Hi Mike,
>
> There is no need to do this through a front end, this is the purpose of
> the CellML API (which is what PCEnv uses to perform the integration).
> The CellML API provides a service called the CIS (CellML Integration
> Service) which is used for integration.
>
> We do have plans to eventually develop a Java bridge, but this is
> something that has been pushed to a lower priority several times so has
> never actually been implemented.
>
> >
> > As competition, these people are also assessing SBML workbench which
> > apparently allows you to do this. I think if they can't easily run
> the
> > CellML model they may shift to SBML soon which would be a shame.
>
> I don't think we should regard SBML as 'competition', SBML and CellML
> solve different problems because CellML is a more general format for
> representing mathematical models, while SBML tackles the problem of
> representing systems of reactions. That said, since CellML is more
> general, we want it to be able to represent any mathematical system
> that
> SBML can represent.
>
> However, it would seem that for the general problem of integrating
> models, CellML would normally be the best choice of format, and I
> believe that, at least in terms of integrator performance, the CellML
> tools are the most developed.
>
> One option in the interim until we have a full Java bridge would be the
> use test program built from the API which allows simulations to be run
> from the command line, and outputs CSV results to standard output.
>
> Best regards,
> Andrew
>
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- [cellml-dev] Pluggable solver for CellML, Andrew, 04/15/2008
- [cellml-dev] Pluggable solver for CellML, Randall Britten, 04/16/2008
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