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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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