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Just for the record: currently seating a few meters away from Hans, David
Nickerson and I suggested him a possible solution to his 'problem'.

For those curious/interested, the solution basically consists in using
David's CSim tool (see https://code.google.com/p/cellml-simulator/). Now,
because Hans wants to solve a reaction/diffusion problem, he shouldn't use
the solver used by CSim, which is CVODE (see
http://computation.llnl.gov/casc/sundials/description/description.html#descr_cvode).
CVODE is a probably the best solver for single cell simulations, but it's
not particularly suitable for multicellular modelling (it requires to be
reset after each diffusion step, something that can be quite time consuming).
So, instead of using CVODE, he should use a simpler solver or, rather, a
solver that doesn't need to reset itself after each diffusion step (or
doesn't take long to do so).

Finally, and for convenience, we also suggested to Hans to annotate the
CellML file(s) he wants to use for his work, and this using OpenCOR (see
http://www.opencor.ws/ and
http://www.opencor.ws/user/plugins/editing/CellMLAnnotationView.html). The
idea is to associate a particular ontological term (which one doesn't
actually matter, as long as the annotation is consistent through the CellML
files he wants to be able to use) to the various model parameters is
interested in. This done, and using CSim, he will be able to query model
parameters using their annotation information. The advantage of this approach
is that all his simulation framework needs to know is that the membrane
potential has, for example, been annotated using this or that ontological
term. Without this annotation, his framework would need to know the name of
the model parameter (and possibly the name of the component in which it was
defined), something that may vary from one model to another.

Alan

> -----Original Message-----
> From:
> cellml-discussion-request AT lists.cellml.org
> [mailto:cellml-discussion-
> request AT lists.cellml.org]
> On Behalf Of
> hans.dierckx AT ugent.be
> Sent: 16 April 2014 01:00
> To:
> cellml-discussion AT lists.cellml.org
> Subject: [[cellml-discussion] ] enable c calls to cellML ?
>
> Hi all,
>
> Inspired by Herbert Sauro's suggestion in this week's CellML workshop, I'd
> like
> to ask whether cellML currently has possibilities to make simple c calls.
> If not, can they be included in the near future?
>
> As many researchers in cardiac modeling, I use my own code to solve the
> reaction-diffusion equations. I know there's much advantage in using 'big'
> software packages, but so is there in code which you fully control and
> understand. It would be great for users like me if we could import cellML
> models to use as a black box to give correct/verified reaction kinetics.
>
> In c-language, I would be looking for calls like
>
> #include "cellMLimports.h"
> / / to enable imports
>
> void import_cellMLmodel(char[] modelname); / / specify the model to be
> imported by a string or char array (by some cellML identifier or URL)
>
> void give_reactionterm(double** u, double* Fu); / / **u is a pointer to an
> array of state variables in one point of the domain / / *Fu is an array
> containing the corresponding reaction term in du/dt =
> F(u) to which the result is written
>
> void update_state(double** u, double dt); / / **u is a pointer to an array
> of
> state variables in one point / / dt is a time interval over which
> du/dt=F(u) is
> integrated at a time resolution needed by the model; the resulting state
> vector is returned to u
>
> void stimulate_point(double **u, double I_amp, double dt, double
> voxelvolume); / / to apply a current stimulus (in physical units)
>
> double give_resting_state(int whichvariable); / / to return the resting
> potential and equilibrium values for state variables
>
> I only mention the c-example as it applies to me, but similar arguments
> apply
> also to calls from other languages (fortran, python, matlab, …). A useful
> extension may be to support also parallel calls, e.g. in openMP.
>
> Many thanks in advance to discuss the possibility,
>
>
> Hans Dierckx
>
> (I am a postdoc in Ghent University, Belgium, currently visiting the
> Auckland
> Bioengineering Institute.)

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• [[cellml-discussion] ] enable c calls to cellML ?, hans.dierckx, 04/16/2014
  • RE: [[cellml-discussion] ] enable c calls to cellML ?, Alan Garny, 04/16/2014
    • Re: [[cellml-discussion] ] enable c calls to cellML ?, Jonathan Cooper, 04/16/2014
      • RE: [[cellml-discussion] ] enable c calls to cellML ?, Alan Garny, 04/16/2014

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