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-------- Original Message --------
Subject: Re: batch processing
Date: Sat, 20 Jul 2013 12:08:54 +1200
From: Andrew Miller
<ak.miller AT auckland.ac.nz>
To: Maxwell Neal
<mneal AT u.washington.edu>
CC: Alan Garny
<alan.garny AT inria.fr>,
Michael Cooling
<m.cooling AT auckland.ac.nz>,
David Nickerson
<d.nickerson AT auckland.ac.nz>

On 20/07/13 05:24, Maxwell Neal wrote:
> Hi all,
>
> I'm setting up a java program to test CellML-SemSim round trips
> over all the CellML models in the repository. Tommy sent me a txt
> file with URLs to all the models and I've been able to download
> them all into a local folder. I've got the CellML API incorporated
> into my program and I'm able to programmatically read the local
> CellML models and output things like the names of components,
> variables, etc.
>
> What I'm wondering is - how do I simulate the models using the
> CellML API and record the numerical output?
>
> Alan you had mentioned there is a "RunCellML" test program in the
> API but I haven't been able to find it in the cellml.jar classes.
> Any help would be appreciated!

Hi Maxwell,

The RunCellML program is a test program used for testing the API,
written in C++, not an API. Because the C++ bindings map closely to
the Java bindings (the Java bindings are automatically generated to
ensure this remains true) once you know how things map to Java, you
can easily translate any CellML API based program from C++ to Java.

The service in the CellML API you want to use is called the CellML
Integration Service (CIS); the documentation (which is language
independent) is here:
http://cellml-api.sourceforge.net/1.13/interfacecellml__services_1_1_cell_m_l_integration_service.html

// You probably already call this somewhere...
System.loadLibrary("java_cellml");
// You will want this to enable the CIS from Java...
System.loadLibrary("java_cis");
// Most users of the CIS also use the CCGS...
System.loadLibrary("java_ccgs");

// You already probably get the CellML Bootstrap like this:
CellMLBootstrap cb =
cellml_bootstrap.CellMLBootstrap.createCellMLBootstrap();
// Similarly you want to bootstrap the CIS so you can run integrations:
CellMLIntegrationService cis =
cellml_bootstrap.CellMLIntegrationService.createCellMLIntegrationService();
// Now read the documentation for CellMLIntegrationService to decide
what you want to do, e.g.:
ODESolverCompiledModel cmod = cis.compileModelODE(someModel);
ODESolverRun run = cis.createODEIntegrationRun(cmod);
run.setStepType(ODEIntegrationStepType.ADAMS_MOULTON_1_12);
run.setResultRange(0.0, 10.0, 1000.0);
run.setStepSizeControl(1E-6, 1E-6, 1.0, 1.0, 1.0);
run.setProgressObserver(yourProgressObserverCallbackObject);
run.start();

BTW do you mind if I forward your question (with my answer) to the
cellml-tools-developers AT lists.cellml.org
mailing list so we have a
public archive of the question and answer? That is the best place for
questions like this.
https://lists.cellml.org/sympa/info/cellml-tools-developers

Best wishes,
Andrew

>
> Many thanks!
>
> M
>
>
> --------------------------------- Maxwell Neal
>
> Post-doctoral researcher Department of Bioengineering University
> of Washington
> mneal AT uw.edu
>
> <mailto:mneal AT uw.edu>
>
> ---------------------------------
>
>
>
>
>
>
>
>
> On Jun 7, 2013, at 1:12 AM, Alan Garny wrote:
>
>> Hi Max,
>>
>> At this point in time, you might want to use the ‘RunCellML’ test
>> program. It is part of the CellML API (you might have to build
>> it). Alternatively, you could use one of David Nickerson’s tools:
>> http://code.google.com/p/cellml-simulator/ (this being said, I am
>> not sure it can directly be used with CellML; it might need a
>> SED-ML file as an input).
>>
>> Alan
>>
>> *From:* Maxwell Neal
>> [mailto:mneal AT u.washington.edu]
>> *Sent:* 07
>> June 2013 04:50 *To:* Alan Garny *Subject:* batch processing
>>
>> Hi Alan,
>>
>> I'd like to be able to perform automated tests on multiple
>> SemGen-exported CellML models and validate their numerical
>> results against those of the original models. So far I've been
>> doing this manually using OpenCell but I was wondering - is
>> there a tool for batch processing a set of CellML models and
>> retrieving their numerical output programmatically?
>>
>> Thanks!
>>
>> M
>>
>>
>> --------------------------------- Maxwell Neal
>>
>> Post-doctoral researcher Department of Bioengineering University
>> of Washington
>> mneal AT uw.edu
>>
>> <mailto:mneal AT uw.edu>
>>
>> ---------------------------------
>>
>>
>>
>>
>>
>>
>>
>>
>

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• [[cellml-dev] ] Fwd: Re: batch processing, Andrew Miller, 07/20/2013

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