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Hi Andrew,

I've been able to load in the CIS library and integrate my models, so thanks
for the help there.

What I'm wondering now is - how do I capture the output from these model runs?

Many thanks!

M

---------------------------------
Maxwell Neal

Post-doctoral researcher
Department of Bioengineering
University of Washington
mneal AT uw.edu
---------------------------------








On Jul 20, 2013, at 5:00 PM,
cellml-tools-developers-request AT lists.cellml.org
wrote:

> cellml-tools-developers Digest Sun, 21 Jul 2013
>
> Table of contents:
>
> 1. [[cellml-dev] ] Fwd: Re: batch processing - Andrew Miller
>
> <ak.miller AT auckland.ac.nz>
>
>
> ----------------------------------------------------------------------
>
> Date: Sat, 20 Jul 2013 14:18:59 +1200
> From: Andrew Miller
> <ak.miller AT auckland.ac.nz>
> Subject: [[cellml-dev] ] Fwd: Re: batch processing
>
> -------- 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>
>>> ---------------------------------
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
>
> ------------------------------
>
>
> End of cellml-tools-developers Digest Sun, 21 Jul 2013
> *********************************************

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• [[cellml-dev] ] Re: cellml-tools-developers Digest Sun, 21 Jul 2013, Maxwell Neal, 07/23/2013
  • Re: [[cellml-dev] ] Re: cellml-tools-developers Digest Sun, 21 Jul 2013, Andrew Miller, 07/23/2013

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