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Posts: 4
Registered:
April 2012
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Finding Stable Points in a system of ODEs
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04 May '12 19:02
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Ayesha,
We've been working on a new SBML interface to APMonitor Modeling Language that can solve very large-scale models in steady-state (dx/dt=0), dynamic simulation, parameter estimation, optimization, etc.
http://apmonitor.com/wiki/index.php/Main/SBML
Once you've converted the SBML model to APM, it can be solved through a web-interface...
http://apmonitor.com/online/view_pass.php
or MATLAB...
http://apmonitor.com/wiki/index.php/Main/MATLAB
or Python...
http://apmonitor.com/wiki/index.php/Main/PythonApp
One of my students, David Grigsby, gave a presentation last week that explains some of the capabilities and future development plans...
http://apmonitor.com/wiki/uploads/Main/apm_sbml_23Apr12.pdf
We're looking for additional researchers to help benchmark APMonitor performance. For example, a complete simulation (to a time of 9000) with the ErbB model takes around 20 seconds. The ErbB Signalling model has the following characteristics:
Parameters: 225
Variables: 504
Intermediates: 827
Equations: 504
We don't know if this is faster than other available software for simulation. Does anyone else have perspective on the simulation speed benchmarks for large-scale models?
Best regards,
John Hedengren
Brigham Young University
john.hedengren@byu.edu
Date: Fri, 4 May 2012 13:24:49 -0700 (PDT)
From: ayesha <ayesha.kalra@gmail.com>
Subject: [sbml-discuss] Finding Stable Points in a system of ODEs
To: sbml-discuss@caltech.edu
Message-ID: <20120504202449.803E8CF049C@notes.caltech.edu>
Content-Type: text/plain; charset="ISO-8859-15"
Hi all
I am simulating a model with ~200 first-order, non-linear system of ODEs. I want to know if there is any way I can find out:
1. If the model has stable points? If so, how many?
2. Is there a good software (free or commercial) for dynamical analysis of ODEs which can handle large no. of non-linear equations?
Thanks
Ayesha
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