Stochastic solvers that pass tests?

[srikiran chandrasekaran]

Hello,

I am trying to locate a stochastic solver that passes the tests in the sbml-test-suite - something that I can reproduce locally. I am also trying to use the SBML TestRunner with COPASI, but I am not sure how to connect them.

[Herbert Sauro]

Check out this:

https://www.biorxiv.org/content/10.1101/181446v1 

it describes a C implementation of the Gillespie direct method and was extensively tested and verified to be correct using the *stochastic* test suite.  It probably won't pass many of the tests in sbml test suite because it doesn't support eg events and other aspects that are not applicable to stochastic solvers

Herbert Sauro 

On Sun, Dec 1, 2019 at 11:53 AM srikiran chandrasekaran <srik...@gmail.com> wrote:

Hello,

I am trying to locate a stochastic solver that passes the tests in the sbml-test-suite - something that I can reproduce locally. I am also trying to use the SBML TestRunner with COPASI, but I am not sure how to connect them.

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[srikiran chandrasekaran]

Oh looks good, thanks!

On Sunday, 1 December 2019 13:18:13 UTC-8, Herbert Sauro wrote:

Check out this:

https://www.biorxiv.org/content/10.1101/181446v1 

it describes a C implementation of the Gillespie direct method and was extensively tested and verified to be correct using the *stochastic* test suite.  It probably won't pass many of the tests in sbml test suite because it doesn't support eg events and other aspects that are not applicable to stochastic solvers

Herbert Sauro 

On Sun, Dec 1, 2019 at 11:53 AM srikiran chandrasekaran <srik...@gmail.com> wrote:

Hello,

I am trying to locate a stochastic solver that passes the tests in the sbml-test-suite - something that I can reproduce locally. I am also trying to use the SBML TestRunner with COPASI, but I am not sure how to connect them.

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[Frank T. Bergmann]

Hello,

 

To answer the specific questions you had regarding COPASI I commented how we run the SBML test suite and the stochastic test suite full information on the links below:

 

SBML test suite:  https://github.com/copasi/COPASI/tree/develop/sbml-testsuite

Stochastic test suite:  https://github.com/copasi/COPASI/tree/develop/stochastic-testsuite

 

Best

Frank

 

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[srikiran chandrasekaran]

Thank you so much!

On Tuesday, 3 December 2019 08:05:39 UTC-8, Frank T. Bergmann wrote:

Hello,

 

To answer the specific questions you had regarding COPASI I commented how we run the SBML test suite and the stochastic test suite full information on the links below:

 

SBML test suite:  https://github.com/copasi/COPASI/tree/develop/sbml-testsuite

Stochastic test suite:  https://github.com/copasi/COPASI/tree/develop/stochastic-testsuite

 

Best

Frank

 

From: sbml-inter...@googlegroups.com <sbml-inter...@googlegroups.com> On Behalf Of srikiran chandrasekaran
Sent: Sunday, December 1, 2019 8:25 PM
To: sbml-interoperability <sbml-inter...@googlegroups.com>
Subject: [sbml-interoperability] Stochastic solvers that pass tests?

 

Hello,

 

I am trying to locate a stochastic solver that passes the tests in the sbml-test-suite - something that I can reproduce locally. I am also trying to use the SBML TestRunner with COPASI, but I am not sure how to connect them.

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