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BhallaLab / moose-core

C++ basecode and python scripting interface
https://moose.ncbs.res.in
GNU General Public License v3.0
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Markov Channels #334

Open dbdorman opened 5 years ago

dbdorman commented 5 years ago

Moose has objects for markov channels and markov rate tables, but I cannot determine how to properly set them up. Is there an example or documentation of creating a markov channel using pymoose?

upibhalla commented 5 years ago

I was not able to find a worked example. There is the in-code documentation that you can see using moose.doc( 'MarkovChannel' ) There is some automated documentation in the code that can be found at https://moose.ncbs.res.in/source/doxygen/cpp/html/annotated.html but I didn't find it to be very helpful. Finally the author of the code is still at NCBS but in a different lab, and is at vishakad@ncbs.res.in -- Upi

dbdorman commented 5 years ago

Thank you, Upi! The function testMarkovChannel() in https://github.com/BhallaLab/moose-core/blob/master/biophysics/testBiophysics.cpp was helpful in showing how to setup and connect 3 necessary objects for simulating a markov channel: a MarkovChannel, a MarkovRateTable, and a MarkovSolver. But I cannot figure out a way to get the step for setting up transition rates for the MarkovRateTable object to work. There are 3 destFinfo functions, set1d, set2d, and setconst, that appear to be used for setting up the transition rates, but calling these from python raises the following: SystemError: NULL result without error in PyObject_Call. So it seems to me that it is not currently possible to simulate a markov channel from pymoose. Thanks for the assistance!

github-actions[bot] commented 4 years ago

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