Simulate voltage-clamp protocols faster

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Simulate voltage-clamp protocols faster #20

Open MichaelClerx opened 6 years ago

MichaelClerx commented 6 years ago

~Test 'method 2' for HH models in Myokit, finish mini-report~
~Auto-detect HH models, use explicit solution?~
~Or rush-larsen?~
~Auto-detect Markov models, use explicit solution?~

Update (2018-11-02):

Eventually, we should have some machinery in the WL for running clamp-only protocols on Markov or HH models, both of which can be solved analytically for fixed voltages.

mirams commented 6 years ago

Yep - just having a nice tidy solver that does exact solutions for MM and HH models for flat voltage steps, then swaps to CVODE for sine wave section, should give nice speed ups.

I would like to get these kind of solvers auto-generated from CellML. Would require figuring out what the transition matrix is for Markov models specified as a system of ODEs.

MichaelClerx commented 6 years ago

I would like to get these kind of solvers auto-generated from CellML. Would require figuring out what the transition matrix is for Markov models specified as a system of ODEs.

Can copy/paste that from Myokit when the time is right! (It uses sympy for this step)

MichaelClerx commented 5 years ago

I'd say this is out of scope now, or possibly a weblab_cg nice-to-have?

Can I close this @jonc125 @mirams ?

mirams commented 5 years ago

Can we have a WL3 tag for longer future tickets, rather than closing them and never finding them again?

jonc125 commented 5 years ago

We certainly don't have to close issues that are out of scope for the BBSRC grant, since everything in scope should be linked to an epic, and we can use those to filter tasks of interest.