Running after uninserting a mechanism

[ted]

other problem:
Using "insert/remove mechanisms" with my model works only on quiet mode. when "quiet mode" and one or more mechanisms were OFF, running simulation doesn't work, nothing happen while it works in "quiet mode"

What version of NEURON are you using?

[Gannier]

What version of NEURON are you using?

I tried with official version 5.9 and 6.0 alpha 891

[ted]

Do your best to trim the model down to a minimal size that reproduces the problem--I mean
REALLY MINIMAL, with as few files and lines of code as possible. Then zip up just those
essential bits and send it to me
ted dot carnevale at yale dot edu
so we can try to diagnose the problem. If it's a NEURON bug, we'll fix it. If it's a bug in your
code, we'll tell you how to fix it.

[Gannier]

Hello Ted,

when trying to do a minimal model I found this problem comes from the session file.
I'm starting from the courtemanche model found at modeldb database.
in the session file, we can found a parameters window like following:

Code: Select all

{
xpanel("soma(0 - 1) (Parameters)", 0)
xlabel("soma(0 - 1) (Parameters)")
xlabel("nseg = 1")
soma.L = 100
xvalue("L","soma.L", 1,"define_shape()", 0, 0 )
soma.diam = 16
xvalue("diam","soma.diam", 1,"", 0, 0 )
soma.cm = 2
xvalue("cm","soma.cm", 1,"", 0, 0 )
soma.gCaL_ICaL = 0.000248
xvalue("gCaL_ICaL","soma.gCaL_ICaL", 1,"", 0, 0 )
soma.gK1_IK1 = 0.0001567
xvalue("gK1_IK1","soma.gK1_IK1", 1,"", 0, 0 )
soma.gKr_IKr = 5.88e-05
xvalue("gKr_IKr","soma.gKr_IKr", 1,"", 0, 0 )
soma.Tauact_IKr = 1
xvalue("Tauact_IKr","soma.Tauact_IKr", 1,"", 0, 0 )
soma.gbNa_ibackg = 1.348e-06
xvalue("gbNa_ibackg","soma.gbNa_ibackg", 1,"", 0, 0 )
soma.gbCa_ibackg = 2.26e-06
xvalue("gbCa_ibackg","soma.gbCa_ibackg", 1,"", 0, 0 )
xpanel(759,230)
}

from the "insert/remove mechanisms", if you uncheck a mechanism found in this parameters window, values display "doesn't exist" and the simulation stops and you cannot restart a new one. However, the problem does not exits in the same conditions in "Quiet mode".

[ted]

That's a symptom, but not much of a clue.

I'm starting from the courtemanche model

A model with a high degree of mechanistic complexity. Trying the original from ModelDB,
I deselected one of the mechanisms and found that the RunControl panel's Init & Run
button seemed not to launch a simulation. However, executing run() at the oc> prompt
produced a segmentation violation that referenced ca_ion--specifically,
hoc_ac_ = cai0_ca_ion
It didn't seem to matter which mechanism I deselected--the same problem occurred.

To me this suggests a problem with the calcium accumulation mechanism Cadynam,
which is formulated in terms of a nasty looking nonlinear first order differential equation.

I don't know what to make of your observation about "Quiet" mode, but the fix, if there is
one, will most likely involve revising the calcium accumulation mechanism.

[ted]

if you uncheck a mechanism found in this parameters window, values display "doesn't exist" and the simulation stops and you cannot restart a new one.

Actually this IS a clue. Closing this xpanel allows the simulation to proceed. You can then
bring up a new "parameter" panel by
NEURON Main Menu / Tools / Distributed Mechanisms / Viewers / Shape Name
and double clicking on "soma" in the list of sections.

And sure enough, clicking on the "old style" RunControl's "Quiet" button allows you to uninsert
mechanisms and still be able to run simulations, even though the numeric fields for the
uninserted mechanisms' parameters contain "doesn't exist" messages.

So I misunderstood your question.

I'm not sure it's a good idea to be able to run simulations when the parameter panel contains
items that don't exist. This seems like a guaranteed way to become confused about what
is, and what isn't, in a model. But having to launch a new parameter panel is awkward.
The problem arises because the parameter panel and the inserter tool are independent
of each other, which forces the user to be the glue between these tools. I suggest that
you use the CellBuilder to specify your model properties. Its Biophysics page integrates
mechanism selection and specification of parameters in a way that avoids this problem.