Search found 5673 matches

by ted
Mon Dec 02, 2019 3:21 pm
Forum: NEURON + Python
Topic: Shape plot update from Python
Replies: 2
Views: 146

Re: Shape plot update from Python

I would like to monitor "cai" variable across shape plot. After I execute this code it shows correctly what I want to monitor, except that it wont update . . . When I specify the same parameters with mouse - it works and the plot is updates. The Programmer's Reference documentation of PlotShape sho...
by ted
Mon Dec 02, 2019 12:09 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Accessing state variables of one mechanisn in another mechanism
Replies: 4
Views: 252

Re: Accessing state variables of one mechanisn in another mechanism

One way would be to make the dependent mechanisms' cAMP variables be POINTERs. Read about setpointer in the Programmer's Reference. For an example, see caL.mod and kir2.mod in ModelDB entry 39949. These mechanisms specify ion channels whose properties are modulated by a second messenger, the concent...
by ted
Sun Dec 01, 2019 11:37 am
Forum: Adding new mechanisms and functions to NEURON
Topic: where to declare cai and cao ?
Replies: 1
Views: 140

Re: where to declare cai and cao ?

At least in two modules for low and high threshold calcium currents read inner and outer calcium concentrations (cai, cao) and compute the GHK equation. Yes, but neither of those NMODL-specified mechanisms WRITEs cai or cao, so their assignment statements cai = something cao = something else do not...
by ted
Tue Nov 26, 2019 4:36 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 451

Re: using diam and L params inside MODL file

Models of diffusion can be implemented with NMODL, but NMODL is best suited for nearly cylindrical geometries--structures in which diameter changes very slowly along the length of a neurite--and under conditions in which concentration gradients and solute fluxes are either predominantly longitudinal...
by ted
Tue Nov 26, 2019 2:53 pm
Forum: NEURON + Python
Topic: How to get synapse offset/position
Replies: 5
Views: 248

Re: How to get synapse offset/position

Good. I hope you're still in an educational mood. The d_lambda rule is a rational basis for specifying the spatial discretization of a model. It involves setting nseg to a value that is a small fraction of the AC length constant at a high frequency. The rationale behind it is developed in the second...
by ted
Mon Nov 25, 2019 1:13 pm
Forum: Other questions
Topic: Could neuron be installed on Windows/MacOS through the command line?
Replies: 2
Views: 209

Re: Could neuron be installed on Windows/MacOS through the command line?

For MacOS the answer is: install from source code. In principle, that should also be doable under MSWin.
by ted
Mon Nov 25, 2019 1:09 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 451

Re: using diam and L params inside MODL file

NMODL code can access properties of the segment to which it is attached. Examples include range variables, such as v, diam, and transmembrane currents. Another is segment surface area, which is known to NMODL as area. To access any of these from inside a mod file, declare them in the ASSIGNED block....
by ted
Sun Nov 24, 2019 12:04 pm
Forum: Getting started
Topic: How to reconstruct the 3D points of a morphology imported by Import3D
Replies: 7
Views: 455

Re: How to reconstruct the 3D points of a morphology imported by Import3D

Is a child section's 0 end xyz always the same as its parent's 1 end xyz? Good question. Looks like you (and probably a lot of other people) have some reading, or maybe re-reading, to do in the Programmer's Reference. The answer is no, and for two reasons. Reason 1. Read the Programmer's Reference ...
by ted
Fri Nov 22, 2019 9:10 pm
Forum: Getting started
Topic: How to reconstruct the 3D points of a morphology imported by Import3D
Replies: 7
Views: 455

Re: How to reconstruct the 3D points of a morphology imported by Import3D

so I can safely assume that Neuron always connects sections end-to-end? Please rephrase the question. I don't quite know what you're asking. What exactly does that x value represent then? If you are asking about the meaning of the value returned by seg.x in statements of the form for seg in somesec...
by ted
Fri Nov 22, 2019 12:48 pm
Forum: Other questions
Topic: Plotting M for IntFire4
Replies: 3
Views: 650

Re: Plotting M for IntFire4

Your first decision is whether to plot M vs. t "on the fly" i.e. while the simulation is executing. If yes, this is most easily done by using NEURON's own plotting features. For example, if your IntFire1 instance was created by this Python statement if1 = h.IntFire1() then print will reveal its hoc ...
by ted
Thu Nov 21, 2019 1:47 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL: COMPARTMENT statement in the KINETIC section
Replies: 2
Views: 182

Re: NMODL: COMPARTMENT statement in the KINETIC section

If you actually have a copy of The NEURON Book , see the discussion in 9.10.1 Modeling diffusion with kinetic schemes . Any reader of this thread who does not have the book may download this earlier draft of chapter 9 https://www.neuron.yale.edu/ftp/ted/book/revisions/chap9indexedref.pdf and read Mo...
by ted
Thu Nov 21, 2019 1:33 pm
Forum: OS X
Topic: NEURON not working properly after update to Catalina and major troubleshooting!
Replies: 3
Views: 315

Re: NEURON not working properly after update to Catalina and major troubleshooting!

Not related to the problem that triggered this thread, but something you need to know: for your ODE-described calcium accumulation mechanism, use derivimplicit rather than cnexp. See Integration methods for SOLVE statements https://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592 in the Hot tips a...
by ted
Thu Nov 21, 2019 1:25 pm
Forum: NEURON + Python
Topic: How to get synapse offset/position
Replies: 5
Views: 248

Re: How to get synapse offset/position

If it is absolutely essential to place "something" at a very particular location along a neurite, then represent the neurite by two sections connected in series, assign each section whatever length you need, and place the "something" at their junction point. Then you are free to use whatever values ...
by ted
Thu Nov 21, 2019 11:30 am
Forum: Getting started
Topic: How to reconstruct the 3D points of a morphology imported by Import3D
Replies: 7
Views: 455

Re: How to reconstruct the 3D points of a morphology imported by Import3D

If a section.parentseg().x = 0.5 and parent_section.n3d = 21, does that mean that section is connected to parent_section somewhere around the 10th-11th 3d xyz point? No. Reflect on the fact that what governs the placement of xyzdiam measurements along the length of an unbranched neurite are the irr...
by ted
Thu Nov 21, 2019 11:06 am
Forum: NEURON hacks
Topic: NMODL file in different folder
Replies: 9
Views: 2320

Re: NMODL file in different folder

On Linux it generates a folder x86_64 . . . The documentation mentions that nrn_load_dll works for Linux, but I don't see a dll file? The file you want to load is x86_64/.libs/libnrnmech.so You realize that, by doing this, you are writing code that will not work under MSWin or MacOS. And unless you...