Search found 5572 matches

by ted
Fri Sep 20, 2019 10:47 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 76

Re: Solving 8 interdependent differential equations

This is not a problem of "magic numbers." There's a bug, either a subtle syntax error in your NMODL code or in NEURON itself. I'll need to work with your NMODL file in a toy model. If the NMODL file can be used by itself in a single compartment model, that's all I'll need. If it requires other mecha...
by ted
Fri Sep 20, 2019 10:39 am
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 99

Re: Filter Mechanism params by NMODL PARAMETER

Brilliant up to a point. The NMODL source code will tell you the default values of parameters. However, it won't tell you the actual value of any parameter used in a particular model implementation, because those can be changed by hoc or Python assignment statements. Also, if mechanism X's PARAMETER...
by ted
Thu Sep 19, 2019 10:58 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 76

Re: Solving 8 interdependent differential equations

I'd suggest changing
SOLVE blrrate METHOD cnexp
to
SOLVE blrrate METHOD derivimplicit
because many of the state variables have very small values and should not become negative.
by ted
Thu Sep 19, 2019 10:27 am
Forum: NEURON + Python
Topic: Filter Mechanism params by NMODL PARAMETER
Replies: 8
Views: 99

Re: Filter Mechanism params by NMODL PARAMETER

mech contains parameters like 'gbar', 'g', 'ica' and so on. Not what I see. Given soma = h.Section(name='soma') soma.insert('hh') then for seg in soma: for mech in seg: print(mech) returns k_ion na_ion hh but no mention of gnabar, gkbar, gl. or el, which are declared in hh.mod's PARAMETER block.
by ted
Thu Sep 19, 2019 10:09 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 76

Re: Solving 8 interdependent differential equations

Does the STATE block declare all of the variables that appear on the LHS of the ODEs?
What are the contents of the BREAKPOINT block?
Is initialization of the state variables correct?
Is PROCEDURE calcparameters() working properly?
by ted
Tue Sep 17, 2019 1:14 pm
Forum: MSWin
Topic: Cannot find executable python3 or python
Replies: 2
Views: 81

Re: Cannot find executable python3 or python

If you're not planning to use Python with NEURON or vice versa, ignore the message. Otherwise, uninstall NEURON completely--COMPLETELY--and then reinstall and accept the "add python to path" option.
by ted
Sat Sep 14, 2019 11:31 am
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 240

Re: can't load mknrndll issue

Are there some other ways that I can run this model without using cmd Nope. after removing the statement { neuron_name = "d151" , I double-clicked the eaps\cells\d151.hoc file and successfully got the shape plot. cell_type = "ca1pyr" } Then I tried to load other hoc files from Neuron Main Menu\File...
by ted
Sat Sep 14, 2019 11:17 am
Forum: Modeling networks
Topic: Decompose LFP into components
Replies: 5
Views: 171

Re: Decompose LFP into components

if I calculate single channel current's (implemented as point-process) contribution to LFP As a point process? What does point process have to do with anything? Most voltage-gated channels are implemented as density mechanisms. The currents they generate have units of mA/cm2 and must be multiplied ...
by ted
Fri Sep 13, 2019 10:50 am
Forum: Modeling networks
Topic: Decompose LFP into components
Replies: 5
Views: 171

Re: Decompose LFP into components

At large distances (more than about 10 x segment length) it is reasonable to treat the segment as a point source of current located at the segment center. A more fastidious approach is to treat each segment as a line source with the same length as the segment, centered at the location of the segment...
by ted
Wed Sep 11, 2019 12:10 pm
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 240

Re: can't load mknrndll issue

Sure. Forget about Windows. Use Linux instead. The code runs without complaint under Linux. Making it work under Windows is going to be a major pain.
by ted
Wed Sep 11, 2019 12:07 pm
Forum: Modeling networks
Topic: Decompose LFP into components
Replies: 5
Views: 171

Re: Decompose LFP into components

Assuming that one or more cells are embedded in a conductive medium that is linear, the potential Vi at any point i in the medium is Vi = SUMMA Zx_j Im_j j where the index j ranges over all compartments in the model, Im_j is the total (i.e. ionic + capacitive) transmembrane current for compartment j...
by ted
Wed Sep 11, 2019 11:40 am
Forum: NEURON + Python
Topic: Export to .hoc with CellBuilder from Python
Replies: 2
Views: 141

Re: Export to .hoc with CellBuilder from Python

but when I try . . . I receive an empty cell in test.hoc. You're starting with a model created by executing statements in Cell_Scnn1a.hoc. Where did the CellBuilder referenced by h.CellBuild() come from? If you created it yourself, it's "empty" (except for a soma section). It's not going to know an...
by ted
Tue Sep 10, 2019 12:29 pm
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 240

Re: can't load mknrndll issue

I also tried auto-launch which didn't work because this model isn't packaged in a way that allows auto-launch to work. How do I know, without even trying it? Two ways. First, auto-launch requires the presence of a mosinit.hoc file. ModelDB entry 84589 doesn't come with a mosinit.hoc file. Second, t...
by ted
Tue Sep 10, 2019 12:18 pm
Forum: Suggestions and Feedback
Topic: can't load mknrndll issue
Replies: 9
Views: 240

Re: can't load mknrndll issue

when I double click mknrndll, these massages shows: Can't load NEURON resources from D:\nrn;C:\nrn/lib/nrn.def[aults] . . . I've downloaded NEURON twice, the first time I downloaded it on D drive, and the second time on C drive. No, you INSTALLED NEURON twice, and now you have at least one broken i...
by ted
Sat Sep 07, 2019 3:37 pm
Forum: MSWin
Topic: cygwin vs msys file path changes, Windows NEURON version
Replies: 1
Views: 147

Re: cygwin vs msys file path changes, Windows NEURON version

Try checking the value returned by neuronhome().