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These basic concepts should be covered in any introductory book or course on cellular biophysics or neurophysiology. Try Foundations of Cellular Neurophysiology by Johnston & Wu. Also try Wikipedia or just search the WWW; searching for membrane capacitance produces these two excellent hits on th...

I started NEURON from "NEURON DEMO." I selected "stylized" model. I want to know which hoc file is corresponding to the stylized model, so I can read the file content and know the anatomical and biological properties of this model. If you are interested in the demonstration prog...

The problem was that the DERIVATIVE block preceded the BREAKPOINT block. To quote Michael Hines, The problem is that sometimes the METHOD in the SOLVE statement determines some of the parsing when the DERIVATIVE block is seen. Because of this problem, nocmodl now prints an error message during mod f...

NMODL source code is organized into blocks. To simplify development and debugging, and avoid problems such as inconsistent units, failed compilation, or runtime errors, there are a few simple rules to follow when organizing NMODL source code. 1. It's always a good idea to put a COMMENT block at the ...

There is no need to recompile. As you said, in the standard distribution of NEURON, the extracellular mechanism has two layers--see http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/mech.html#extracellular --but the default values of all of its parameters are such that neither layer h...

The Vector class does have an interpolate method, but it is only first order interpolation. You might as well do it right to start with. Referring to the documentation of the Vector class's record method http://www.neuron.yale.edu/neuron/static/docs/help/neuron/general/classes/vector/vect.html#recor...

2) How could I return the value of the last NetCon[id] so that I could change the numbers in the spkid vector to be more straight forward? Whoops... I noticed that there was another argument to netcon.record that solves this. In the for loop where the spike times are recorded just change one line t...

1) Why does the code fragment for netcon.record (Prog Ref) include the final, objref netcon Destroying the NetCon prevents reusing the NetCon for some other purpose, which would have the side effect of interfering with the recording. In the Programmer's Reference see http://www.neuron.yale.edu/neur...

FOR_NETCONS was introduced earlier this year. Google search from NEURON's home page generates several hits, including this one which is most informative: What's new? extends the NET_RECEIVE block by introducing the FOR_NETCONS statement. ie FOR_NETCONS(same, args, as, netreceive) { stmt } which iter...

Federal funding agencies and journals have fairly strict data sharing policies regarding sequence data. The "instructions for authors" for almost every scientific journal includes a statement that sequence data are to be deposited in a publically-accessible database such as Genbank, DNA Da...

I read that the assigned block is a block whereby it is possible to declare two types of variables: 1. variables given outside mod file and used in every mechanism and 2. statements inside mod file - unknown dependent variables in differential equations Would an example of the first be declaring gl...

zhbrass wrote:The one I am trying to modify is in a .mod file.

Then you have two choices:
change the mod file
or
use a Channel builder to set up a new mechanism that has the same biophysical properties
as those that are specified by the mod file, then modify the Channel Builder.

Sure. Anything that can be done to specify channel properties in the first place, can be done to modify them afterward. To review the basic properties, click on the Properties button http://www.neuron.yale.edu/neuron/static/docs/chanlbild/hhstyle/basicprop.html and to examine the gating properties, ...

Do you want channel noise or synaptic noise? For the former, use a Channel Bulider to implement stochastic gating--see the Channel Builder tutorial (link is here http://www.neuron.yale.edu/neuron/docs ). For the latter, use an ExpSyn or Exp2Syn driven by an event stream generated by a NetStim. via a...

The Channel Builder is for specifying the properties of the channel per se, i.e. its ionic selectivity, GHK vs. ohmic IV relationship, number of gating states and their kinetics, etc.. Channel density is an attribute of the section into which the channel mechanism has been inserted, and is managed w...