creating cell type

Moderator: wwlytton

Post Reply
Amal Afzal Shaikh

creating cell type

Post by Amal Afzal Shaikh »

hello ted,
i want to create a cell type which i can use in networks.. if i use gui, then i need to go to management of cell builder then cell type and save the type in hoc file.. but that cell type is not appearing in network builder's artificial cell list which consists of netsim,intfire1..etc.. pls help..
thanx in advance...
ted
Site Admin
Posts: 5786
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Post by ted »

Have you already worked through part 2 of the Network Builder tutorial?
http://www.neuron.yale.edu/neuron/stati ... /main.html
if i use gui, then i need to go to management of cell builder then cell type and save the type in hoc file.. but that cell type is not appearing in network builder's artificial cell list
A cell class exported from the CellBuilder is a hoc file that specifies a type of model
biophysical cell. It cannot be used with the GUI tools for building networks, and even if it
could, it is not an artificial spiking cell class so it would not appear in the ArtCellGUI tool.
The only way to add new classes of artificial spiking cells is to write a new model
specification in NMODL, then compile that mod file.

If you have a model cell, specified by a CellBuilder, that you would like to use as a cell class
in the Network Builder, here's how to proceed:
Make sure that the CellBuilder's "Continuous Create" is OFF (i.e. no check mark in the box).
Save that CellBuilder to a session file all by itself (use the Print & File Window Manager; if
you don't know how to do this, see this item in the FAQ list
Q: What is a ses (session) file? Can I edit it?
).

Exit NEURON.

Then restart NEURON, and load the CellBuilder's ses file.
Click on Build / Network Cell / From CellBuilder
A new window pops up. The right column in this tool has a list of all CellBuilders that are
open (for this example, there will only be one CellBuilder in the list). Click on the name
of your CellBuilder, then click on the "Use Selection" button.
You will now see a NetReadyCellGUI tool, and its associated SynTypeGUI tool.
You should click on your CellBuilder's Close button.
You are now ready to specify what kinds of synapses should be attached to your
biophysical model cell (with the SynTypeGUI tool), and where they are to be located
(with the NetReadyCellGUI tool), as described in Network Builder Tutorial 2
http://www.neuron.yale.edu/neuron/stati ... /main.html
Amal Afzal Shaikh

nmodl

Post by Amal Afzal Shaikh »

Thanx a lot Ted for clearing my doubt.. i hv gone thru chpt 11 fo modelling of networks..i hv a basic doubt .. do we write the nmodl code in text document? wht extension do v save the doc? is it by using extension .mod? thn hw do v compile the mod file?

thanx in advance..
ted
Site Admin
Posts: 5786
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: nmodl

Post by ted »

Amal Afzal Shaikh wrote:do we write the nmodl code in text document?
What nmodl code? I didn't say anything about nmodl.
{quote]wht extension do v save the doc?[/quote]
What doc?
hw do v compile the mod file?
What mod file?
Post Reply