Code for Lists of Synaptic Connections

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johnawolf
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Joined: Wed Jun 08, 2005 4:48 pm
Location: University of Pennsylvania
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Code for Lists of Synaptic Connections

Post by johnawolf »

Hi all,

Does anyone (Bill?) have a chunk of code that does a nice job of displaying all the NetCons in a network sorted by either precell or postcell? We are having problems printing the contents of netconlist...

TIA,

John

ted
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Post by ted »

Assuming you have a List of all cells in your network, why not do something like this:

Code: Select all

// allcells is a List of all cells in the net
objref ncs_by_pre, ncs_by_post, tmplist
ncs_by_pre = new List()
ncs_by_post = new List()
// element ii of ncs_by_pre will be a List of netcons whose source is allcells.object(ii)
for ii = 0, allcells.count()-1 {
  tmplist = cvode.netconlist(allcells.object(ii), "", ""))
  ncs_by_pre.append(tmplist)
  tmplist = cvode.netconlist("", allcells.object(ii), ""))
  ncs_by_post.append(tmplist)
}
for ii = 0, allcells.count()-1 {
  print allcells.object(ii), " is a source for"
  for jj = 0, ncs_by_pre.object(jj).count()-1 print ncs_by_pre.object(jj)
  print "and receives afferent streams via"
  for jj = 0, ncs_by_post.object(jj).count()-1 print ncs_by_post.object(jj)
  print ""
}
I haven't tested this, but barring a typo it should work--although its output will be ugly.

wwlytton
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network organziation

Post by wwlytton »

I go in the other direction -- I put the network together in a database and then use this to view and manipulate connectivity -- then I load the db into neuron

alternatively I do have some code that reads out of cvode.netconlist to produce the database

however you mentioned that you are having some trouble with netconlist() -- maybe this is the place to start -- what kind of trouble?

Bill

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