problems using the Network Builder

[ted]

I'm working through chapter 11, and have gotten stuck on step 11.4.5 where it tells me to toggle the time step from global to local. When I open the Numerical Method Selection window my "current model type" is set to <*no model*> and therefore does not allow me to choose Local Step. I thought I'd followed all the steps, can you tell what I need to do to fix this?

If no model exists and you're using the Network Builder (NetGUI tool), I bet you haven't clicked on that tool's "Create" button (par. 3 and Fig. 11.13 on p. 318).

[tseredynski]

Thanks for the help ted. Unfortunately I have clicked on the "create" button... here's a screen shot of what windows I think are relevant:



Wish that image was a bit clearer...

Any other guesses? Any other information I can provide you with to give you ideas?

Thanks

EDIT: FYI, I have been able to work through most of the remainder of the chapter and run the simulation, plotting the occurrence of spikes. Not sure what this means regarding the lack of a "model." I am currently unable to change things like the weight and tau values via the GUI, but am working on it. I give you this information in case it helps determine what exactly I'm lacking...

[ted]

I just now threw together a toy net with two model cells--biophysical model cell specified by the CellBuilder, and a NetStim, with the latter sending events to an ExpSyn attached to the former. I'm not getting any error messages at all. What do you see when you execute the command
psection()
or
forall psection()
at the oc> prompt?
Also, exactly what version of NEURON are you using--what is the first line that hoc prints when NEURON starts?

[tseredynski]

psection() and forall psection() give:



I wonder if I compiled my cell model correctly.. I copied out Listing 11.1 and used mknrndll to build a dll file. I then opened nrngui and loaded the dll file. From there I continued on from step 11.4.1. Anything sound wrong about this?

[ted]

The messages mean there is no model. Either there is a problem in how you are using the Network Builder GUI tools, or there is a problem in the code you copied from Chapter 11, or both. Have you worked through the Network Builder tutorials on the Documentation page?
http://www.neuron.yale.edu/neuron/docs
They're simple and fairly quick and should familiarize you with proper GUI usage. Once you have done those, you might try working through chapter 11 again. If you find an error in that chapter or continue to run into difficulty, please let me know.

Two other items:
1. I split these new posts off from the old thread because they diverged so much from the original topic that they deserved a separate thread. In doing that, somehow I managed to split your first post into a third thread. I had to copy it, then paste it into my reply (see way above). So much for the ease of using GUI tools.
2. In the future, when quoting text output from NEURON please just copy and paste the text directly into your message, then select it and click on the "Code" button above the text entry area. This is quicker and uses less space than snapshotting a window and posting it as a bitmap.

[tseredynski]

Thank you ted. I had not worked through that tutorial yet, as I thought chapter 11 also served as one. I'll do as you suggested and let you know the outcome.

Also, I'll keep your posting suggestions in mind for the future, thank you.

- Tyler

[ted]

I had not worked through that tutorial yet, as I thought chapter 11 also served as one.

Yes, except that the online tutorial is of more recent vintage and less complicated, so has lower risk of deviation between what was current "then" vs. what is current now, and presents users with fewer traps and opportunities to make their own mistakes.

[tseredynski]

Hi ted,

Got the same results attempting the Network Builder Tutorial (Tutorial 1 : Making Networks of Artificial Neurons) from Documentation. I attempted it twice, and tried to make sure I didn't miss any steps... Sorry, but I'm attaching another picture...

It shows I have the ArtCellGUI window open w/ cells defined, the NetGUI with network defined and create button checked, a simulation ran, and the Numerical Method Section that will not allow me to check the Local Step button b/c the current model type is "<*no model*>". I don't know what I'm doing wrong... I even did this tutorial on a different computer, so I doubt its a software problem...

As additional information I am running Neuron 7.2, which seems to have a slightly different VariableTimeStep window from the tutorial.

[ted]

What is the first line printed by NEURON when it starts--it will look something like
NEURON -- VERSION 7.3 (692:32dfec6adae7) 2012-06-13
but the exact version number and date will be helpful.
What operating system are you using?

[tseredynski]

First line:

NEURON -- Release 7.2 (562:42a47463b504) 2011-12-21

OS's attempted:

Windows XP Pro run in Virtual Box on Mac OS X 10.7.4
Windows 7.0

[tseredynski]

Is there any other information I can supply you with, or recommendations I can try?

Thanks for your help.

[ted]

Well, looking at the most recent picture you posted, it looks like some model does exist--otherwise the spike rasters in the SpikePlot window would not exist. Are you sure you don't have more than one instance of NEURON running, one with a valid model, and the other without a model?

[tseredynski]

Well, I completely restarted the Windows session and the virtualBox program, and rebuilt the tutorial model from scratch, only opening the GUI once, and got the same results. Under these circumstances I believe only one instance could be running...

[tseredynski]

Okay, what if we look at the .hoc code? I've generated the .hoc code after completing part 1 of the online Network Builder tutorial:

Code: Select all

// Artificial cells no longer need a default section.
//Network cell templates
//Artificial cells
//   S_NetStim
//   C_IntFire1


begintemplate S_NetStim
public pp, connect2target, x, y, z, position, is_art
objref pp
proc init() {
  pp = new NetStim()
}
func is_art() { return 1 }
obfunc connect2target() { localobj nc
  nc = new NetCon(pp, $o1)
  if (numarg() == 2) { $o2 = nc }
  return nc
}
proc position(){x=$1  y=$2  z=$3}
endtemplate S_NetStim

begintemplate C_IntFire1
public pp, connect2target, x, y, z, position, is_art
objref pp
proc init() {
  pp = new IntFire1()
}
func is_art() { return 1 }
obfunc connect2target() { localobj nc
  nc = new NetCon(pp, $o1)
  if (numarg() == 2) { $o2 = nc }
  return nc
}
proc position(){x=$1  y=$2  z=$3}
endtemplate C_IntFire1

//Network specification interface

objref cells, nclist, netcon
{cells = new List()  nclist = new List()}

func cell_append() {cells.append($o1)  $o1.position($2,$3,$4)
   return cells.count - 1
}

func nc_append() {//srcindex, tarcelindex, synindex
  if ($3 >= 0) {
    netcon = cells.object($1).connect2target(cells.object($2).synlist.object($3))
    netcon.weight = $4   netcon.delay = $5
  }else{
    netcon = cells.object($1).connect2target(cells.object($2).pp)
    netcon.weight = $4   netcon.delay = $5
  }
  nclist.append(netcon)
  return nclist.count - 1
}

//Network instantiation

  /* S0 */  cell_append(new S_NetStim(),   -101,    23, 0)
  /* C1 */  cell_append(new C_IntFire1(),   -60,    22, 0)
  /* S0 -> C1    */  nc_append(0, 1, -1,  2,1)


Are you able to post a copy of functional code, in which a local time step was allowed to be defined? Either by looking at my code, or us comparing the two, perhaps we can notice what my issue is. Because at first glance of my code, seeing as how I have templates defined, and a network instantiated... I clearly have a model, no?

[ted]

Model View says there is one instance each of NetStim and IntFire1. hoc confirms that these are NetStim[0] and IntFire1[0], and that the former projects events to the latter via NetCon[0] which has weight 2 and delay 1.

Are you able to post a copy of functional code, in which a local time step was allowed to be defined?

Try
cvode_active(1)
cvode.use_local_dt(1)