www.neuron.yale.edu

Hi, Sorry I guess I posted a bit too much code and actually missed the essential bit. I initialise the random process right before I call pnm.create(), which calls the obfunc that creates the cells. Willl that make sure that the that the seed from ranind is used in the obfunc? Here is the code bit t...

Hi, I am trying to parallelise a network model I had used previously, as we are now in the lucky situation to have a beowulf cluster available for simulations. I have adapted my network model based on a few examples posted in ModelDB (especially the parallel olfactory bulb network model.) I am curre...

Hi, I personally would go along with detlefvonberg who pointed out that Wiki is both flexible enough to let users easily contribute to the knowledge base but has mechanisms to protect final versions of content from being modified. Further on I was not thinking of "just another" place to lo...

Hi NEURON users, As a NEURON beginner it is quite hard to find a solution to a specific problem either if I have a problem with writing hoc code or using the gui. I do know all the places to look at (programmers reference, NEURON site at Yale/Duke, NEURONDB, tutorials, manuals, NEURON Book), but as ...

Hi this is about importing again: I received a file reconstructed cell which was used in Neuron simulations (possibly an earlier version). It seems to be in .swc format. Unfortunately the import through the 3d import tool doesnt work (and cvapp cant read the file either). I tried to change the first...

Hi! We are trying to use Condor for running Neuron jobs on a grid of linux machines. My rather general questions are: 1) Has anyone ever tried to use Neuron with Condor? 2) It is required that all jobs submitted to nodes in the grid use a statically linked executable. Is is possible to "compile...

Another error occurs when restoring the savestate of a single cell modell (save state after running, write to file, open in a modified copy hoc to read state): Assertion failed: file ../nrncvode/netcvode.cpp, line 3594 /usr/local/nrn/x86_64/bin/nrniv: cursize_ < vrd->t_->capacity() in pfc_pc.hoc ne...

Sorry, I guess I have to clarify this: If I use savestate in the sugessted way (and using the modified init proc from above, t=0 commented out, in the hoc that opens the state): ... IBnetstate = new SaveState() IBnetstate.save() ... I do get this error during saving the state: /usr/local/nrn/x86_64/...

I do admit the code above is not very elegant... Anyhow, an altered version of that code seems to save the state but the problem remains that this state saved by neuron is not readable to that same version of neuron?! It seems like neuron wants to have a 5.6 binary file but it is 5.7. So maybe it ha...

Thanks again! tried to save state, load similar hoc file and read state file, error was: /usr/local/nrn/x86_64/bin/nrniv: Bad SaveState binary file Not version 5.6 in transrun2.hoc near line 58 IBnetstate.fread(fo) ^ SaveState[0].fread(File[1]) 2. States are saved in a binary format using data struc...

Hi, the network I am simulating has a very long transient before it settles into the dynamic regime I am interested in. My idea is now to use SaveState() to save the network state after the transient and then run a sweep of simulations starting of at that point. My questions are: How can you set the...

Hi, my soma is not 400 um long (that would be a quite a big soma, huh?). Here's an image of the cell: http://www.pion.ac.uk/~ulli/opics/cell.jpg You can clearly see that the maximum distance should be around 600 µm. But dist = 94.361069 140.46154 535.17393 224.15504 289.46572 297.22658 422.05326 549...

Hi, Another very basic question, but I could not find an answer in the forum or elsewhere: I have a morphological model of a pyramidal cell and I am trying to determine voltage attenuation in the cell depending on the distance to the soma. The cell builder (after importing the morphology / or cvapp)...

Spines seem to be coded by the position of their head. An example from my Neurolucida ascii file: ( (Color Red) (Dendrite) ... ( 8.77 -18.01 -11.75 0.87 S2) ; R-1, 6 <( 9.68 -16.96 -11.50 0.65 S2)> ; Spine ... No value equals another, so I guess the base is not coded. This can be easily seen in anot...

The zigzags do appear in cvapp and in Neuron, - but they are not seen under Neuroexplorer from Neurolucida - and they are not seen on the axon of the cell which has no spines! So only spiny part s of the cell show that zigzag like shape. To put this better I add some figures. The cell in the Neuroex...