Search found 8 matches

by szabolcs
Tue Nov 22, 2011 11:32 am
Forum: Anatomically detailed models
Topic: parametrized subsets
Replies: 3
Views: 2215

Re: parametrized subsets

Thank you for the detailed response including the example. The situation I am facing is slightly different though. I am in the process of building (in fact, mostly porting from GENESIS) a detailed cell model I created earlier, which includes a total of about 15 different biophysical mechanisms in a ...
by szabolcs
Mon Nov 21, 2011 11:54 am
Forum: Anatomically detailed models
Topic: parametrized subsets
Replies: 3
Views: 2215

parametrized subsets

Dear All, Is there a way to define subsets in the Cell Builder in a parametric way (e.g., include all sections which are less than 300 micrometers away from the soma)? If not, is there a simple way to achieve this using the hoc interpreter, such that the subset definitions are used subsequently by t...
by szabolcs
Tue Mar 01, 2011 8:44 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Problem with saturating synapse model
Replies: 8
Views: 4724

Re: Problem with saturating synapse model

Thanks for the detailed response. While a fix for this is being developed (allow specification of the self-event that is to be moved?), the interim workaround is to limit each instance of the saturating synapse mechanism AMPA_S to a single input stream per instance--that is, one NetCon per AMPA_S in...
by szabolcs
Thu Feb 17, 2011 6:34 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Problem with saturating synapse model
Replies: 8
Views: 4724

Re: Problem with saturating synapse model

OK, you have discovered a bug in the mod file. Declaring the variables RANGE or GLOBAL is not the fix. Yes, I realize that these are two independent issues - still, I do not understand why the synapse model does not work at all (with any kind of input) when parameters such as synaptic time constant...
by szabolcs
Wed Feb 16, 2011 10:25 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Problem with saturating synapse model
Replies: 8
Views: 4724

Re: Problem with saturating synapse model

Thanks for the reply. By "defining an additional type of synapse in analogy to the two existing ones," I meant only that the synapse defined by the ampa.mod file had to be added to the cell template "StandardIF" in PyNN which already had two other (simpler, non-saturating) synapses. However, this is...
by szabolcs
Tue Feb 15, 2011 11:04 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Problem with saturating synapse model
Replies: 8
Views: 4724

Problem with saturating synapse model

I am trying to use the the saturating synapse model described in Chapter 10 of the NEURON Book in a network simulation. I compile the .mod file listed as ampa.mod in the book, and then attempt to drive a generic conductance-based linear integrate-and-fire neuron through synapses of this type. I actu...
by szabolcs
Mon Aug 09, 2010 10:28 am
Forum: UNIX/Linux
Topic: Parallel Neuron with Python support on an Opteron server
Replies: 2
Views: 2889

Re: Parallel Neuron with Python support on an Opteron server

Thank you for your help. Rebuilding mpich2 with shared library support was indeed the necessary first step, but then I also had to modify the setup.py script to get rid of an error caused in mpic++ by the remaining empty references to the missing iv libraries. In the end, I managed to make it work -...
by szabolcs
Fri Aug 06, 2010 12:25 pm
Forum: UNIX/Linux
Topic: Parallel Neuron with Python support on an Opteron server
Replies: 2
Views: 2889

Parallel Neuron with Python support on an Opteron server

Dear All, I am trying to install Neuron 7.1 with MPI and Python support, but without X11 on an Opteron blade server running Fedora 9, with the ultimate goal of using it with PyNN. I can compile Neuron with the Python interpreter (using the options --with-nrnpython=/usr/bin/python --with-paranrn --wi...