Search found 41 matches

by rth
Wed Apr 10, 2013 6:16 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 10028

Re: mixed model of artificial and conduction-based cells

maybe we can insert two modules, one for current and the other one for threshold (POINT_PROCESS), but how the latter one will reach the u variable in current module, I don't know....
by rth
Wed Apr 10, 2013 6:03 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 10028

Re: mixed model of artificial and conduction-based cells

yes Bill, because NET_RECEIVE section can exist only in POINT_PROCESS module.
by rth
Wed Apr 10, 2013 5:43 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 10028

Re: mixed model of artificial and conduction-based cells

Well, here is a first shot. Module for current, izhcur.mod TITLE IzhikevichCurrent COMMENT It is a dirty trick for implementation of Izhikevich model as a non-specific current. This mod file treats Izhikevich model as v'=(Iizh(v)+i)/cm where Iizh=e*v^2+f*v+g-u; u is treated as gating variable Do not...
by rth
Wed Apr 10, 2013 11:39 am
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 10028

Re: mixed model of artificial and conduction-based cells

Thank you, Bill. Right now I have a question. You use vv, because v is embedded in standard segment. Why can we not use variable v and i in standard segment for Izh. model? We can rewrite his model as v'=(Izh(v)+I)/c and where Izh(v)=e*v*v+f*v+g+u - is the non-specific current, c is equal 1 and u is...
by rth
Tue Apr 09, 2013 12:07 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 10028

mixed model of artificial and conduction-based cells

I'm trying to make a mixed model, where some multicompartment or single-compartment cells may be arbitrarily replaced by Izhikevich model(39948). Conditions of Izh. model should be the same as for conduction-based cells: the same Exp2Syn synapses, InNp noise current generator and so on. I'm not sure...
by rth
Wed Oct 10, 2012 2:51 am
Forum: Modeling networks
Topic: Simulating intermittent barrage of network activity
Replies: 9
Views: 5804

Re: Simulating intermittent barrage of network activity

Hi Ted, Maybe a little bit off-top. I use NetStim->NetCon->Exp2Syn system to get a barrage of synaptic inputs on distal dendrites of 8 compartments pyramidal cell model. (The code is too long and too simple to post it here) It worked very nice and did what I want until I tried to run simulation with...
by rth
Mon Jun 25, 2012 12:15 pm
Forum: UNIX/Linux
Topic: GUI through SSH connection
Replies: 2
Views: 2630

Re: GUI through SSH connection

Thanks, -isaty works.
by rth
Mon Jun 25, 2012 12:13 pm
Forum: UNIX/Linux
Topic: NEURON installation with Python and MPICH2
Replies: 7
Views: 6227

Re: NEURON installation with Python and MPICH2

Does --enable-shared --enable-sharedlibs=gcc turn on -fPIC flag gcc? I'm not sure. Anyway with CFLAGS="-fPIC" and CXXFLAGS="-fPIC" under 1.4.1 (latest) version on MPICH2 it works good.
by rth
Fri Jun 22, 2012 5:51 pm
Forum: UNIX/Linux
Topic: GUI through SSH connection
Replies: 2
Views: 2630

GUI through SSH connection

We have problem to run nrngui with X11 tunneling. Every user has authorized_keys for connection to nodes without password. if user logs in to node and runs nrngui: $ssh cn0 cn0>nrngui the standard NEURON's menu appears, but if user runs neuron without log in: $ssh cn0 nrngui it can see black square ...
by rth
Fri Jun 22, 2012 1:11 pm
Forum: UNIX/Linux
Topic: NEURON installation with Python and MPICH2
Replies: 7
Views: 6227

Re: NEURON installation with Python and MPICH2

I've solved it. We need to add CFLAGS="-fPIC" and CXXFLAGS="-fPIC" as a parameters for ./configure
by rth
Fri Jun 22, 2012 10:54 am
Forum: UNIX/Linux
Topic: NEURON installation with Python and MPICH2
Replies: 7
Views: 6227

Re: NEURON installation with Python and MPICH2

I have same problem. My OS OpenSUSE 12.1, $uname -a Linux beowolf 3.1.0-1.198-default #1 SMP Thu Nov 3 14:45:45 UTC 2011 (187dde0) x86_64 x86_64 x86_64 GNU/Linux configuration for MPICH2 version 1.4.1p1 $export RSHCOMMAND=ssh; ./configure --prefix=/usr/local/paranrn --enable-f77 --enable-fc --enable...