Search found 54 matches

by oren
Thu Jan 30, 2014 12:37 pm
Forum: Other questions
Topic: Is it possible to know if a section is in sectionlist
Replies: 7
Views: 1870

Re: Is it possible to know if a section is in sectionlist

Is it possible to know if a section is in sectionlist? One problem with your code is that it corrupts the section list that you are trying to test. sl.append() ensures that n1 will be >=1, so if n1==0{ sl.remove()} is guaranteed to fail to remove the appended section. Another problem is that it won...
by oren
Wed Jan 29, 2014 7:54 pm
Forum: Other questions
Topic: Is it possible to know if a section is in sectionlist
Replies: 7
Views: 1870

Is it possible to know if a section is in sectionlist

Is it possible to know if a section is in sectionlist? For example soma{ print = sectionlist.in()} What I managed to do is sl = new SectionList() soma { sl.append() n1 = sl.unique() if n1==0{ sl.remove()} } Then id n1>0 I know that the section was in the sectionlist. Is this method good? Is there an...
by oren
Wed Jan 22, 2014 4:25 am
Forum: Parallel NEURON
Topic: ParallelNetManager Example does not work
Replies: 4
Views: 7183

Re: ParallelNetManager Example does not work

Thank you Ted, I removed the lines : pnm.pc.runworker pnm.pc.done But it still does not work,Same error Code... And as I mention the code work on the old cluster. But I forgot to mention that the old cluster runs NEURON -- VERSION 7.3 (728:52f3a2a66b5f) 2012-08-17 And the new cluster runs NEURON -- ...
by oren
Mon Jan 20, 2014 10:40 am
Forum: Parallel NEURON
Topic: ParallelNetManager Example does not work
Replies: 4
Views: 7183

Re: ParallelNetManager Example does not work

I managed to advance in finding what the problem is. I tired to run the simulation each time with different number of nodes/cell's mpiexec -n $NSLOTS ${NRNIV} -mpi -c "{ncell=$NSLOTS}" bstest.hoc NSLOTS = [4,8,12,20,25,35,45,60,80,90,100,120,123] In our cluster there are 228 nodes. It seems that the...
by oren
Sun Jan 19, 2014 9:25 am
Forum: Getting started
Topic: Record current
Replies: 7
Views: 3901

Re: Record current

Follow up question: If I want to record the current passing from 1 segment to the other. Is it possible? Example: I have a dendrite with 3 segments, And I want to know how to record the current the 2th segment received from the 3rd segment and the current the 2nd segment received from the 1th segmen...
by oren
Sun Jan 19, 2014 7:13 am
Forum: Parallel NEURON
Topic: ParallelNetManager Example does not work
Replies: 4
Views: 7183

ParallelNetManager Example does not work

Hello, We have a new cluster in our lab, and it seems to work with some parallel code. But fail's with other codes: For example, when I try to run this example: http://www.neuron.yale.edu/neuron/static/new_doc/modelspec/programmatic/network/parnet.html#ParallelNetManager load_file("stdrun.hoc") tsto...
by oren
Sun Dec 29, 2013 3:39 am
Forum: Getting started
Topic: Fano factor
Replies: 4
Views: 5746

Re: Fano factor

Thank You Ted. I have fixed the code to get so now it give the right results. // Test Fano factor objref syn, sti , con, Vec, Vec1, hist create soma insert pas Vec = new Vector() syn = new Exp2Syn(0.5) sti = new NetStim(0.5) sti.interval = 100 sti.start = 10 sti.number = 500000 sti.noise = 1 con = n...
by oren
Wed Dec 25, 2013 8:37 am
Forum: Getting started
Topic: Fano factor
Replies: 4
Views: 5746

Fano factor

Hello, I am trying to see if the synaptic events that are created from netstim with noise=1 have a Fano Factor http://en.wikipedia.org/wiki/Fano_factor of 1 (as should be for a Poisson distribution) This is my code // Test Fano factor objref syn, sti , con, Vec, Gra, Vec1 create soma insert pas Vec ...
by oren
Mon Nov 11, 2013 4:27 pm
Forum: Getting started
Topic: Help in understanding the terms in a code
Replies: 3
Views: 2321

Re: Help in understanding the terms in a code

Hello ram, g = new Graph() // create a new graph ( like figure in matlab) addplot(g, 0) // add the graph to the graphList[0] so it will be updated each run. g.size(0,tstop,-100,100) // sets the axis limits .size(xstart, xstop, ystart, ystop) g.addvar("soma.v(x)",3,2) // (.., color_index, brush_index...
by oren
Thu Oct 24, 2013 9:26 am
Forum: Getting started
Topic: start GUI with graph that contain many variables
Replies: 1
Views: 1335

start GUI with graph that contain many variables

Hello, I'm trying to investigate a model form modeldb. The model contain a network of cells. I want to do the investigation with the GUI, and I'm trying to plot in a graph the voltage of all the neruon's soma's. I can just start Neuron and do Graph/Voltage axis... and add all cells soma's. but this ...
by oren
Thu Oct 24, 2013 9:07 am
Forum: Getting started
Topic: floor and ceil function
Replies: 2
Views: 1771

Re: floor and ceil function

Ted,
Thank you
by oren
Wed Oct 23, 2013 3:21 am
Forum: Getting started
Topic: floor and ceil function
Replies: 2
Views: 1771

floor and ceil function

Hello, Is there a floor and ceil function in neuron? I know that I can use int for floor function , but what about ceil? ( I can not do floor + 1 because sometimes I can get a int number) I notice that in NMOD http://www.neuron.yale.edu/neuron/static/docs/nmodl/nmodlfunc.html there are ceil and floo...
by oren
Tue Aug 13, 2013 2:58 am
Forum: Getting started
Topic: forsec ... stack empty
Replies: 2
Views: 2547

Re: forsec ... stack empty

Thank You Ted, Now I understand.

This is my new code and it work.

Code: Select all

objref Leaff
Dist = new Vector()
forsec terminals {
   Leaff = new SectionRef()
         while (Leaff.has_parent){
      Leaff.sec { ...CODE... }
      Leaff.parent {
                Leaff = new SectionRef
}
                
}
}

by oren
Mon Aug 12, 2013 9:50 am
Forum: Getting started
Topic: forsec ... stack empty
Replies: 2
Views: 2547

forsec ... stack empty

Hello, I have a neuron model and I am trying to get the route from each leaf ( terminal ) to the routh. First I use this code to get a list of all terminals objref tree tree = new SectionList() soma[0] distance() soma[0] tree.wholetree() objref terminals, thisone terminals = new SectionList() forsec...
by oren
Mon Jul 01, 2013 4:31 am
Forum: Getting started
Topic: pause function
Replies: 3
Views: 3827

Re:

No, but you can fake it with startsw(). proc pause() { local t0 t0 = startsw() while (startsw()-t0 < $1) { } } Normally in Matlab I use the pause option, so that I can plot with delay multiplay graphs on the same plot. and see them add to the graph one by one in 0.5 s interval( Each 0.5s new one ad...