Search found 41 matches

by bremen
Tue Dec 12, 2017 11:01 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 12340

Re: Spike source and target sections

Where exactly did you change the label 'soma' to 'soma_C''? in the original imported file? in the netpyne netParams? I just tried replacing 'soma' with 'soma_C' in another example, and worked ok. So it might be that you are not replacing the label consistently, or some other bug. Feel free to send ...
by bremen
Sat Dec 09, 2017 8:15 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 12340

Re: Spike source and target sections

I have found a strange behavior with the somatic section. I have imported the C_cell population and placed some synapses directly on the soma, as seen in experiments. It generates no errors if the C_cell template somatic section is named 'soma'. If i change that to 'soma_C' or any other combination,...
by bremen
Fri Dec 08, 2017 7:55 am
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 5730

Netpyne on clusters

Hi I've been using, for last two months, a Julich cluster, based on "knight landing" (Xeon Phi) CPUs, in which i have created a virtual env, to contain all pythons modules and a locally compiled NEURON installation, as a Python module too. Doing "from netpyne import specs, sim" generates and import ...
by bremen
Fri Dec 08, 2017 6:10 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 12340

Re: Spike source and target sections

Thank you. After defining some custom code for the connectivity to be passed to 'connList', everything runs great, in a small scale net of 40 neurons. I'll have to add another neuronal type but my AMD 1800x is starting to be too small for the scale i need to reach. I have tried to install netpyne, o...
by bremen
Wed Dec 06, 2017 5:13 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 12340

Re: Spike source and target sections

'synsPerConn' solved the problem. Thank you. To complete this part i have a last question: 1) {'preConds': {'pop': 'A_pop'}, 'postConds': {'pop': 'B_pop'} Is it possibile to define a certain member of the A_pop to connect to a certain member of B_pop? A_pop = 5cells and B_pop = 5cells For example to...
by bremen
Mon Dec 04, 2017 7:38 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 12340

Re: Spike source and target sections

My bad. I changed the numbering scheme in my main trunk, instead of changing it in the branch i am using for these tests. Now it reports: "Number of connections on node 3: 5" For the moment, there are 5 cellA to each cellB even thou the final connectivity will be 1:1. I can see a very small variatio...
by bremen
Fri Dec 01, 2017 3:45 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 12340

Re: Spike source and target sections

Hi Salvador. Thank you. I tried your suggestions but i get a "list index out of range": synMechs = [self.addSynMech(synLabel=params['synMech'], secLabel=synMechSecs[i], loc=synMechLocs[i]) for i in range(synsPerConn)] IndexError synMechs = [self.addSynMech(synLabel=params['synMech'], secLabel=synMec...
by bremen
Mon Nov 27, 2017 4:53 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 12340

Re: Spike source and target sections

Hi Salvador, thank you. 1) I have added the axonal section to the "cellRule" and recorded a voltage trace from it. It works perfectly. 2) Based on the tutorial i was able to set a "synMechParams" for an AMPA syn mechanism and a "connParams": netParams.connParams['A_pop->B_pop'] = {'preConds': {'pop'...
by bremen
Sat Jun 03, 2017 4:16 pm
Forum: Parallel NEURON
Topic: How to build network model for coreNeuron 
Replies: 24
Views: 25647

Re: How to build network model for coreNeuron 

I have done more testing. The code of my previous post is fine. The problem was that, the other two models, generated no spikes in Coreneuron. In both models i have tables in the mods and i just discovered that, if not specified in the code, they are active by default. This explaine the absence of s...
by bremen
Sat Jun 03, 2017 8:51 am
Forum: Parallel NEURON
Topic: How to build network model for coreNeuron 
Replies: 24
Views: 25647

Re: How to build network model for coreNeuron 

Hi. I have expanded my test network with three different cell types (python/Neuron implementation), linked to specific parts of the gidlist list. In pseudo code: for i in gidlist: if gid < x: append.Celltype1 elif gid > x and <y: append.Celltype2 else: append.Celltype3 I have no issues recording spi...
by bremen
Wed Apr 26, 2017 7:54 am
Forum: Parallel NEURON
Topic: How to build network model for coreNeuron 
Replies: 24
Views: 25647

Re: How to build network model for coreNeuron 

Hello. I have done the installation of Coreneuron, following the tutorial on the official github, and, when i run ringtest, everything is fine. Then i modified ringtest, with one of my models, and tested it in parallel. With NEURON and MPI on 4 cores, it runs correctly and the results are valid. The...