Search found 58 matches

by salvadord
Mon Jan 15, 2018 11:05 am
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 9
Views: 7454

Re: VERSION RELEASES

# Version 0.7.6 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.6 - Added option to order raster spike trains by multipe tags (eg. ['pop', 'y']) - Enable providing a 2D list of spike times to VecStim populations - Added exception handling to analysis functions - Updated saveLoadV1 examples...
by salvadord
Wed Dec 13, 2017 10:26 am
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 1336

Re: Netpyne on clusters

try adding this at the top of the main script you are calling:

Code: Select all

import matplotlib; matplotlib.use('Agg')
by salvadord
Tue Dec 12, 2017 10:37 am
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 1336

Re: Netpyne on clusters

Seems like there is some issue with matplotlib -- can you import it by itself outside of netpyne?

You can use the command line option '-nogui' (this sets netpyne.__gui__ to False) to avoid importing graphic-related modules -- but you won't be able to use the most analysis functions.
by salvadord
Tue Dec 12, 2017 10:33 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 14
Views: 4169

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 m...
by salvadord
Tue Dec 12, 2017 10:11 am
Forum: NetPyNE
Topic: Bug in plasticity option
Replies: 1
Views: 977

Re: Bug in plasticity option

You can find the stdp.mod file here: https://github.com/Neurosim-lab/netpyne ... m/stdp.mod

let me know if that works
by salvadord
Wed Dec 06, 2017 3:19 pm
Forum: NetPyNE
Topic: plotRatePSD
Replies: 1
Views: 2176

Re: plotRatePSD

Andrew, The issue was due to a bug introduced in a recent change to plotRatePSD(). I have fixed it and pushed to the 'development' github branch of netpyne. It will be released in next version. You can use it now by cloning this github branch. Alternatively, you can just pass a dict with the color f...
by salvadord
Wed Dec 06, 2017 3:12 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 14
Views: 4169

Re: Spike source and target sections

Yes, you can select any arbitrary conn pattern using the 'connList' argument: http://neurosimlab.org/netpyne/referenc ... vity-rules
by salvadord
Mon Dec 04, 2017 10:58 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 14
Views: 4169

Re: Spike source and target sections

With a probability of 1, you should be getting Npre*Npost connections, where Npre,Npost is the number of cells in the presyn,postsyn populations. If you only got 5 conns, it might be you have Npre=5, Npost=1 ? Also, if you want more that 1 synapse per connection use the 'synsPerConn' argument -- see...
by salvadord
Sun Dec 03, 2017 9:13 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 14
Views: 4169

Re: Spike source and target sections

Perhaps the cell is not being imported correctly and those sections don't exist?

Can you share your full code? Either as a link to a repo (eg. github) or zip file to salvadordura@gmail.com

Thanks
by salvadord
Sun Dec 03, 2017 3:17 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 9
Views: 7454

Re: VERSION RELEASES

# Version 0.7.5 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.5 - Improved NeuroML conversion support - Make cfg.checkErrors = True by default, but set to False if using multiple cores or batch - Added methods to rename netParams dict keys in a nested format (needed for GUI) - Added anal...
by salvadord
Tue Nov 28, 2017 10:13 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 14
Views: 4169

Re: Spike source and target sections

Stefano, The sections must exist in the cell rule in order to be able to connect to them. But if you are importing an existing cell I assume these section will already exist. To target these sections in the connParams rule, you can just use a list of strings e.g. netParams.connParams['A_pop->B_pop']...
by salvadord
Tue Nov 28, 2017 10:01 am
Forum: NetPyNE
Topic: Error: sec had previously been connected to parent sec
Replies: 1
Views: 3078

Re: Error: sec had previously been connected to parent sec

Hi Sergio, Just remove the line: netParams.cellParams['goc'] = goc_cellRule When you use the importCellParams() it already stores the imported rule in netParams, in this case in netParams[‘Golgi_2007’] (since label=‘Golgi_2007’). Therefore you were duplicating the cell rule by storing it in cellPara...
by salvadord
Tue Nov 28, 2017 10:00 am
Forum: NetPyNE
Topic: Error: sec had previously been connected to parent sec
Replies: 1
Views: 3078

Error: sec had previously been connected to parent sec

Received by email: "Hello Salvador, I get this message when I use importCellParams: Notice: <netpyne.cell.CompartCell object at 0x7f74a36621d0>.dend_2(0) had previously been connected to parent <netpyne.cell.CompartCell object at 0x7f74a36621d0>.soma(1) Here's the code: goc_cellRule = netParams.impo...
by salvadord
Mon Nov 27, 2017 12:20 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 14
Views: 4169

Re: Spike source and target sections

Hi Stefano, Thanks for for your question, and for trying out NetPyNE. Yes, it is possible to do what you are asking: 1) you can set the source of the action potential by simply adding the 'spikeGenLoc' ("spike generation location") to that section in the cell rule; e.g. say you want it at a section ...
by salvadord
Mon Nov 27, 2017 12:03 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 14
Views: 4169

Spike source and target sections

Question received by email: "Hi Salvador. I have just started using your Netpyne framework, to test the possibility to build a network with "particular characteristics". I was able to import two of my Python/neuron HH models and to define the code to see their basic behaviour, with or without a curr...