Search found 12 matches

by BBAmp
Wed Jun 29, 2011 9:43 am
Forum: Other questions
Topic: Checkpointing
Replies: 2
Views: 1088

Re: Checkpointing

excellent.
by BBAmp
Tue Jun 28, 2011 2:22 pm
Forum: Other questions
Topic: Checkpointing
Replies: 2
Views: 1088

Checkpointing

Hello, I haven't seen this question asked in any relevant forum. My lab has a NEURON simulation that consumes a little too much RAM and I was wondering if it is possible to save the values of all state variables at a particular time and restart the simulation with exactly those values. Thank you, -Y...
by BBAmp
Thu Nov 18, 2010 12:48 pm
Forum: NEURON + Python
Topic: Raster plots in Python
Replies: 5
Views: 6678

Re: Raster plots in Python

This documentation is for plotting raster plots ONLY. Please refer to the online documentation of pylab, NEURON, and Python to learn more about plotting NEURON/Python data. 1. Python Raster Plots for NEURON/Python Simulations This section assumes all your cells and parameters have been initialized i...
by BBAmp
Tue Nov 16, 2010 7:03 pm
Forum: NEURON + Python
Topic: Raster plots in Python
Replies: 5
Views: 6678

Re: Raster plots in Python

Hello, Thank you for your replies. I took a similar approach to what you suggested and figured out what was wrong. My project currently involves taking a simulation coded entirely in NEURON and graph all output in python. It turns out I was pointing the netcon object to h.PM .soma(.5)._ref_v (where ...
by BBAmp
Thu Oct 28, 2010 12:26 pm
Forum: NEURON + Python
Topic: Raster plots in Python
Replies: 5
Views: 6678

Raster plots in Python

Hello, Is is possible to create a raster plot of a network of cells using pylab the same way I can record and create a graph of the membrane potentials of cells? I've tried following the syntax used in the NEURON documentation to the best of my ability: tobj = h.NetCon(h.PM[0].soma(.5)._ref_v, h.nil...
by BBAmp
Wed Aug 18, 2010 1:07 pm
Forum: NEURON + Python
Topic: Changing custom channel parameters through Python
Replies: 10
Views: 6130

Re: Changing custom channel parameters through Python

Great, that will prove to be very useful.

Thanks for the help!

-Youngmin
by BBAmp
Mon Aug 16, 2010 3:20 pm
Forum: NEURON + Python
Topic: Changing custom channel parameters through Python
Replies: 10
Views: 6130

Changing custom channel parameters through Python

Hello, I understand the syntax for assigning values to an "internal" object like a soma is something like: for seg in soma: seg.hh.gnabar = 0.11 to change the gnabar of hh. I am currently trying to do something similar for a parameter defined in an ses file. I have a soma defined through Python (som...
by BBAmp
Mon Apr 05, 2010 2:05 pm
Forum: NEURON + Python
Topic: Mining Code from Channel Builder
Replies: 7
Views: 2928

Re: Mining Code from Channel Builder

Thank you very much for your help. After a little more tweaking I have been able to get the results I wanted.

-YMP
by BBAmp
Sat Apr 03, 2010 1:35 pm
Forum: NEURON + Python
Topic: Mining Code from Channel Builder
Replies: 7
Views: 2928

Re: Mining Code from Channel Builder

Hi again, Is there a way to change the values set by the ses files through python? For example if I created a denisty mechanism called A where the default gmax is 0.1. I then insert the mechanism into the python defined soma with h('insert A') and verify that it indeed exists in the python soma with...
by BBAmp
Fri Apr 02, 2010 6:00 pm
Forum: NEURON + Python
Topic: Mining Code from Channel Builder
Replies: 7
Views: 2928

Re: Mining Code from Channel Builder

OS: Linux Mint Version: NEURON 7.1 Python version: 2.6.2 I double checked the mechanisms and they are indeed density mechanisms. According to psection the mechanisms were placed properly but I am still not getting the results I am looking for. I am starting to think I am not using the NetCon command...
by BBAmp
Sun Mar 28, 2010 8:44 pm
Forum: NEURON + Python
Topic: Mining Code from Channel Builder
Replies: 7
Views: 2928

Re: Mining Code from Channel Builder

Thank you for your reply. I was able to load the ses file but when I tried to insert one of my mechanisms with the command soma.insert('A') it says A is not a density argument name. I've also tried creating a soma in hoc using h('create soma') and tried h.soma.insert('A') but I got the the same erro...
by BBAmp
Fri Mar 26, 2010 2:53 pm
Forum: NEURON + Python
Topic: Mining Code from Channel Builder
Replies: 7
Views: 2928

Mining Code from Channel Builder

Hello, I am currently working on translating a NEURON model into Python and I would like to know if there is a way to get Channel Builder info/code from the GUI into something Python can use. I know how to get the hoc code as well as a text file info of the channel density mechanisms specified by ch...