Search found 57 matches

by RBJ
Sat Sep 30, 2017 11:16 am
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28817

Re: the Qt platform plugin

OK, thanks it actually was an August release I think, but I went for re-install anyway. Naturally I can't run any of my scripts now, so I am making a very fresh start. The banner NOW is: NEURON -- VERSION 7.5 master (6b4c19f) 2017-09-25 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2016 Se...
by RBJ
Sun Aug 27, 2017 3:22 am
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28817

Re: the Qt platform plugin

If you start the bash terminal supplied by the NEURON 7.5 installation, and unset PYTHONHOME and then run nrnpyenv,sh it will print a number of environment variables needed for python to work when launching nrniv. In fact nrnpyenv.sh is automatically run when you start the bash terminal and exports...
by RBJ
Sun Aug 27, 2017 3:05 am
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28817

Re: the Qt platform plugin

Are you able to import neuron from the regular Python prompt? If so, consider that as a work-around; i.e. launch your simulation through python instead of through NEURON. If not, that can be fixed by adjusting your PYTHONPATH and maybe NEURONHOME environment variables. No I'm sorry that doesn't wor...
by RBJ
Mon Aug 21, 2017 3:19 pm
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28817

Re: the Qt platform plugin

Thanks, yes Matplotlib works fine through Python itself (Anaconda2), but exporting those environmental variables did not do the trick. Same error. I am thinking that somewhere among all my environmental variables there is probably a backslash where there should be a forward slash or visa versa? It's...
by RBJ
Wed Aug 16, 2017 5:36 pm
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28817

Re: the Qt platform plugin

So this still doesn't work for me, but I see the

Code: Select all

def Section(name):
  h("create "+name)
  return h.__getattribute__(name)
"trick" illustrated on this very site serves as an alternative. Allowing full use of the Neuron GUI!
by RBJ
Sun Aug 13, 2017 3:21 pm
Forum: MSWin
Topic: the Qt platform plugin
Replies: 20
Views: 28817

the Qt platform plugin

Hello All, I have tended to work in HOC.... but am moving now to Python. I get this error: "This application failed to start because it could not find or load the Qt platform plugin "windows" in "". " ..when I try to run any script that includes from matplotlib import pyplot pyplot.figure(figsize=(8...
by RBJ
Wed Sep 14, 2016 12:15 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Temperature dependence with the Channel Builder
Replies: 7
Views: 10019

Re: Temperature dependence with the Channel Builder

That works beautifully (modifying an existing xpanel with reference to ...the manual). It is superinteractive now.
Thank you very much
by RBJ
Thu Sep 08, 2016 1:31 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Channel Builder Ion Permeability Ratios
Replies: 13
Views: 9698

Re: Channel Builder Ion Permeability Ratios

Yes thank you. My "vtrp" comment/thought was a bit rash. Couldn't see the wood for the trees there. The Zip you uploaded works really well, has corrected this and a few other small errors I made and I am now adapting my code in line with these examples!
Thanks
R.
by RBJ
Wed Sep 07, 2016 6:45 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Channel Builder Ion Permeability Ratios
Replies: 13
Views: 9698

Re: Channel Builder Ion Permeability Ratios

Thank you so much for that Ted! I am downloading now and will thoroughly examine these examples later in the week when I get time. The temperature aspect is indeed key. As for the actual ion movements; GHK approach vs Ohmic with "Vtrp" as the reversal potential, I probably need to think about the bi...
by RBJ
Wed Sep 07, 2016 6:07 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Temperature dependence with the Channel Builder
Replies: 7
Views: 10019

Re: Temperature dependence with the Channel Builder

OK, got this one now I think. With slightly more careful reading of the documentation I see: These functions either execute code contained in an arbitrary, possibly generated-at-runtime string or load code from a file potentially chosen at runtime Therefore I have created a text file with the code f...
by RBJ
Tue Sep 06, 2016 1:04 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Temperature dependence with the Channel Builder
Replies: 7
Views: 10019

Re: Temperature dependence with the Channel Builder

Hello there, This discussion went cold 11 years ago after a successful solution, but may I ask a follow up question. Within the HOC I can easily read temperature, calculate appropriate rate constants and write these to: ChannelBuild[3].aliases.aCO.A=rate That works nicely when I followed those exact...
by RBJ
Mon Sep 05, 2016 10:48 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Channel Builder Ion Permeability Ratios
Replies: 13
Views: 9698

Re: Channel Builder Ion Permeability Ratios

Hi All, I think I have solved this issue now. To avoid any charge balance issues and timestep delays (discussed above). I now created a non-specific ion kschannel with chosen TRP Vrev and gmax of zero . Now the simulated mixed permeability "trp" channel merrily gates according to the various transit...
by RBJ
Wed Aug 31, 2016 7:33 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Channel Builder Ion Permeability Ratios
Replies: 13
Views: 9698

Re: Channel Builder Ion Permeability Ratios

Small update; I have created the channel "tedeq" with permeability for eq valence 2, equilibrium potential +50mV. I've created a mechanism (NMODL) that is supposed to translate this to an ica in the first instance simply returning ica=ieq, then I was going to develop that later. Charge balance issue...
by RBJ
Tue Aug 30, 2016 7:21 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Channel Builder Ion Permeability Ratios
Replies: 13
Views: 9698

Re: Channel Builder Ion Permeability Ratios

Thank you very much indeed. A little more background in case other viewers are wondering what I am up to with single channel building/modelling. We are recording and modelling TRP channel expressing neurones, and ultimately aim to include temperature, osmolarity and calcium feedback regulation, in a...
by RBJ
Mon Aug 29, 2016 6:16 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Channel Builder Ion Permeability Ratios
Replies: 13
Views: 9698

Re: Channel Builder Ion Permeability Ratios

Thank you very much for that Ted. . . I'll investigate this approach. I think that probably the IV relationship is surprisingly linear, as you suggested (I have data on this at my office). I do need to track ca movement though. I will experiment some more.
Thanks again
Richard