Search found 19 matches

by cafischer
Wed Feb 07, 2018 4:34 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Direction of current in point process
Replies: 2
Views: 1378

Re: Direction of current in point process

Thanks a lot!
I found this mechanism 3 years ago, so I don't remember where I found it (I guess on modeldb). Could well be that it is already fixed now.
by cafischer
Tue Feb 06, 2018 3:43 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Direction of current in point process
Replies: 2
Views: 1378

Direction of current in point process

I am using a model for an Ornstein-Uhlenbeck Process (see below). It is defined as a point process. What does this imply regarding the direction of current? Is i > 0 depolarizing the cell, so that the equation for a one-compartment model would be c_m dV/dt = -I_ion + I_syn or is it - I_syn? INDEPEND...
by cafischer
Fri Dec 01, 2017 3:28 am
Forum: Getting started
Topic: Dynamic clamp?
Replies: 9
Views: 11665

Re: Dynamic clamp?

I think we misunderstood. I want to use the SEClamp as a conductance clamp. So I should play my time dependent conductance g(t) into SEClamp.rs, right? But then I did not know how to set the reversal potential of the, as synapse abused, SEClamp. ------------------------------------------------------...
by cafischer
Thu Nov 30, 2017 11:07 am
Forum: Getting started
Topic: Dynamic clamp?
Replies: 9
Views: 11665

Re: Dynamic clamp?

So if the SEClamp replaces: i = g * (v - e) then rs is the equivalent for 1/g. But what is the equivalent for e. How can I set that in the SEClamp? --------------------------------------------------------------------------------------------------------------------------------------------------------...
by cafischer
Wed Jul 12, 2017 3:28 am
Forum: Modeling networks
Topic: Bug in Exp2Syn?
Replies: 2
Views: 5759

Bug in Exp2Syn?

When I was playing around with synapses in a neuron model, I figured out that the start of current change in Exp2Syn is delayed by 1 time step (which is not the case in ExpSyn). See the code below for a minimal example. I found this behavior strange and found out that A and B in Exp2Syn already chan...
by cafischer
Fri Jun 02, 2017 6:05 am
Forum: UNIX/Linux
Topic: Bug: CVode - stdrun.hoc - tstop
Replies: 1
Views: 8336

Bug: CVode - stdrun.hoc - tstop

When loading stdrun.hoc before declaring and setting CVode to 1 the simulation will not run until tstop but stop at some earlier point. However when reversing the order everything is fine and the simulation stops at tstop. In the documentation it says that a cvode will be created when loading stdrun...
by cafischer
Thu Jun 01, 2017 6:19 am
Forum: Other questions
Topic: Injecting any kind of current under adaptive integration
Replies: 1
Views: 4378

Injecting any kind of current under adaptive integration

Injecting any kind of current works very well when the time steps are fixed. You can just play a vector of the current into an IClamp. However, when using adaptive integration the best you can do is to turn continuous on and you will have a linear interpolation of your discrete current. But is there...
by cafischer
Mon Mar 07, 2016 3:35 am
Forum: Other questions
Topic: How to access and plot derivatives of variables?
Replies: 9
Views: 6116

Re: How to access and plot derivatives of variables?

I am still not 100% sure what icap is. I made a test with a single-compartment model where I compared icap with the negative sum of all ionic currents plus the injected current and found that there where differences between those two which reduced with increasing step size. This suggests that icap i...
by cafischer
Fri Mar 04, 2016 5:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: What does cnexp do?
Replies: 4
Views: 7014

Re: What does cnexp do?

I would like to learn more about the the integtrators that are used within cnexp in a fixed time step simulation. So if the user does not set manually secondorder = 0, then gating variables of ion channels are always computed analytically (using symbolic manipulation software)? When won't they be co...
by cafischer
Wed Mar 02, 2016 6:13 am
Forum: Adding new mechanisms and functions to NEURON
Topic: What does cnexp do?
Replies: 4
Views: 7014

What does cnexp do?

I could not find a description or reference of the cnexp method in the NEURON documentation and the NEURON book. I would like to know which method it is (equations, reference). All the source code is at your disposal, but here is a brief summary. I like to think of cnexp as more of a "directive" fo...
by cafischer
Wed Feb 24, 2016 9:53 am
Forum: Getting started
Topic: time shift in SEClamp
Replies: 5
Views: 6503

Re: time shift in SEClamp

Thanks for the elaborate explanations! I was thinking about the last part again. I said that: I want to know the current flowing through a certain ion channel inserted in the membrane in response to a given membrane potential ideally resembling the clamped potential. As you explained that the SEClam...
by cafischer
Mon Feb 08, 2016 9:51 am
Forum: Getting started
Topic: time shift in SEClamp
Replies: 5
Views: 6503

Re: time shift in SEClamp

As I understand it know without ion channels the equation is cm * dV/dt = i_clamp = (V_clamp - Vm) / R_clamp Assuming you use the forward-Euler (V_new = V_old + dV/ dt * dt) for the integration (which is not the case in NEURON) then: V_new = V_old + (V_clamp - V_old) * dt / (cm * R_clamp) = dt/(cm*R...
by cafischer
Fri Feb 05, 2016 8:50 am
Forum: Getting started
Topic: time shift in SEClamp
Replies: 5
Views: 6503

time shift in SEClamp

I played a vector into a SEClamp and then recorded the membrane potential to see whether it matches the played vector but it did not. Firstly the beginning can be quite different if v_init does not match the first value in the played vector. But also the second value still did not match. Secondly, a...
by cafischer
Fri Feb 05, 2016 4:23 am
Forum: Other questions
Topic: Check the cable equation
Replies: 3
Views: 2092

Re: Check the cable equation

I think you mean this place where I used numpy magic: icap_from_v = np.concatenate((np.array([0]), np.diff(v)/np.diff(t))) * Cm In a for loop this would be: icap_from_v = np.zeros(len(v)) for i in range(1, len(v)): icap_from_v[i] = (v[i] - v[i-1]) / (t[i] - t[i-1]) * Cm But I don't know how to make ...
by cafischer
Thu Feb 04, 2016 12:20 pm
Forum: Other questions
Topic: Check the cable equation
Replies: 3
Views: 2092

Check the cable equation

I wanted to check the cable equation implemented in NEURON which says that: cm * dV/dt - I_inj = - sum(i_ion) (ignoring axial currents) The following code is a minimal example of doing this whereby I computed the left hand side of the equation in two different ways: from neuron import h import numpy...