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.

## Search found 19 matches

- 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**

- 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...

- 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. ------------------------------------------------------...

- 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? --------------------------------------------------------------------------------------------------------------------------------------------------------...

- 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...

- 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...

- 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...

- 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...

- 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...

- 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...

- 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...

- 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...

- 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...

- 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 ...

- 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...