Search found 5416 matches

by ted
Thu Feb 21, 2019 10:51 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How to change parameter used in NMODL for channel kinetics in hoc
Replies: 5
Views: 60

Re: How to change parameter used in NMODL for channel kinetics in hoc

From the problem you're having, it's clear that you haven't read The NEURON Book, so let me start by suggesting two papers for you to read. One is The NEURON simulation environment which we published in Neural Computation (NOT the paper with the same title that was published in Arbib's book). The ot...
by ted
Wed Feb 20, 2019 9:33 am
Forum: Optimization
Topic: Optimizing PROCEDURE equations in mod files
Replies: 5
Views: 5716

Re: Optimizing PROCEDURE equations in mod files

I don't think I have that mod file on this machine. No matter; a better example is hh.mod, which you will find in NEURON's source code under nrn/src/nrnoc
by ted
Wed Feb 20, 2019 1:06 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How to change parameter used in NMODL for channel kinetics in hoc
Replies: 5
Views: 60

Re: How to change parameter used in NMODL for channel kinetics in hoc

How do you know that you changed the value of any particular parameter. Pick one, show me the hoc statement(s) you used to change it, and show me the hoc statement(s) that confirm that you actually changed it.
by ted
Tue Feb 19, 2019 11:11 am
Forum: Hot tips
Topic: Turning adaptive integration ("CVODE") on and off
Replies: 3
Views: 9108

Re: Turning adaptive integration ("CVODE") on and off

cvode_active() follows the longstanding convention that 1 means True or On, 0 means False or Off
by ted
Mon Feb 18, 2019 2:35 pm
Forum: Getting started
Topic: How to read multiple data values into an array
Replies: 1
Views: 41

Re: How to read multiple data values into an array

You might find it easier to set up arrays with Python. Whether you are or aren't already familiar with Python, you might consider learning about both Python and NEURON by working through this tutorial https://neuron.yale.edu/neuron/static/docs/neuronpython/index.html . If you prefer to stick with ho...
by ted
Mon Feb 18, 2019 11:16 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 6888

Re: Driving synaptic event using vecStim

I should update vecstim.mod to make it compatible with CoreNEURON. The file distributed with NEURON is called vecevent.mod, even though it defines the properties of an ARTIFICIAL_CELL class called VecStim. Among my own files, I find something called vecstim.mod from 2002, the source code for which ...
by ted
Tue Feb 12, 2019 11:47 am
Forum: Other questions
Topic: Segmentation Fault when calling BBSaveState.save_test()
Replies: 3
Views: 242

Re: Segmentation Fault when calling BBSaveState.save_test()

Sorry this response took such a long time. I decided to start with a parallelized network model that is known to work--specifically, ringpar.hoc, which implements the parallelized model of the ring network in Hines ML, Carnevale NT (2008) Translating network models to parallel hardware in NEURON J. ...
by ted
Mon Feb 11, 2019 2:32 pm
Forum: NEURON + Python
Topic: Optimizing single cells programmatically
Replies: 3
Views: 108

Re: Optimizing single cells programmatically

If their workflow doesn't require actual fiddling with the old InterViews-based graphical interface, the code should work even on hardware that doesn't have a graphical interface, or under an OS that doesn't have its own GUI--the non-gui objects, variables, methods etc. will still work and be fully ...
by ted
Mon Feb 11, 2019 2:09 pm
Forum: OS X
Topic: Trouble Compiling Mod2 Files on Virtual Environment
Replies: 1
Views: 96

Re: Trouble Compiling Mod2 Files on Virtual Environment

How are you "importing neuron"? Exactly what code did you execute?
by ted
Mon Feb 11, 2019 2:05 pm
Forum: NEURON + Python
Topic: Optimizing single cells programmatically
Replies: 3
Views: 108

Re: Optimizing single cells programmatically

they use NEURON's MultipleRunFitter tool with the GUI (in HOC). I would like to do this step entirely using Python as the interpreter Did they really? Actually use the MRF's graphical user interface? Or did they just create an instance of a class, then call that class's methods from Python? After b...
by ted
Wed Feb 06, 2019 10:35 pm
Forum: Other questions
Topic: See what a vector is recording from ?
Replies: 3
Views: 157

Re: See what a vector is recording from ?

The Vector class documentation mentions no such method because there isn't one. At the present time, the only way to discover what variable a Vector might be recording is to analyze the model's instrumentation code yourself. Start with
grep record *hoc
or
grep record *py
by ted
Wed Feb 06, 2019 10:31 pm
Forum: Modeling networks
Topic: Is there any network model using extracellular mechanism in simulating DBS
Replies: 1
Views: 92

Re: Is there any network model using extracellular mechanism in simulating DBS

I am not aware of any published modeling studies of extracellular stimulation of networks in which the target of the simulation was a network model. That doesn't mean that no such papers exist.
by ted
Sun Feb 03, 2019 1:28 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 233

Re: eca calculation

For the benefit of others who may read this-- hines points out that the model setup code in demofit1.hoc executes forall if(ismembrane("ca_ion")) { . . . ion_style("ca_ion",0,1,0,0,0) . . . } after a calcium channel mechanism has been inserted into the soma. This overrides the "automatic ion_style" ...
by ted
Fri Feb 01, 2019 6:40 pm
Forum: Hot tips
Topic: Driving a synapse with recorded or precomputed spike events
Replies: 7
Views: 8089

Re: Driving a synapse with recorded or precomputed spike events

I could not find a manual for VecStim VecStim isn't mentioned in the Programmer's Reference because, unlike NetStim, it's not a built-in feature of NEURON--even though its source file vecevent.mod is included in an "examples" subdirectory that is packaged with NEURON's source code (which is all the...
by ted
Fri Feb 01, 2019 5:06 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 233

Re: eca calculation

Correction to my post from 1/31-- cai is a state, and its value is initialized in cad.mod. so b2 b1 b0 should be 1 1 1 and the 7 bit number is 1 1 1 0 1 1 1 So why does ion_style"ca_ion") return 1 0 0 0 1 0 0 0 ? According to that value, eca is NOT recalculated at every advance, eca is NOT calculate...