Search found 6036 matches

by ted
Thu Aug 11, 2022 9:58 pm
Forum: NEURON + Python
Topic: POINTER is not thread safe
Replies: 6
Views: 161

Re: POINTER is not thread safe

I was not able to open the links you shared in the previous thread Hmm, the Forum automatically (and incorrectly) "promoted" those to incorrect URLs. I have now revised that post. Alternatively, you could try modeldb.science/3815 and modeldb.science/3264 entered into your browser's URL fi...
by ted
Wed Aug 10, 2022 7:28 pm
Forum: NEURON + Python
Topic: POINTER is not thread safe
Replies: 6
Views: 161

Re: POINTER is not thread safe

The sample mod file provided has several fatal problems. non-Ascii character in line 42 This is trivially easy to fix; unfixed, it could cause a lot of trouble. Has it been resolved? Strong hint: stick with the ASCII character set until this particular limitation of NMODL code has been resolved. The...
by ted
Wed Aug 03, 2022 2:34 pm
Forum: NEURON + Python
Topic: mechanisms written in python?
Replies: 5
Views: 104

Re: mechanisms written in python?

AG synthesis? arachidonoylglycerol? The best way to do this depends on the details of your conceptual model for what's going on. Presumably you have already expressed your conceptual model in the form of a reaction scheme or mathematical equations. My question at this point is: what aspects of your ...
by ted
Wed Aug 03, 2022 11:42 am
Forum: NEURON + Python
Topic: mechanisms written in python?
Replies: 5
Views: 104

Re: mechanisms written in python?

is it in principle possible to have a network where some of my mechanisms are given as mod files while others are written in python? In principle, with software all things are possible. Do everything with Python. Or with C or C++. Or assembly language. Then you'll have complete liberty to do anythi...
by ted
Tue Aug 02, 2022 10:38 am
Forum: NEURON + Python
Topic: mechanisms written in python?
Replies: 5
Views: 104

Re: mechanisms written in python?

Python is slow. NMODL code is compiled to produce binary libraries which execute orders of magnitude faster. Read Hines, M.L. and Carnevale, N.T. Expanding NEURON's Repertoire of Mechanisms with NMODL. Neural Computation 12:995-1007, 2000. or, better, download and read the "expanded preprint&qu...
by ted
Tue Jul 26, 2022 11:14 pm
Forum: NEURON + Python
Topic: Recording synaptic currents
Replies: 4
Views: 151

Re: Recording synaptic currents

Suppose foo is an instance of the GABAa class that was created by the statement foo = h.GABAa(dend3(0.5)) # attaches an instance of GABAa to the segment of dend3 that contains location 0.5 Then foo.i is the Python name for the current generated by foo. If you want to record the time course of foo.i ...
by ted
Mon Jul 25, 2022 11:38 pm
Forum: NEURON + Python
Topic: Recording synaptic currents
Replies: 4
Views: 151

Re: Recording synaptic currents

The key to measuring something is to know what it is called. Actually you've got it half right. Your syntax is correct. The problem is, there's no such variable as target.soma(0.5)._ref_i that is, for any given segment seg, seg.i does not exist. I know nothing about your synaptic mechanisms, so I do...
by ted
Wed Jul 20, 2022 6:28 pm
Forum: OS X
Topic: Can't Load .mod files in Python Script
Replies: 4
Views: 84

Re: Can't Load .mod files in Python Script

That works for now, on a particular hardware platform with a particular directory structure. But it plants a problem that will crop up as soon as you share your code with someone who uses a machine with an Intel CPU, or a GPU. And it may become more of a problem in the future, if you make your code ...
by ted
Wed Jul 20, 2022 11:47 am
Forum: OS X
Topic: Can't Load .mod files in Python Script
Replies: 4
Views: 84

Re: Can't Load .mod files in Python Script

First, for the benefit of future readers of this thread--in the second code example in the previous message, "som.insert('klt')" is just an accidental misspelling. In the actual code that Liz_Stan_88 executed, the statement must have been "soma.insert('klt')"; if not, there would...
by ted
Tue Jul 19, 2022 10:41 am
Forum: NEURON + Python
Topic: Can the simulation results of Python and HOC be different?
Replies: 5
Views: 130

Re: Can the simulation results of Python and HOC be different?

Pleaze zip up whatever hoc, py, ses, and mod files are needed to reproduce your findings and email them to ted.carnevale@yale.edu so I can see what is happening.
by ted
Mon Jul 18, 2022 4:59 pm
Forum: MSWin
Topic: Insert Mechanisms in Matlab
Replies: 1
Views: 67

Re: Insert Mechanisms in Matlab

Most mechanisms used in NEURON are specified by code written in NMODL. To use them with NEURON it is necessary to compile the NMODL code with mknrndll (if you're using MSWin) or nrnivmodl (if you're using Linux or MacOS). If you then launch NEURON in the same directory where you compiled the NMODL f...
by ted
Mon Jul 18, 2022 11:01 am
Forum: NEURON + Python
Topic: Can the simulation results of Python and HOC be different?
Replies: 5
Views: 130

Re: Can the simulation results of Python and HOC be different?

Here are some suggestions that may help you with debugging: 1. For initial tests, why use a super long run time to study a very transient phenomenon? Examining results will be easier if you start the stimulus at, say, 5 ms, and limit run time to 30 ms or so. 2. To debug your model, use the introspec...
by ted
Sat Jul 09, 2022 12:41 am
Forum: Modeling networks
Topic: GUI Network Builder: Modeling 20 synapses as 1
Replies: 5
Views: 351

Re: GUI Network Builder: Modeling 20 synapses as 1

if there was something that needed to be changed on a fundamental level, I would have to do that myself For any given model define A to be the set of "all things that can be done without writing more code." The problem is how to decide what belongs to A and what does not. If I wanted to m...
by ted
Thu Jun 30, 2022 5:18 pm
Forum: Modeling networks
Topic: GUI Network Builder: Modeling 20 synapses as 1
Replies: 5
Views: 351

Re: GUI Network Builder: Modeling 20 synapses as 1

First, I should mention that my previous reply was not as clear as it should have been. Please take a look at the revised version above. I wanted to make the program in a GUI for individuals who are not experienced in coding That is certainly doable. Just use hoc and/or Python to build the model net...
by ted
Mon Jun 27, 2022 11:11 am
Forum: Modeling networks
Topic: GUI Network Builder: Modeling 20 synapses as 1
Replies: 5
Views: 351

Re: GUI Network Builder: Modeling 20 synapses as 1

The Network Builder is designed for prototyping simple networks that have only a few cells and a few synaptic connections (where "few" means maybe half a dozen at most; more than that would exceed the patience of most mortals). Also, the Network Builder doesn't allow more than a single ins...