Search found 5410 matches

by ted
Tue Feb 12, 2019 11:47 am
Forum: Other questions
Topic: Segmentation Fault when calling BBSaveState.save_test()
Replies: 3
Views: 179

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: 79

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: 79

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: 79

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: 123

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: 68

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: 166

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: 8004

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: 166

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...
by ted
Thu Jan 31, 2019 6:13 pm
Forum: Hot tips
Topic: Driving a synapse with recorded or precomputed spike events
Replies: 7
Views: 8004

Re: Driving a synapse with recorded or precomputed spike events

"A VecStim is an event source" means that a VecStim is similar to any other artificial spiking cell, e.g. an instance of the NetStim class or of one of the IntFire classes. For any of these, the usage pattern is 1. Create an instance of the target that is to be driven by events. The target could be ...
by ted
Thu Jan 31, 2019 5:29 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 166

Re: eca calculation

The documentation leads one to believe that the numeric result returned by ion_style("name_ion") can be interpreted as the 7 bit binary value b6 b5 b4 b3 b2 b1 b0 where b1 b0 is c_style b2 is cinit b4 b3 is e_style b5 is einit b6 is eadvance However, as you have noted, soma print ion_style("ca_ion")...
by ted
Thu Jan 31, 2019 1:18 am
Forum: Hot tips
Topic: Driving a synapse with recorded or precomputed spike events
Replies: 7
Views: 8004

Re: Driving a synapse with recorded or precomputed spike events

An instance of the VecStim class is an event source. It generates events. Use NetCons to convey those events to the target synaptic mechanism(s).
by ted
Thu Jan 31, 2019 1:16 am
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 166

Re: eca calculation

Good question. Read the Programmer's Reference documentation of ion_style.
by ted
Mon Jan 28, 2019 10:35 pm
Forum: UNIX/Linux
Topic: nrnivmodl compiling in Linux
Replies: 8
Views: 8903

Re: nrnivmodl compiling in Linux

Thanks, rgerkin. Installation and configuration tips are always welcome.
by ted
Sat Jan 26, 2019 11:57 am
Forum: Other questions
Topic: Segmentation Fault when calling BBSaveState.save_test()
Replies: 3
Views: 179

Re: Segmentation Fault when calling BBSaveState.save_test()

There have been many bug fixes and improvements since 7.5. Suggest you remove 7.5 and update to the latest version of NEURON (7.6.5), just in case that takes care of the problem. With regard to your test program, why call pc.set_maxstep before even a single NetCon delay has been specified? Why invok...