Search found 1579 matches

by hines
Thu Jan 24, 2019 8:56 am
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 1917

Re: Running secondary networks in isolation

You've convinced me that removing cells from a simulation without destroying them is a useful feature. I've concluded that the basic functionality will have a straightforward implementation. More rarely used combinations of features that will break the system can raise errors until the implementatio...
by hines
Wed Jan 23, 2019 6:00 pm
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 1917

Re: Running secondary networks in isolation

I was completely unaware that Nengo can create a NEURON Section. I don't know very much about Nengo but thought it had its own native implementation of models. Can you point me to a document that explains more of the Nengo workflow related to NEURON. As I think about the possibility of removing a Se...
by hines
Wed Jan 23, 2019 3:58 pm
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 1917

Re: Running secondary networks in isolation

Sorry. I'm not quite seeing the problem yet. I'm hearing that when build_connection is called, that you need to build something that you can optimize and then throw it away. Can you not also save the relevant info of each build_connection call (and return value) in set/dict/list for later simulation...
by hines
Tue Jan 22, 2019 5:30 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: KINETIC block for enzymatic reaction
Replies: 1
Views: 830

Re: KINETIC block for enzymatic reaction

I suspect that the solver has been tricked into thinking the system is linear and can be solved in a single iteration. Ie the changes in Rafi and RafPi are computed with constant rates (for that time step) that will be computed based on the entry values of Rafi and RafPi. Unfortunately, my experienc...
by hines
Tue Jan 22, 2019 4:36 pm
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 1917

Re: Running secondary networks in isolation

It is not possible to not simulate created cells in NEURON. I can imagine this is a problem if the expense of setting up a network takes a long time. Otherwise, the best way to proceed is to destroy the previous network and setup only a network needed for the next phase. This can be most easily done...
by hines
Sat Dec 22, 2018 1:10 pm
Forum: NEURON + Python
Topic: Compling Problem
Replies: 21
Views: 16652

Re: Compling Problem

Looks like I have a bad substitution line in nrn/src/nrnpython/setup.py.in which reads @setup_extra_link_args@ = [ epre+libdirs[0],epre+libdirs[1] ], and should get replaced in setup.py with either extra_link_args = [ epre+libdirs[0],epre+libdirs[1] ], or #extra_link_args = [ epre+libdirs[0],epre+li...
by hines
Thu Dec 20, 2018 3:09 pm
Forum: MSWin
Topic: Windows 10 install problem
Replies: 2
Views: 2794

Re: Windows 10 install problem

NEURON -- VERSION 7.6.2 master (f5a1284) 2018-08-15
The latest standard distribution is 7.6.3.
I have hope but not certainty that that will fix your problem. At any rate it makes sense to begin diagnosing with that as there have
been a few changes in the files that would be related to your issues.
by hines
Fri Dec 14, 2018 10:53 am
Forum: Other questions
Topic: Impedance methods change the location
Replies: 5
Views: 1498

Re: Impedance methods change the location

The extended impedance behavior is now the same as for the default impedance calculation. That is, interleaved calculations of transfer and input impedance work properly without having to reset the input stimulus location for transfer. So the behavior now corresponds to the existing documentation. N...
by hines
Tue Dec 11, 2018 8:40 am
Forum: Other questions
Topic: Impedance methods change the location
Replies: 5
Views: 1498

Re: Impedance methods change the location

The documentation needs to be updated to reflect this behavior. The default calculation is able to efficiently combine the calculation of transfer impedance everywhere given a specific current stimulus location and input impedance everywhere. After a compute, it is possible just read off the values ...
by hines
Wed Nov 28, 2018 8:17 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 1740

Re: Nested for loops over SectionList objects

Please try the latest version. I inadvertently reffed the section list iterators twice which prevents deletion of the SectionList
See commit a3d1233b
by hines
Tue Nov 27, 2018 11:29 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 1740

Re: Nested for loops over SectionList objects

A fix for nested SectionList iteration in python has been pushed to the github repository. I use the test: $ cat slseq.py from neuron import h a = [h.Section(name='s%d'%i) for i in range(3)] sl = h.SectionList() for s in a: sl.append(sec=s) for s in sl: print(s) print("") for x in sl: for y in sl: p...
by hines
Tue Nov 27, 2018 9:03 am
Forum: NEURON + Python
Topic: Nested for loops over SectionList objects
Replies: 5
Views: 1740

Re: Nested for loops over SectionList objects

The following is intended behavior >>> sl = h.SectionList() >>> sl.allsec() Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'hoc.HocObject' object has no attribute 'allsec' that is, the allsec method is restricted to the <HocTopLevelInterpreter>. The changeset ...
by hines
Fri Nov 02, 2018 9:02 am
Forum: Getting started
Topic: Program functions between Mac and Windows
Replies: 3
Views: 1485

Re: Program functions between Mac and Windows

Please email me a zip file with all the mod, py, ses, hoc files needed along with instructions on launching the model to produce the result to michael.hines@yale.edu . I will try to reproduce the problem, diagnose, and fix the issue. There are two dimensions here: (mac, mswin) and (7.4, 7.6) as well...
by hines
Tue Oct 30, 2018 5:11 pm
Forum: Getting started
Topic: compiling issues on Mac
Replies: 6
Views: 1994

Re: compiling issues on Mac

Instead of dragging the mod file, try dragging the folder containing the two mod files on to the mknrndll icon
by hines
Fri Oct 26, 2018 9:29 pm
Forum: Getting started
Topic: compiling issues on Mac
Replies: 6
Views: 1994

Re: compiling issues on Mac

Is the hoc file in the same folder as the mod file? Dragging the mod file (or its folder) onto the mknrndll icon should create an x86_64 folder in the folder that contained the mod file. Verify this is the case. If you launch nrniv in this folder (now containing the x86_64) folder from a terminal, y...