Search found 1543 matches

by hines
Mon Feb 18, 2019 12:08 pm
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 6888

Re: Driving synaptic event using vecStim

vecevent.mod has been updated to be compatible with CoreNEURON. See https://github.com/neuronsimulator/nrn/commit/7adabc176763386031a9c88ef5218a64f9402219 This kind of VERBATIM code is quite painful. I need to consider an NMODL syntax for easily describing the use of Random variables and Vectors in ...
by hines
Mon Feb 18, 2019 11:47 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 6888

Re: Driving synaptic event using vecStim

i've updated vecevent.mod (VecStim)
Just need to test with coreneuron.
When it is working I'll push to the github repository and mention that here.
by hines
Thu Feb 14, 2019 8:53 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 6888

Re: Driving synaptic event using vecStim

look at nrn/src/nrnoc/netstim.mod for an analogy. You need to replace POINTER with BBCOREPOINTER and introduce
bbcore_write and bbcore_read implementations. Anything containing the string BBCORE is of interest.
I should update vecstim.mod to make it compatible with CoreNEURON.
by hines
Fri Feb 01, 2019 6:48 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 233

Re: eca calculation

Using
neurondemo -python
#select release model

Code: Select all

from neuron import h
bin(int(h.ion_style("ca_ion", sec=h.terminal)))
yields
'0b11110111'
If you send me the code fragment that returns

Code: Select all

>>> bin(136)
'0b10001000'
I can look into it in more detail.
by hines
Fri Feb 01, 2019 8:53 am
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 233

Re: eca calculation

from nrn/src/nrnoc/eion.c /*the bitmap is 03 concentration unused, nrnocCONST, DEP, STATE 04 initialize concentrations 030 reversal potential unused, nrnocCONST, DEP, STATE 040 initialize reversal potential 0100 calc reversal during fadvance 0200 ci being written by a model 0400 co being written by ...
by hines
Mon Jan 28, 2019 4:46 pm
Forum: NEURON + Python
Topic: how to delete a Point Process object
Replies: 11
Views: 2726

Re: how to delete a Point Process object

is there a reason
I don't know the reason yet.
In my notebook, the output from that function shows up in the terminal
Today I pushed a fix in the master branch of github.com/neuronsimulator/nrn that directs the output of
h.allobjects() to stdout of Python.
by hines
Mon Jan 28, 2019 9:00 am
Forum: NEURON + Python
Topic: how to delete a Point Process object
Replies: 11
Views: 2726

Re: how to delete a Point Process object

Something mysterious is going on with jupyter that I can't yet quite figure out. Can you work around the problem with print (soma.psection()) Everytime Jupyter default pretty prints the result of soma.psection(), the hoc reference count of the POINT_PROCESS is incremented and never gets decremented ...
by hines
Sat Jan 26, 2019 10:31 am
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 317

Re: Running secondary networks in isolation

You only need to call sec.simulate(0) for one section in a cell and all the sections in that cell will follow along. However, if you call sec.simulate(0) for several or all of the sections in a cell it should not matter as any after the first will do nothing. for sec in neuron.h.allsec(): sec.simula...
by hines
Thu Jan 24, 2019 9:00 pm
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 317

Re: Running secondary networks in isolation

Ok. The do-not-simulate branch is ready to try. the log message is commit 0ebc0f8ff10ddd68b8cd3fe12cfb5e78bd9dd6a5 (HEAD -> do-not-simulate, origin/do-not-simulate) Author: Michael Hines <michael.hines@yale.edu> Date: Thu Jan 24 13:38:54 2019 -0500 nrn.Section.simulate(False) causes the entire tree ...
by hines
Thu Jan 24, 2019 8:56 am
Forum: Modeling networks
Topic: Running secondary networks in isolation
Replies: 11
Views: 317

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: 317

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: 317

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: 212

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: 317

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: 12497

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...