Search found 5188 matches

by ted
Mon May 21, 2018 11:32 pm
Forum: Getting started
Topic: Models Without Spatial Data
Replies: 5
Views: 64

Re: Models Without Spatial Data

Please answer yes or no: is the citation Galvis D, Wu W, Hyson RL, Johnson F, Bertram R. A distributed neural network model for the distinct roles of medial and lateral HVC in zebra finch song production. J Neurophysiol. 118:677-692, 2017 ? Given the complexity of the model described in that paper, ...
by ted
Mon May 21, 2018 12:49 pm
Forum: Getting started
Topic: Models Without Spatial Data
Replies: 5
Views: 64

Re: Models Without Spatial Data

Need a little more information. Is this a completely abstract model, e.g. an artificial spiking cell with an "activation" state variable with a rest value of 0 and spike threshold of 1? A model of chemical reactions that occur in a well stirred volume? A model of channel gating? A single compartment...
by ted
Fri May 18, 2018 11:40 am
Forum: UNIX/Linux
Topic: Interviews Not Installing
Replies: 3
Views: 54

Re: Interviews Not Installing

We're not going to make any progress if this discussion jumps from one item to another, piling one unresolved issue on top of another. First let's resolve the first issue, and then we'll go on to the next. Here's the first issue raised by your previous post: As instructed in earlier posts, I went in...
by ted
Thu May 17, 2018 3:38 pm
Forum: UNIX/Linux
Topic: Interviews Not Installing
Replies: 3
Views: 54

Re: Interviews Not Installing

As instructed in earlier posts, I went into src/lib folder and executed make. That's guaranteed not to work. We need to correct that--in which posts did you find that instruction? Are you installing from the gzipped tar file, or did you clone the git repository? In either case, you want to cd iv th...
by ted
Thu May 17, 2018 3:33 pm
Forum: UNIX/Linux
Topic: NEURON and Python Installation on Ubuntu 16.04
Replies: 1
Views: 51

Re: NEURON and Python Installation on Ubuntu 16.04

src is in nrn, the root directory of NEURON's source code, which is where you executed ./configure ...
by ted
Thu May 17, 2018 8:40 am
Forum: Parallel NEURON
Topic: Network Parallelization
Replies: 5
Views: 55

Re: Network Parallelization

When we run the network as 'python init.py' and as 'mpiexec -n 1 python -mpi init.py', should generate same number of spikes, right? That is one indication of properly parallelized code. Another is that results produced by parallelized code should be identical to the results of a serial implementat...
by ted
Thu May 17, 2018 8:26 am
Forum: Parallel NEURON
Topic: Network Parallelization
Replies: 5
Views: 55

Re: Network Parallelization

Is it possible to place source gids and Target gids on same host? Properly implemented parallel code should work regardless of the host on which any particular spike source or target is located. The purpose of distributing cells over multiple hosts is to achieve load balance, which is critically im...
by ted
Mon May 14, 2018 10:53 am
Forum: Parallel NEURON
Topic: Network Parallelization
Replies: 5
Views: 55

Re: Network Parallelization

The NetStim is indeed a spike source, so in principle it could be assigned a gid. But before doing that, consider the three leading reasons why one would assign a gid to a spike source. 1. At least one of its targets exists on a different host. 2. Load balance. 3. Convenience of recording the events...
by ted
Fri May 11, 2018 12:00 pm
Forum: Modeling networks
Topic: Error using 2 different cells with network gui
Replies: 3
Views: 78

Re: Error using 2 different cells with network gui

The following note is for the benefit of others who may read this thread. The problem may have been caused by the fact that the CellBuilders that belonged to the NetReadyCellGUI tools (which are used to set up biophysical model cell classes) were in "Continuous Create" mode. That led to many collisi...
by ted
Thu May 10, 2018 4:44 pm
Forum: Reaction-diffusion in NEURON
Topic: Negative concentrations
Replies: 5
Views: 106

Re: Negative concentrations

In a system with so many reactions it seems likely that at least a few will involve state variables that are much smaller than others. For such cases, it is often useful to use state-specific error tolerance scale multipliers. NEURON's GUI simplifies this task tremendously. 1. Make sure you have imp...
by ted
Tue May 08, 2018 10:17 am
Forum: Modeling networks
Topic: Error using 2 different cells with network gui
Replies: 3
Views: 78

Re: Error using 2 different cells with network gui

I haven't seen this happen before; will have to be able to reproduce the problem in order to find out what's wrong and how to fix it. If you zip up the files needed to reproduce it and email that file to ted dot carnevale at yale dot edu I'll tell you what I find out. I'll need the .ses files for th...
by ted
Mon May 07, 2018 11:52 am
Forum: Hot tips
Topic: Caveats about anatomically detailed model cells
Replies: 0
Views: 66

Caveats about anatomically detailed model cells

After you import morphology data, always examine a Shape plot of the resulting model cell for possible problems. 1. Z axis artifact. This appears as sudden jumps parallel to the Z axis. Morphology files with Z axis artifact are useless for modeling. The Shape plot's default view is a projection of t...
by ted
Mon May 07, 2018 11:21 am
Forum: Modeling networks
Topic: net_send call in NET_RECEIVE
Replies: 4
Views: 112

Re: net_send call in NET_RECEIVE

The best way to implement a refractory period is with events. Indeed, events are also the best way to implement a "cosmetic spike" because, unlike your present implementation, (1) the "spike" will have a fixed duration independent of dt, and (2) there will be no need to move the "threshold" back and...
by ted
Sun May 06, 2018 1:30 pm
Forum: NetPyNE
Topic: Import json format of morphology to NetPyNE
Replies: 2
Views: 77

Re: Import json format of morphology to NetPyNE

After you import morphology data, always examine a Shape plot of the resulting model cell for three possible problems: 1. Z axis artifact. This appears as sudden jumps parallel to the Z axis. Morphology files with Z axis artifact are useless for modeling. The Shape plot's default view is a projectio...
by ted
Fri May 04, 2018 4:56 pm
Forum: Other questions
Topic: extracellular stimulation with adaptive time step integration
Replies: 3
Views: 93

Re: extracellular stimulation with adaptive time step integration

Does that mean the adaptive time step method won't work with my model, using extracellular stimulation? This discussion doesn't contain enough information to decide anything. Factors that determine whether adaptive integration succeeds include how your model has been discretized in space, the imple...