Search found 14 matches

by agmccrei
Wed Jan 24, 2018 1:37 pm
Forum: Other questions
Topic: NetStim Fractional Randomness: Mathematical Notation?
Replies: 3
Views: 865

Re: NetStim Fractional Randomness: Mathematical Notation?

Right, so my understanding of how fractional randomness is implemented is that for each interspike interval, the interval is dependent on the values set for s.interval and s.noise (assuming s = new NetStim(x)). Specifically, the magnitude of the value of s.noise (from 0 to 1) will control the propor...
by agmccrei
Fri Jan 19, 2018 4:19 pm
Forum: Other questions
Topic: NetStim Fractional Randomness: Mathematical Notation?
Replies: 3
Views: 865

NetStim Fractional Randomness: Mathematical Notation?

Hello, I don't have a strong formal background in mathematics here, but I want to describe some of the mechanisms used in NEURON. Specifically, I am not sure if I have the correct mathematical notation for describing how fractional randomness is implemented in NEURON's NetStim function. So far, I ha...
by agmccrei
Sun Feb 26, 2017 2:18 am
Forum: Parallel NEURON
Topic: Accessing ParallelContext() while in Python
Replies: 2
Views: 4951

Re: Accessing ParallelContext() while in Python

I actually found what looks to be a (embarrassingly) simple solution to my initial query. In fact, I am somewhat embarrassed I had not realized this before. Instead of running the ParallelContext twice for two separate problems, I could just run my hoc "simulation" function (i.e. h.f()) at the begin...
by agmccrei
Thu Feb 23, 2017 6:21 pm
Forum: Parallel NEURON
Topic: Accessing ParallelContext() while in Python
Replies: 2
Views: 4951

Re: Accessing ParallelContext() while in Python

One quick thing to add is that in the simplified code, when I do not create the ParallelContext in the hoc file (i.e. I comment out execution of the "SynParamSearch.hoc" file in the "init.py" file) and I create it in the python code with pc = h.ParallelContext(), the parallelization works fine. Simi...
by agmccrei
Thu Feb 23, 2017 5:36 pm
Forum: Parallel NEURON
Topic: Accessing ParallelContext() while in Python
Replies: 2
Views: 4951

Accessing ParallelContext() while in Python

Hello, I am fairly new to parallel processing and I am running into a somewhat odd problem while trying to access and re-use a previously used ParallelContext(). When I first use a ParallelContext in my hoc code to run a parameter search (i.e. simulate many iterations of my models) using a bulletin ...
by agmccrei
Mon Jan 16, 2017 10:43 pm
Forum: Parallel NEURON
Topic: Using Multisplit on NSG
Replies: 2
Views: 4820

Re: Using Multisplit on NSG

Thank you for your reply Dr. Carnevale. I tried doing as you suggested, but I only seem to be receiving a slightly more detailed version of the previous error: stderr.txt: Use of uninitialized value in multiplication (*) at /opt/sdsc/bin/ibrun line 99. Use of uninitialized value in multiplication (*...
by agmccrei
Mon Jan 02, 2017 6:51 pm
Forum: Parallel NEURON
Topic: Using Multisplit on NSG
Replies: 2
Views: 4820

Using Multisplit on NSG

Hello, I am new to parallel processing in NEURON but it has become necessary to implement due to the increasing complexity of my model and the size of parameter searches that I am running. I am running repeated simulations of a morphologically detailed multi-compartment model with 1903 Exp2Syn synap...
by agmccrei
Mon Nov 14, 2016 1:12 am
Forum: Modeling networks
Topic: Inacurrate Number of Spikes While Using Random Netstim
Replies: 5
Views: 6176

Re: Inacurrate Number of Spikes While Using Random Netstim

In my scenario, the input spike train ISI statistics to the cell type that I am modelling are not characterized and so, it is not clear whether modelling them using random sampling from a negexp distribution is appropriate in the first place (since there are other potential ISI distributions - see r...
by agmccrei
Sun Nov 13, 2016 4:54 pm
Forum: Modeling networks
Topic: Inacurrate Number of Spikes While Using Random Netstim
Replies: 5
Views: 6176

Re: Inacurrate Number of Spikes While Using Random Netstim

Thank you for your reply Dr. Carnevale. You mean you got fewer spikes than you expected. Why would you expect to get even 1 spike in every run? Given a negexp distribution with mean ISI > 0, for any finite simulation duration there is a nonzero probability that no spikes at all will be observed duri...
by agmccrei
Fri Nov 11, 2016 6:39 pm
Forum: Modeling networks
Topic: Inacurrate Number of Spikes While Using Random Netstim
Replies: 5
Views: 6176

Inacurrate Number of Spikes While Using Random Netstim

Hello, I am trying to run a parameter search by varying the number of excitatory and inhibitory synapses on a multi-compartment model as well as their corresponding presynaptic firing rates. It is also important that these presynaptic spikes occur at random times. For the presynaptic spike parameter...
by agmccrei
Mon Sep 05, 2016 10:07 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Trying to Make/Debug an Input Current Mod File
Replies: 1
Views: 5200

Re: Trying to Make/Debug an Input Current Mod File

Hello again, So I was recently directed to the following Github repository: https://github.com/pozzorin/GIFFittingToolbox/tree/HBP_Simplification/src/HBP/NEURON ... which is in the Human Brain Project (HBP) branch of the GIF fitting python repository. Inside is the "gif.mod" file which, it seems, mo...
by agmccrei
Wed Aug 17, 2016 12:49 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Trying to Make/Debug an Input Current Mod File
Replies: 1
Views: 5200

Trying to Make/Debug an Input Current Mod File

Hello, I've been attempting to develop a mod file to re-create an input current similar to what was used in Pozzorini et al (2015). Unfortunately, I'm finding that this task is a bit outside of my wheelhouse as I have not yet needed to make mod files. As it stands, I'm not sure if I have mistakes in...
by agmccrei
Mon Feb 22, 2016 6:25 pm
Forum: Other questions
Topic: Using save_session on Neuroscience Gateway (NSG)
Replies: 1
Views: 664

Using save_session on Neuroscience Gateway (NSG)

I am currently running simulations on NSG where I have input session files containing my multi-compartment model and several MultipleRunFitter windows. In the simulations the code iteratively optimizes the synaptic parameters of a single synapse for each compartment. The optimized parameters are sav...
by agmccrei
Fri Sep 11, 2015 2:44 am
Forum: Anatomically detailed models
Topic: Questions about geometry & area(x)
Replies: 1
Views: 5071

Questions about geometry & area(x)

I'm having some trouble understanding how area(x) is calculated in the morphology of my model. My basic understanding is that when a morphology is imported into NEURON, it is specified using the pt3dadd function, which specifies the segments as truncated cones/frusta. Furthermore, despite having man...