Search found 14 matches

by samnemo
Tue Nov 13, 2018 12:45 pm
Forum: Employment and educational opportunities
Topic: Postdoc in auditory thalamocortical system modeling & data analysis
Replies: 0
Views: 1383

Postdoc in auditory thalamocortical system modeling & data analysis

A computational neuroscience postdoctoral position is available at the Nathan Kline Institute for Psychiatric Research under the auspices of a NIH R01 (MPI: Peter Lakatos, Sam Neymotin). The aim of our project is to develop/utilize computer models of the auditory thalamocortical system to investigat...
by samnemo
Tue Oct 30, 2018 10:34 am
Forum: HNN: Human Neocortical Neurosolver
Topic: HNN at SFN 2018
Replies: 0
Views: 1664

HNN at SFN 2018

We are pleased to announce that we will be presenting the following HNN workshops, posters, and related research at the Society for Neuroscience Annual Meeting in San Diego in November. Computational Psychiatry: http://computationalpsychiatry.org/cp18/ When: 11/2, 11:00 AM - 12:20 PM Lecture – Steph...
by samnemo
Thu Oct 11, 2018 3:20 pm
Forum: HNN: Human Neocortical Neurosolver
Topic: Tutorials on simulating ERPs/Rhythms using HNN
Replies: 2
Views: 1546

Re: Tutorials on simulating ERPs/Rhythms using HNN

Poisson inputs are recorded and saved by HNN. The format of spk.txt is: column 1 = spike times, column 2 = identifier If you look at param.txt you will see a line with something like this: extpois: [1350, 1619] that indicates that identifiers 1350 through 1619 are associated with Poisson inputs. You...
by samnemo
Wed Sep 05, 2018 11:05 am
Forum: HNN: Human Neocortical Neurosolver
Topic: Tutorials on simulating ERPs/Rhythms using HNN
Replies: 2
Views: 1546

Tutorials on simulating ERPs/Rhythms using HNN

We recently released a new set of tutorials ( https://hnn.brown.edu/index.php/tutorials/ ), describing how to use HNN to simulate some of the most commonly observed patterns in MEG/EEG data, including event related potentials, and low frequency rhythms (alpha/beta/gamma). We welcome any feedback/com...
by samnemo
Wed Sep 05, 2018 11:01 am
Forum: HNN: Human Neocortical Neurosolver
Topic: Installation Issues
Replies: 4
Views: 1734

Installation Issues

If anyone has installation issues/questions, please let us know. We can help troubleshoot any problems here. Also note, that to simplify the HNN installation process, we have created Virtual Box application images, available at https://hnn.brown.edu/ .
by samnemo
Fri May 11, 2018 4:39 pm
Forum: HNN: Human Neocortical Neurosolver
Topic: HNN: Human Neocortical Neurosolver
Replies: 0
Views: 1739

HNN: Human Neocortical Neurosolver

We recently built the Human Neocortical Neurosolver (HNN; https://hnn.brown.edu), a user-friendly software tool that gives researchers/clinicians the ability to test and develop hypotheses on circuit mechanisms underlying EEG/MEG data in an easy-to-use environment. The foundation of HNN is a computa...
by samnemo
Fri Jan 01, 2016 11:31 am
Forum: Reaction-diffusion in NEURON
Topic: New multiscale (molecular/net) neocortex model on ModelDB
Replies: 0
Views: 8938

New multiscale (molecular/net) neocortex model on ModelDB

A new paper, Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex, was recently accepted to Neuroscience . The paper describes a model that links molecular to neuronal network dynamics using NEURON's reaction-diffusion module. The model is available here...
by samnemo
Thu Dec 18, 2014 1:23 pm
Forum: Reaction-diffusion in NEURON
Topic: New reaction-diffusion model on ModelDB
Replies: 6
Views: 7752

New reaction-diffusion model on ModelDB

A new paper, Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model , was recently accepted to Neural Computation . The paper describes an electrochemical model that uses NEURON's new reaction-diffusion features, and may therefore serve as a templ...
by samnemo
Wed Jun 18, 2014 4:11 am
Forum: Reaction-diffusion in NEURON
Topic: Basic modelling question
Replies: 7
Views: 12359

Re: Basic modelling question

should cai increase = is there any current through your channel?
by samnemo
Wed Jun 18, 2014 4:09 am
Forum: Reaction-diffusion in NEURON
Topic: Basic modelling question
Replies: 7
Views: 12359

Re: Basic modelling question

for access to continuerun you can do: h.load_file("stdrun.hoc")

can you post output showing the problem you're still having connecting rxd and the mod mechanism?
by samnemo
Wed Jun 04, 2014 12:25 pm
Forum: Reaction-diffusion in NEURON
Topic: Basic modelling question
Replies: 7
Views: 12359

Re: Basic modelling question

Hi Stephan, The setup looks correct. To link the calcium current in your mod file to changes in intracellular calcium concentration you should make sure you're using the ca ion in your mod file, eg with this: USEION ca READ cai,cao WRITE ica The name = 'ca' is required in your rxd.Species setup, whi...
by samnemo
Sat Dec 14, 2013 11:15 am
Forum: NEURON + Python
Topic: nrnpython+matplotlib gui thread hangs
Replies: 1
Views: 1839

nrnpython+matplotlib gui thread hangs

I'm having some issues using matplotlib plots from the hoc side with nrnpython due to threading issues. The problem is that the matplotlib gui thread seems to prevent response from the hoc interpreter. Previously, the code sequence below was effective in dealing with this issue (similar to ipython i...
by samnemo
Mon Oct 28, 2013 12:13 pm
Forum: Specific models
Topic: X-axis changes scale when adding color to plot
Replies: 2
Views: 10971

Re: X-axis changes scale when adding color to plot

Hi Sanjay, You just need to pass the correct arguments to the Vector plot function. Here are the docs for that: http://www.neuron.yale.edu/neuron/static/new_doc/programming/math/vector.html#Vector.plot Since you want to specify a dt and a color you'll have to use this call: vec.plot(graphobj, x_incr...
by samnemo
Tue Jun 26, 2012 1:39 pm
Forum: NEURON + Python
Topic: python & hoc strings
Replies: 1
Views: 11240

python & hoc strings

I am trying to modify a hoc string from within a mod file (strtest.mod code below) and want to be able to do this using both hoc and python. When I call the code in test.py there's no error when running using NEURON h(command) syntax, but when using h.variablename syntax, I get an error. Although th...