Giter Club home page Giter Club logo

arbor-usc-collab's Introduction

Granule and Basket Cells

This repository contains the Neuron and Arbor implementations and simulations of

  1. A single basket cell
  2. A single granule cell

Morphologies

  1. The basket cell is a single soma model
  2. The granule cell reads the morphology from output0_updated.swc in the morphologies directory

Density Mechanisms

The basket and granule cells both have the following mechanisms inserted on the soma and dendrites:

  1. borgka.mod
  2. cagk.mod
  3. cat.mod
  4. ccanl.mod
  5. gskch.mod
  6. ichan2.mod
  7. lca.mod
  8. nca.mod

There are 2 versions of the modfiles present in neuron/modfiles and neuron/modfiles_arb. The files in neuron/modfiles_arb have been edited to not use the TABLE feature which is supported in Neuron but not Arbor. Adding the TABLE feature is an optimization that changes the simulation results significantly. For accurate voltage measurement comparison, we use neuron/modfiles_arb for the neuron simulation.

For benchmarking performance, the TABLE feature (neuron/modfiles) can be used for the neuron simulations.

Parameters

Various parameters can be set in param_basket.json and param_granule.json.

Stimulus

A series of spikes is delivered to a synapse on the basket/granule cell. The spike times are read from param_basket.json and param_granule.json.

Running the examples

Neuron:

$ cd neuron
$ nrnivmodl modfiles_arb
$ python2 test_granulecell.py ../param_granule.json
OR
$ python2 test_basketcell.py ../param_basket.json

Running the examples will generate a plot

Arbor:

Installing Arbor:

Compiling the example:

$ cd arbor/granule
OR
$ cd arbor/basket

$ mkdir build && cd build
$ cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/arbor/installation -DCMAKE_BUILD_TYPE=release
$ make

Running the example:

$ ./arbor-granule ../../../param_granule.json
OR
$ ./arbor-basket ../../../param_basket.json

Plotting the results:

Running the examples will generate voltages.json. To plot the results, you can use the provided tsplot script:

$ python2 tsplot.py arbor/granule/build/voltages.json
OR
$ python2 tsplot.py arbor/basket/build/voltages.json

arbor-usc-collab's People

Contributors

noraabiakar avatar

Watchers

 avatar  avatar  avatar  avatar

Forkers

noraabiakar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.