Introductory Tutorial: Edinburgh Summer School 2012
The tutorial will introduce students to PSICS. No prior experience is required. You will need a simple text editor such as Notepad or Emacs to modify models. An XML-aware editor such as the one in Eclipse makes editing models easier but it not essential.
- Motivation for developing PSICS and the importance of stochastic ion channel simulations, Matt Nolan (15 mins)
- Development and functionality of PSICS, Robert Cannon (15 mins)
- Tutorial overview (5 mins)
1: Getting started with PSICS
Installing PSICS and running a model. Full details are in the getting started section of the user guide.
2: Stochastic ion channel gating in the Hodgkin Huxley model
Starting with the standard rallpack model, first run it deterministically, then try varying the single channel conductance while keeping the total maximum conductance density the same. How does changing the single channel properties affect the behaviour?
3: More detailed modeling
Two possible starting points are listed below. Also feel free to pursue your own questions and make use of the tutors while they are there to help.
Option 1: Effects of stochasticity on synaptic integration
Using the mode from ModelDB accession 128043 investigate how stochastic ion channels influence synaptic integration.
- simulate response of deterministic CA1 neuron to distributed synaptic input
- simulate response of stochastic CA1 neuron to distributed synaptic input
- identify channel populations with greatest influence on stochastic integration of synaptic responses
Option 2: Passive modeling
Although PSICS was initially developed for studying stochastic ion channels, it can also be used for passive models. Using morphologies from this site or from NeuroMorpho.org with synaptic conductances applied explore how the positions and timing of synaptic inputs affects depolarizations at the soma in a passive model.