PSICS - the Parallel Stochastic Ion Channel Simulator
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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.

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.

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 with synaptic conductances applied explore how the positions and timing of synaptic inputs affects depolarizations at the soma in a passive model.

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