NEURON Discussion Group
We are no longer meeting, but I am keeping this up for reference. We will be starting an XPP/AUT discussion group in the Fall of 2008. If you would like to be added to the email list and be informed of when the discussion group will meet just Email Me. Anyone is welcome to join us and if you have an interest do not let lack of experience keep you from coming. Below is a list (reverse chronological order) of what we have talked about so far and the files all have contributed (just click the blue text usually labled "code" or "here" to download).
Mar-02-2007
We talked about Ca2+ yet again. We are all happy with the unit conversions in our internal Ca2+ dynamics file. We spent some time making the pump slightly more realistic mostly by checking units. We started our work on Ca2+ diffusion which was led by Michael. There was quite a bit of code worked out which can be found below.
Michael has provided some code in which he worked out basic longitudinal diffusion using a kinetic scheme. The code is available here and should prove quite useful in understanding how to get diffusion to work in NEURON before implementing shells and buffers.
Mark has provided some code, available here, which describes a Michaelis-Menten style Ca2+ pump.
Feb-23-2007
We talked more about modeling Ca2+. It seems that to implement both Ca2+ accumulation and a Ca2+ pump in two separate .mod files you must have the pump file write to ICa and can not directly affect the concentration of Ca2+ as it can only be written to once. We also discovered the unit checker needs better documentation.
Michael has provided the following code to illustrate the strategy. Currently the pump is Michael-described as crude. All of the .mod files are well commented and to get it all to run just extract the zip, compile by dragging the whole folder to mknrndll and then drag the CaDemo.hoc file to the nrngui.
We also found a tutorial for the unit checker (modlunit) and can be accessed here: http://www.snl.salk.edu/~pjthomas/neuron/munit.html
More thourough documentaion on the unit checker is available on Alain Destexhe's webpage:
http://cns.iaf.cnrs-gif.fr/files/units.html
Feb-16-2007
Collin gave us an introduction to modeling internal Ca2+ dynamics using NEURON. He worte a few files which include a Ca2+ channel, a conversion from Ca2+ current to internal Ca2+ concentration and a Ca2+-activated K+ current (SK). The files can be found here.
Feb-02-2007
Chris showed us how to make a model ion channel using published data. He fit the model to the data from this paper by Marco Martina and Peter Jonas. To do this he claims he needed only a boltzman curve desribing the activation and inactivation variables as well as their time constants. He has provided the mod file as well as two mathematica notebooks used to fit boltzman curves and time constant curves. The files can be found here.
Jan-26-2007
Michael showed us how to use the vector class to inject arbitrary waveforms into a model neuron. He provided some code which is very well-documented and can be obtained here.
Jan-19-2007
We talked about NMODL, which is the extension language to NEURON. If you are interested in using ion channels that are not the Hodkin-Huxley described Na+ and K+ current then you want to learn NMODL. The only thing close to documentation for this language can be found here. Chris commented the K+ channel mod file example found in that documentation, get it here (right-click and save target as).
Jan-12-2007
We talked about how to install NEURON. Basically you should visit the main NEURON site, and download the "Precompiled code" for your machine type. If you have a mac, you should download the "powerpc code" if you have a G4 or G5 chip and you should get the "i686 apple dmg" if you have an intel (core duo) chip. This package contains a number of things and three are of main interest to you:1) "NRNGUI" this is the main program and you should open your .hoc files with this 2) "MKNRNDLL" this allows you to use files that end in ".mod" to do this you should drag a folder containing you .hoc file and .mod files to this program and it will compile the mod files 3) "MODLUNIT" This is the unit checker, to use it write a .mod file and drag it to this to check the unit consistency. SPECIAL NOTE: If you have are running Mac OSX then you need to download and install the developer tools, mknrndll needs the gcc compiler which is included in this package.
It is highly suggested that you check out the following tutorial which is very good at getting the beginner up to speed.