diff --git a/README.md b/README.md new file mode 100644 index 0000000..d22ee58 --- /dev/null +++ b/README.md @@ -0,0 +1,64 @@ +# This code accompanies the publication + +Schmidt-Hieber C, Bischofberger J. (2010) +Fast sodium channel gating supports localized and efficient +axonal action potential initiation. +*J Neurosci* 30:10233-42 + +Send comments to c.schmidt-hieber_at_ucl.ac.uk + +## INSTALLATION + +1. Install the required Python modules: + NumPy ([http://numpy.scipy.org](http://numpy.scipy.org)) + SciPy ([http://www.scipy.org/SciPy](http://www.scipy.org/SciPy)) + Matplotlib ([http://matplotlib.sourceforge.net/index.html](http://matplotlib.sourceforge.net/index.html)) + + Installation instructions can be found on the respective web sites. + +2. NEURON and Python + Install NEURON with Python support. At the time of writing, + the binary distribution won't do and you'll have to compile + NEURON from source. + + See [http://www.davison.webfactional.com/notes/installation-neuron-python/](http://www.davison.webfactional.com/notes/installation-neuron-python/) + for instructions. + +3. Optional + To solve kinetic gating schemes without NEURON, you'll need pyqmatrix: + + [http://code.google.com/p/pyqmatrix](http://code.google.com/p/pyqmatrix) + +## USAGE + +1. Compile the mechanism files in the mod directory: +``` +$ nrnivmodl mod +``` + +2. Run the example simulations: + +- Simple current-clamp simulation +``` +$ python ap.py +``` + +- Voltage-clamp simulation comparing Q-Matrix and NEURON results: +``` +$ python qmatrix.py +``` + +## CHANGELOG + +na8st-1.1 (1.1) + + * Pointing out discrepancies in \bar{g}_{Na} computations. + Thanks to Steffen Platschek for pointing this out. + + -- Christoph Schmidt-Hieber Sun, 20 Oct 2011 13:41:23 +0000 + +20150903 a patch (contributed by Arnd Roth and emailed by Christoph +Schmidt-Hieber) that adds temperature dependence was applied to +mod/na8st.mod. + +20250602 Converted README to Markdown. diff --git a/README.txt b/README.txt deleted file mode 100644 index 9a2a591..0000000 --- a/README.txt +++ /dev/null @@ -1,57 +0,0 @@ -This code accompanies the publication: - -Schmidt-Hieber C, Bischofberger J. (2010) -Fast sodium channel gating supports localized and efficient -axonal action potential initiation. -J Neurosci 30:10233-42 - -Send comments to c.schmidt-hieber_at_ucl.ac.uk - -INSTALLATION - -1. Install the required Python modules: -NumPy (http://numpy.scipy.org) -SciPy (http://www.scipy.org/SciPy) -Matplotlib (http://matplotlib.sourceforge.net/index.html) - -Installation instructions can be found on the respective web sites. - -2. NEURON and Python -Install NEURON with Python support. At the time of writing, -the binary distribution won't do and you'll have to compile -NEURON from source. - -See -http://www.davison.webfactional.com/notes/installation-neuron-python/ -for instructions. - -3. Optional -To solve kinetic gating schemes without NEURON, you'll need pyqmatrix: - -http://code.google.com/p/pyqmatrix - -USAGE - -1. Compile the mechanism files in the mod directory: -$ nrnivmodl mod - -2. Run the example simulations: - -# Simple current-clamp simulation -$ python ap.py - -# Voltage-clamp simulation comparing Q-Matrix and NEURON results: -$ python qmatrix.py - -CHANGELOG - -na8st-1.1 (1.1) - - * Pointing out discrepancies in \bar{g}_{Na} computations. - Thanks to Steffen Platschek for pointing this out. - - -- Christoph Schmidt-Hieber Sun, 20 Oct 2011 13:41:23 +0000 - -20150903 a patch (contributed by Arnd Roth and emailed by Christoph -Schmidt-Hieber) that adds temperature dependence was applied to -mod/na8st.mod.