From 2241d188bde0043bbb886dcfb0d66ceff7be1d39 Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Mon, 2 Jun 2025 14:03:40 -0400 Subject: [PATCH] Standardized README to Markdown format --- README.html | 57 ----------------------------------------------------- README.md | 46 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+), 57 deletions(-) delete mode 100644 README.html create mode 100644 README.md diff --git a/README.html b/README.html deleted file mode 100644 index f9cb1e7..0000000 --- a/README.html +++ /dev/null @@ -1,57 +0,0 @@ -
-This is the README for a model associated with the paper:
-
-Chapman JB, Johnson EA, Kootsey JM. (1983) Electrical and Biochemical
-Properties of an Enzyme Model of the Sodium Pump 
-J. Membrane Biol. 74, 139-153
-
-This implementation was created by Michael Hines.
-
-Generates figures 2-12. Fig 9 unidirectional fluxes were computed using
-equations 13,14 from
-Feher JJ, Biophys J. 1984 June; 45(6): 1125b
-http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1434995
-
-The lines are not labeled but they are easy to
-compare with the figures in the paper.
-
-The mod file can be simplified by removing the calculation and storage
-of the individual forward and reverse fluxes, i.e. rf[] and rb[].  For
-use in a more complex model, this mod file should be modified with
-USEION statements to use na and k ion concentrations and generate ina
-and ik. The dynamic directory shows an example of this by extending
-the Chapman et al simulations using nai, ki, and atp as states, which,
-in the presence of leak channels for na, k and non-specific ions,
-produce reasonable na and k gradients. See dynamic/README.
-
-Usage:
-Simply auto-launch from ModelDB or compile the mod files under
-
-MSWIN:
------
-
-Use mknrndll (change directory to the one expanded from the archive
-and click "make nrnmech.dll").  Then run by double clicking the
-mosinit.hoc file in a windows explorer.
-
-MAC OS X
---------
-
-Drag and drop the expanded folder from this archive onto the mknrndll
-icon.  Drag and drop the mosinit.hoc file onto the nrngui icon.
-
-Linux/Unix
-----------
-
-Change directory to the expanded folder and type these two lines:
-nrnivmodl
-nrngui mosinit.hoc
-
-Once the simulation is started
-------------------------------
-
-Simply press the buttons to reproduce figures.  For example pressing
-the "Figure 2-3" button leads to:
-
-screenshot
-
diff --git a/README.md b/README.md new file mode 100644 index 0000000..988ef5c --- /dev/null +++ b/README.md @@ -0,0 +1,46 @@ +# README for the Model Associated with the Paper + +Chapman JB, Johnson EA, Kootsey JM. (1983) Electrical and Biochemical +Properties of an Enzyme Model of the Sodium Pump +*J. Membrane Biol.* 74, 139-153 + +This implementation was created by Michael Hines. + +Generates figures 2-12. Fig 9 unidirectional fluxes were computed using +equations 13,14 from +Feher JJ, *Biophys J.* 1984 June; 45(6): 1125b +[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1434995](http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1434995) + +The lines are not labeled but they are easy to compare with the figures in the paper. + +The mod file can be simplified by removing the calculation and storage of the individual forward and reverse fluxes, i.e. rf[] and rb[]. For use in a more complex model, this mod file should be modified with USEION statements to use na and k ion concentrations and generate ina and ik. The dynamic directory shows an example of this by extending the Chapman et al simulations using nai, ki, and atp as states, which, in the presence of leak channels for na, k and non-specific ions, produce reasonable na and k gradients. See dynamic/README. + +## Usage + +Simply auto-launch from ModelDB or compile the mod files under + +### MSWIN + +Use mknrndll (change directory to the one expanded from the archive and click "make nrnmech.dll"). Then run by double clicking the mosinit.hoc file in a windows explorer. + +### MAC OS X + +Drag and drop the expanded folder from this archive onto the mknrndll icon. Drag and drop the mosinit.hoc file onto the nrngui icon. + +### Linux/Unix + +Change directory to the expanded folder and type these two lines: +``` +nrnivmodl +nrngui mosinit.hoc +``` + +## Once the Simulation is Started + +Simply press the buttons to reproduce figures. For example pressing the "Figure 2-3" button leads to: + +![screenshot](./screenshot.jpg) + +--- + +2025-06-02: Converted README to Markdown. \ No newline at end of file