From b6e60b1ec6220e3e9b33e70e14eac11bbd33e5a5 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Thu, 21 Oct 2021 10:06:30 +0200
Subject: [PATCH] Polish GJ example readme (#1726)
---
example/gap_junctions/gap_junctions.cpp | 2 +-
example/gap_junctions/readme.md | 50 +++++++++++++++++--------
2 files changed, 35 insertions(+), 17 deletions(-)
diff --git a/example/gap_junctions/gap_junctions.cpp b/example/gap_junctions/gap_junctions.cpp
index 08a67b5c..28e4330b 100644
--- a/example/gap_junctions/gap_junctions.cpp
+++ b/example/gap_junctions/gap_junctions.cpp
@@ -315,7 +315,7 @@ arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration)
decor.place(arb::mlocation{0, 1}, arb::gap_junction_site{}, "local_0");
decor.place(arb::mlocation{0, 1}, arb::gap_junction_site{}, "local_1");
- // Attach a stimulus to the second cell.
+ // Attach a stimulus to the first cell of the first group
if (!gid) {
auto stim = arb::i_clamp::box(0, stim_duration, 0.4);
decor.place(arb::mlocation{0, 0.5}, stim, "stim");
diff --git a/example/gap_junctions/readme.md b/example/gap_junctions/readme.md
index a338020c..c334c2d2 100644
--- a/example/gap_junctions/readme.md
+++ b/example/gap_junctions/readme.md
@@ -1,26 +1,44 @@
# Gap Junctions Example
+A miniapp that demonstrates how to build a network with gap junctions.
-A miniapp that demonstrates how to describe how to build a network with gap junctions.
+## Cells
+Cells have a simple ball-and-stick morphology with gap junctions attached at the
+end of the soma. The following mechanisms are assigned to the complete cell
-##Structure:
-Cells are structured into groups that are inter-connected by gap junctions; Groups are
-connected by synapses. The first cell of the first group (top left in diagram) has a
-current stimulus.
+- `nax`: `gbar=0.04`, `sh=10`
+- `gbar`: `gbar=0.0001`
+- `kamt`: `gbar=0.004`
+- `pas`: `e=-65 mV`, `g=1/12000`
+```
+Soma (A=500π µm^2)
+
+ /\\\\\\\
+( ))))))) ()=================) Dendrite (l=300 µm, r=1.5 µm)
+ \///////
+ *
+ GJ
+```
+
+## Network
+Cells are structured into groups ('cables') that are inter-connected by gap
+junctions; Groups are connected by synapses. The first cell of the first group
+(top left in diagram) has a current stimulus.
```
-c --gj-- c --gj-- c --gj-- c --gj-- c
- |
- syn
- |
-c --gj-- c --gj-- c --gj-- c --gj-- c
-|
-syn
-|
-c --gj-- c --gj-- c --gj-- c --gj-- c
+ c --gj-- c --gj-- c --gj-- c --gj-- c # Cable 0
+ ^ |
+ I_s syn
+ |
+ c --gj-- c --gj-- c --gj-- c --gj-- c # Cable 1
+ |
+ syn
+ |
+ c --gj-- c --gj-- c --gj-- c --gj-- c # Cable 2
+ |
+ ...
```
-
## Tunable parameters
* _n_cables_: number of groups of cells connected by gap junctions.
* _n_cells_per_cable_: number of cells in a group.
@@ -42,4 +60,4 @@ An example parameter file is:
"sim-duration": 100,
"print-all": false
}
-```
\ No newline at end of file
+```
--
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