Merge branch 'master' of https://github.com/arbor-sim/nsuite

validation/rc-exp2syn-spike/README.md

@@ -1,15 +1,49 @@
-Placeholder doc: expand and move to nsuite docs.
+Model rc-exp2syn-spike
+======================
 
-* Model comprises two cells, each with a single compartment
-soma and passive channels together with a double-exponential
-synapse.
-* The synpase on the first cell is triggered at t = 0.
-* The synapse on the second cell is triggered by a spike generated
-on the first cell via a connection with configurable delay.
-* Times to first threshold crossing (spike) on each cell is recorded.
+This model comprises a single source cell connected to a number of
+target cells via a range of delays.
 
-Pass criterion: checks difference in spike times against
-a supplied `max_error` parameter, which hand-wavingly is
-set to three times dt. (Realistically, the pass criterion
-should be more relaxed.)
+Each cell has a single compartment with passive dynamics and a
+single double exponential synapse. The source cell, with label
+zero, has the synapse triggered at time _t_ = 0.
 
+When a cell membrane potential crosses the threshold value, it
+will generate a spike; the spike from the source cell is
+delivered to the target cell _k_ with quasirandom delay
+_d_ = _d₀_ + { _k_ φ }, where φ = (√ 5 − 1)/2.
+
+Each cell is equivalent to an RC circuit with two exponentially
+decaying current sources of opposite sign and different time
+constants.
+
+The fixed electrical parameters are as follows:
+
+| Parameter                  | Value   |
+|----------------------------|---------|
+| Total membrane resistance  | 100 MΩ  |
+| Total membrane capacitance | 0.01 nF |
+| Reversal potential         | -65 mV  |
+| Initial membrane voltage   | -65 mV  |
+| Synaptic time constants    | 0.5 ms  |
+|                            | 4.0 ms  |
+
+Test parameters
+---------------
+
+
+| Parameter   | Interpretation                                      |
+|-------------|-----------------------------------------------------|
+| `dt`        | maximum simulation integration timestep [ms]        |
+| `g0`        | initial current of exponential current sources [µS] |
+| `mindelay`  | minimum connection delay _d₀_ [ms]                  |
+| `threshold` | spiking threshold [mV]                              |
+| `ncell`     | total number of cells (including source)            |
+| `max_error` | acceptance threshold for spike time differences     |
+
+Acceptance critera
+------------------
+
+The recorded spike times from each cell should differ from the
+reference times by at most 3·_dt_. (This is set explicitly as
+the `max_error` test parameter.)

validation/rc-exp2syn-spike/default.param

@@ -1,3 +1,4 @@
+ncell=101
 dt=0.01
 g0=0.1
 mindelay=3.3

validation/rc-exp2syn-spike/generate-rc-exp2syn-spike

@@ -28,9 +28,10 @@ nsamp = 300
 ts = np.linspace(0., tend, num=nsamp)
 
 output, params = stdarg.parse_run_stdarg()
-param_vars = ['g0', 'mindelay', 'threshold']
+param_vars = ['g0', 'mindelay', 'threshold', 'ncell']
 for v in param_vars:
     if v in params: globals()[v] = params[v]
+ncell = int(ncell)
 
 # Voltage on one cell given by ODE:
 #

validation/rc-expsyn/README.md

@@ -0,0 +1,35 @@
+Model rc-expsyn
+===============
+
+The model describes a single compartment cell with passive dynamics and
+a single exponential synapse, that is triggered at time t = 0.
+
+This is equivalent to an RC circuit with an exponentially decaying
+current source.
+
+The fixed electrical parameters are as follows:
+
+| Parameter                  | Value   |
+|----------------------------|---------|
+| Total membrane resistance  | 100 MΩ  |
+| Total membrane capacitance | 0.01 nF |
+| Reversal potential         | -65 mV  |
+| Initial membrane voltage   | -65 mV  |
+| Synaptic time constant     | 1 ms    |
+
+Test parameters
+---------------
+
+
+| Parameter | Interpretation |
+|-----------|----------------|
+| `dt`      | maximum simulation integration timestep [ms] |
+| `g0`      | synaptic current at time _t_ = 0 [µS] |
+
+
+Acceptance critera
+------------------
+
+The relative error in membrane voltage should be within 1% of
+the reference value at time _t_ = 10 ms.
+