Week 12 report (August 12 to August 18)

Revisiting Human-readable export work and create mdexport device mode.

Associated pull request: #37

To provide flexibility as well as standard representation, we decided to use a class with expand functions that can generate standard markdown text and also can be override to modify the default words and representations. That was something very satisfying and there were many insightful feedbacks from my mentor to improve the structure and wordings.

Choosing markdown was a good choice, as converting to LaTeX or pdf are very easy.

The markdown output of COBAHH example is,

Network details

The Network consists of 1 simulation run ___________________________

Duration of simulation is 1. s

Synapses defined:

From neurongroup_subgroup_1 to neurongroup

Pathways:

On pre of event spike statements: $gi$ += $wi$ executed

Constants:

$wi$ : $67. nS$
From neurongroup_subgroup to neurongroup

Pathways:

On pre of event spike statements: $ge$ += $we$ executed

Constants:

$we$ : $6. nS$

StateMonitor defined:

Monitors variable: $v$ of neurongroup, for members: 1,10,100.

NeuronGroup defined:

Name neurongroup, with population size 4000.

Dynamics:

$\frac{d}{d t} ge$ ← $- \frac{1.0.ge}{taue}$ , where unit of $ge$ is S

$\frac{d}{d t} v$ ← $\frac{- g_{kd}.n^{4}.\left(- EK v\right) - g_{na}.h.m^{3}.\left(- ENa v\right) ge.\left(Ee - v\right) gi.\left(Ei - v\right) gl.\left(El - v\right)}{Cm}$ , where unit of $v$ is V

$\beta_{m}$ ← $\frac{1.4}{ms.{exprel}{\left(\frac{- VT - 40.mV v}{5.mV} \right)}}$ , where unit of $\beta_{m}$ is Hz

$\alpha_{h}$ ← $\frac{0.128.e^{\frac{VT 17.mV - v}{18.mV}}}{ms}$ , where unit of $\alpha_{h}$ is Hz

$\beta_{n}$ ← $\frac{0.5.e^{\frac{VT 10.mV - v}{40.mV}}}{ms}$ , where unit of $\beta_{n}$ is Hz

$\frac{d}{d t} h$ ← $\alpha_{h}.\left(1 - h\right) - \beta_{h}.h$ , where unit of $h$ is rad

$\alpha_{m}$ ← $\frac{1.28}{ms.{exprel}{\left(\frac{VT 13.mV - v}{4.mV} \right)}}$ , where unit of $\alpha_{m}$ is Hz

$\beta_{h}$ ← $\frac{4.0}{ms.\left(e^{\frac{VT 40.mV - v}{5.mV}} 1\right)}$ , where unit of $\beta_{h}$ is Hz

$\frac{d}{d t} gi$ ← $- \frac{1.0.gi}{taui}$ , where unit of $gi$ is S

$\alpha_{n}$ ← $\frac{0.16}{ms.{exprel}{\left(\frac{VT 15.mV - v}{5.mV} \right)}}$ , where unit of $\alpha_{n}$ is Hz

$\frac{d}{d t} m$ ← $\alpha_{m}.\left(1 - m\right) - \beta_{m}.m$ , where unit of $m$ is rad

$\frac{d}{d t} n$ ← $\alpha_{n}.\left(1 - n\right) - \beta_{n}.n$ , where unit of $n$ is rad

exponential_euler method is used for integration

Events:

Event spike, after $v \gt - 20.mV$ , with refractory $3. ms$

Constants:

$taue$ : $5. ms$ , $Ee$ : $0. V$ , $Cm$ : $200. pF$ , $taui$ : $10. ms$ , $ENa$ : $50. mV$ , $El$ : $-60. mV$ , $Ei$ : $-80. mV$ , $VT$ : $-63. mV$ , $gl$ : $10. nS$ , $g_{na}$ : $20. uS$ , $EK$ : $-90. mV$ , $g_{kd}$ : $6. uS$

Initializers defined:

Variable $v$ of neurongroup initialized with $El mV.\left(5.{randn}{\left(- \right)} - 5\right)$ to all members. Identifier associated: $El$ : $-60. mV$
Variable $ge$ of neurongroup initialized with $nS.\left(15.0.{randn}{\left(- \right)} 40.0\right)$ to all members
Variable $gi$ of neurongroup initialized with $nS.\left(120.0.{randn}{\left(- \right)} 200.0\right)$ to all members

Synaptic Connections defined:

Connection from neurongroup_subgroup to neurongroup, with probabilty $0.02$
Connection from neurongroup_subgroup_1 to neurongroup, with probabilty $0.02$

Written on August 12, 2020