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Making predefined populations

Erik A. Roberts edited this page Jul 31, 2018 · 7 revisions

Naming convention

Predefined populations are stored in text files (e.g., 'IB.pop') and simulated by passing the file name to dsSimulate (e.g., dsSimulate('IB')) or by equating population equations to it in the DynaSim specification structure (see example).

What to include

A population file describes a system/model, e.g. of a particular type of neuron. This file essentially stores a predefined specification. The syntax is identical to using the equation notation with a cell array of strings, except for the addition of the populationName: line at the top, and the strings being written without the apostrophe: '.

% populationName:

% ODEs
dV2/dt=(@current+E-V+R.*Iapp+@current)./tau; V(0)=reset

% ICs

% Parameters
%  Mixed between semicolon separated lists and separate lines
Iapp=0; gNaF=100; gKDR=5; gM=1.5; Cm=1
reset=-75; thresh=-55; tau=10; R=10; E=-70

Inspired by feedback from Matt Ning