File: tutorial_1a_the_simplest_brian_program.txt

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 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114 .. currentmodule:: brian Tutorial 1a: The simplest Brian program *************************************** Importing the Brian module ~~~~~~~~~~~~~~~~~~~~~~~~~~ The first thing to do in any Brian program is to load Brian and the names of its functions and classes. The standard way to do this is to use the Python ``from ... import *`` statement. :: from brian import * Integrate and Fire model ~~~~~~~~~~~~~~~~~~~~~~~~ The neuron model we will use in this tutorial is the simplest possible leaky integrate and fire neuron, defined by the differential equation: tau dV/dt = -(V-El) and with a threshold value Vt and reset value Vr. Parameters ~~~~~~~~~~ Brian has a system for defining physical quantities (quantities with a physical dimension such as time). The code below illustrates how to use this system, which (mostly) works just as you'd expect. :: tau = 20 * msecond # membrane time constant Vt = -50 * mvolt # spike threshold Vr = -60 * mvolt # reset value El = -60 * mvolt # resting potential (same as the reset) The built in standard units in Brian consist of all the fundamental SI units like second and metre, along with a selection of derived SI units such as volt, farad, coulomb. All names are lowercase following the SI standard. In addition, there are scaled versions of these units using the standard SI prefixes m=1/1000, K=1000, etc. Neuron model and equations ~~~~~~~~~~~~~~~~~~~~~~~~~~ The simplest way to define a neuron model in Brian is to write a list of the differential equations that define it. For the moment, we'll just give the simplest possible example, a single differential equation. You write it in the following form:: dx/dt = f(x) : unit where ``x`` is the name of the variable, ``f(x)`` can be any valid Python expression, and ``unit`` is the physical units of the variable ``x``. In our case we will write:: dV/dt = -(V-El)/tau : volt to define the variable ``V`` with units ``volt``. To complete the specification of the model, we also define a threshold and reset value and create a group of 40 neurons with this model. :: G = NeuronGroup(N=40, model='dV/dt = -(V-El)/tau : volt', threshold=Vt, reset=Vr) The statement creates a new object 'G' which is an instance of the Brian class :class:`NeuronGroup`, initialised with the values in the line above and 40 neurons. In Python, you can call a function or initialise a class using keyword arguments as well as ordered arguments, so if I defined a function ``f(x,y)`` I could call it as ``f(1,2)`` or as ``f(y=2,x=1)`` and get the same effect. See the Python tutorial for more information on this. For the moment, we leave the neurons in this group unconnected to each other, each evolves separately from the others. Simulation ~~~~~~~~~~ Finally, we run the simulation for 1 second of simulated time. By default, the simulator uses a timestep dt = 0.1 ms. :: run(1 * second) And that's it! To see some of the output of this network, go to the next part of the tutorial. Exercise ~~~~~~~~ The units system of Brian is useful for ensuring that everything is consistent, and that you don't make hard to find mistakes in your code by using the wrong units. Try changing the units of one of the parameters and see what happens. Solution ~~~~~~~~ You should see an error message with a Python traceback (telling you which functions were being called when the error happened), ending in a line something like:: Brian.units.DimensionMismatchError: The differential equations are not homogeneous!, dimensions were (m^2 kg s^-3 A^-1) (m^2 kg s^-4 A^-1)