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BrainGrid

A project to facilitate construction of high-performance neural simulations

4. Configuring the model

Now that you have run through a quick test and made sure you have a working BrainGrid repository, it is time to learn how to use it!

We will be going through this in a few steps:

  1. First, we will look at how to implement a quick and dirty model and simulation parameters, which will involve putting together all the files that BrainGrid uses as inputs.

  2. Second, we will configure BrainGrid to use a GPU (you’ve already seen how to do it with a single thread). And then we will run the simulation.

  3. Lastly, we will collect BrainGrid’s output and examine a few ways one might actually visualize the data.

Ready? Okay.

4.1 Inside the Config files

There are two config files needed to run a simulation on BrainGrid:

  1. The input (or “stimulation”) file - SimInfoParams
  2. The model configuration - ModelParams

First, we are going to go through using a built-in model. This is by far the easiest route - if you have a quick idea you want to play with that uses a grid of Izhikivich or LIF neurons, go for it! As long as you only want to use excitatory and inhibitory neurons, this is the way to go. I’ll show you how to specify the parameters you want and then run the simulation.

If on the other hand, you have a more complicated model in mind - such as using different types of neurotransmitters, then you will have to get your hands dirty writing some C++ code. Don’t worry though, I’ll walk you through that too.

4.2.2 Use built-in models

Let’s go through the steps required to use a built-in model.

Take a look at test-tiny.xml file that is under BrainGrid/validation directory:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Parameter file for the DCT growth modeling -->
<!-- This file holds constants, not state information -->
<SimInfoParams>
   <!-- size of pool of neurons [x y z] -->
   <PoolSize x="2" y="2" z="1"/>
   <!-- Simulation Parameters -->
   <SimParams Tsim="1.0" numSims="1"/>
   <!-- Simulation Configuration Parameters -->
   <SimConfig maxFiringRate="200" maxSynapsesPerNeuron="200"/>
   <!-- Random seed - set to zero to use /dev/random -->
   <!-- TODO: implement support for this -->
   <Seed value="1"/>
   <!-- State output file name, this name will be overwritten if -o option is specified -->
   <OutputParams stateOutputFileName="test-tiny-out.xml"/>
</SimInfoParams>

<ModelParams>
   <NeuronsParams class="AllLIFNeurons">
      <!-- Interval of constant injected current -->
      <Iinject min="13.5e-09" max="13.5e-09"/>
      <!-- Interval of STD of (gaussian) noise current -->
      <Inoise min="1.0e-09" max="1.5e-09"/>
      <!-- Interval of firing threshold -->
      <Vthresh min="15.0e-03" max="15.0e-03"/>
      <!-- Interval of asymptotic voltage -->
      <Vresting min="0.0" max="0.0"/>
      <!-- Interval of reset voltage -->
      <Vreset min="13.5e-03" max="13.5e-03"/>
      <!-- Interval of initial membrance voltage -->
      <Vinit min="13.0e-03" max="13.0e-03"/>
      <!-- Starter firing threshold -->
      <starter_vthresh min="13.565e-3" max="13.655e-3"/>
      <!-- Starter reset voltage -->
      <starter_vreset min="13.0e-3" max="13.0e-3"/>
   </NeuronsParams>
   
   <SynapsesParams class="AllDSSynapses">
   </SynapsesParams>
   
   <ConnectionsParams class="ConnGrowth">
      <!-- Growth parameters -->
      <GrowthParams epsilon="0.60" beta="0.10" rho="0.0001" targetRate="1.9" minRadius="0.1" startRadius="0.4"/>
   </ConnectionsParams>

   <LayoutParams class="FixedLayout">

      <!-- If FixedLayout is present, the grid will be laid out according to the positions below, rather than randomly based on LsmParams -->
      <FixedLayoutParams>
         <!-- 0-indexed positions of endogenously active neurons in the list -->
         <A>0</A>

         <!-- 0-indexed positions of inhibitory neurons in the list -->
         <I>1</I>
        
         <!--
         original 10x10 (not updated for 30x30)
            9 . . . . . . . A . .
            8 . . . . . . . . . .
            7 . A . . A . . . . .
            6 . . . . . . I A . .
            5 . . . . . . . . . .
            4 . A . . A . . . . .
            3 . . . I . . . A . .
            2 . . . . . . . . . .
            1 . A . . A . . . . .
            0 . . . . . . . A . .
              0 1 2 3 4 5 6 7 8 9
         -->
      </FixedLayoutParams>
   </LayoutParams>
</ModelParams>

This is a typical example of a model configuration file that you must give to use BrainGrid. This type of file is mandatory - BrainGrid won’t run without specifying model parameters. Even if you plan on writing your own model from “scratch”, you may want to read this section anyway.

You can see that this file is a pretty standard XML file. It has tags that specify what each section is, like <SimInfoParams> and end tags that end said section, like </SimInfoParams>. Within each section, you can have sub-sections ad infinitum (in fact, XML files follow a tree structure, with a root node which branches into a top level of nodes, which branch into their own nodes, which branch, etc.)

Notice the <!-- Parameter file for the DCT growth modeling --> Anything that follows that pattern (i.e., <!-- blah blah blah --> is a comment, and won’t have any effect on anything. It is good practice to comment stuff in helpful, far-seeing ways.

On to the actual parameters.

SimInfoParams

The first set of parameters that BrainGrid expects out of this file is stored in the SimInfoParams node. These parameters are required no matter what your model is. Here you must specify the:

ModelParams

The next set of parameters is the ModelParams. These parameters are specific to your model. Later, when we go through the “from scratch” example (where you will code up your own model using C++ to provide utmost flexibility), you will specify what goes here. But for now, we are using a built in model - specifically LIF (leaky integrate and fire), just to see what’s expected. You must specify the:

» Next: 5. Examples

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