insilicoNeuronal Network Simulation C++ Library

Pranav KulkarniProgrammer, Dr Collins Assisi Lab,IISER Pune

Agenda

● Introduction● Library Design● File Structure● Usage

○ Boost.odeint and example○ Example in Computational Neuroscience○ Memory management○ Data access mechanism

● Example code● Links

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Introduction

About● insilico is a C++ library for writing Neuronal Network

Simulations in Computational Neuroscience● Developed using C++11, a modern language standard for C++● An easy-to-use application programming interface (API)

Dependencies● Boost.odeint● GCC 4.7+

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Library Design

4

File Structure

5

Usage

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Boost.odeint

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About● Boost is collection of free portable C++ source libraries● Boost.odeint is a modern C++ library for numerically

solving Ordinary Differential Equations● Developed by Dr Karsten Ahnert and Dr Mario

Mulansky● Homepage: http://headmyshoulder.github.io/odeint-v2/● Part of Boost C++ Library since September 2012

Boost.odeint Example: Lorenz system

// Function that contains dx/dt corresponding to each x

void lorenz( const state_type &x , state_type &dxdt , double t ) {

dxdt[0] = sigma * ( x[1] - x[0] );

dxdt[1] = R * x[0] - x[1] - x[0] * x[2];

dxdt[2] = -b * x[2] + x[0] * x[1];

}

// Main function

int main(int argc, char **argv)

{

state_type x = { 10.0 , 1.0 , 1.0 }; // initial conditions

integrate( lorenz , x , 0.0 , 25.0 , 0.1 , write_lorenz );

} 8

Example: HH Neuron Model

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Modeling

Neuron Input File insilico’s Memory Mapping

dxdt:4,

v:-65,

m:0.1,

h:0.9,

n:1,

iext:-5,

del:0.02,

sd:0.5;10

HH Neuron in insilico

1 class HH_Neuron : public Neuron {

2 private:

3 I_Na i_na_component;

4 I_K i_k_component;

5 I_Leak i_leak_component;

6 public:

7 void ode_set(state_type& variables, state_type& dxdt, const double t, const unsigned id) {

8 i_na_component.current(variables, dxdt, t, id);

9 i_k_component.current(variables, dxdt, t, id);

10 i_leak_component.current(variables, dxdt, t, id);

11 double I_Na = engine::neuron_value(id, "I_Na");

12 double I_K = engine::neuron_value(id, "I_K");

13 double I_Leak = engine::neuron_value(id, "I_Leak");

14 double I_Ext = engine::neuron_value(id, "I_Ext");

15

16 int v_index = engine::neuron_index(id, "v");

17 dxdt[v_index] = - I_Na - I_K - I_Leak + I_Ext;

18 }

19 }; 11

I_Na current in insilico

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1 class I_Na {

2 private:

3 double gna = 120, ena = 115;

4 public:

5 void current(state_type& variables, state_type& dxdt,

const double t, const unsigned id) {

6 int v_index = engine::neuron_index(id, "v");

7 int m_index = engine::neuron_index(id, "m");

8 int h_index = engine::neuron_index(id, "h");

9 double v = variables[v_index];

10 double m = variables[m_index];

11 double h = variables[h_index];

.. // ...snipped...

16 dxdt[m_index] = (alpha_m * (1-m) - beta_m * m);

17 dxdt[h_index] = (alpha_h * (1-h) - beta_h * h);

18

19 engine::neuron_value(id, "I_Na", (gna * pow(m, 3) * h * (v - ena)));

20 }

21 };

Links

● insilico’s Homepagehttp://www.iiserpune.ac.in/~collins/insilico/

● insilico’s Mailing List a.k.a. Developer Channelhttps://groups.google.com/forum/#!forum/insilico

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Thank You!

Questions?

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