spyks

spyks is a tool for building and simulating simple, dynamical neuron models. It places a strong emphasis on efficient modification of parameters, because it's primarily intended for use in data assimilation applications where the goal is to estimate parameters and unmeasured states from recorded data. It is very much a work in progress.

In general, a dynamical neuron model comprises a set of ordinary differential equations dX/dt = F(X, t, θ) that determine how the state of the neuron X evolves in time. The components of the state vector include the membrane voltage and the (in)activation states of the various currents that contribute to the voltage. In the classical Hodgkin-Huxley model, these additional variables, called m, h, and n, obey first-order kinetics. In many phenomenological models, the voltage diverges when the neuron spikes, and the model must also include a rule for resetting the state when this occurs. The vector θ comprises parameters that govern the behavior of the system (for example, the reversal potential of the fast sodium current or the half-activation voltage of a delayed-rectifier potassium current). Parameters are assumed to be constant over the analysis interval.

In spyks, models are specified in a YAML document that contains at a minimum, the equations of motion in symbolic form and values for all of the parameters and state variables. The model may also include a reset rule. Values are specified with physical units for dimensional analysis and reduced errors from unit mismatches. Here's an example for the classic Hodkin-Huxley model. We're using hyperbolic tangents to parameterize the steady-state activation and time-constant functions for historical reasons (the derivatives are more numerically stable).

---
name: nakl
description: biophysical neuron model with minimal Na, K, leak conductances
author: dmeliza
version: 1.0
state:
  V: -70 mV
  m: 0
  h: 0
  n: 0
forcing:
  Iinj: 0 pA
equations:
  V: 1/C * ((gna*m*m*m*h*(Ena - V)) + (gk*n*n*n*n*(Ek - V)) + (gl*(El-V)) + Iinj)
  m:
    inf: (1+tanh((V - vm)/dvm))/2
    tau: (tm0 + tm1 * (1 - tanh((V - vmt)/dvmt)**2))
  h:
    inf: (1+tanh((V - vh)/dvh))/2
    tau: (th0 + th1 * (1 - tanh((V - vht)/dvht)**2))
  n:
    inf: (1+tanh((V - vn)/dvn))/2
    tau: (tn0 + tn1 * (1 - tanh((V - vnt)/dvnt)**2))
parameters:
  C: 250 pF
  gna: 120 nS
  Ena: 50 mV
  gk: 20 nS
  Ek: -77 mV
  gl: 0.3 nS
  El: -54.4 mV
  vm: -40 mV
  dvm: 15 mV
  tm0: 0.1 ms
  tm1: 0.4 ms
  vmt: -40 mV
  dvmt: 15 mV
  vh: -60 mV
  dvh: -15 mV
  th0: 1 ms
  th1: 7 ms
  vht: -60 mV
  dvht: -15 mV
  vn: -55 mV
  dvn: 40 mV
  tn0: 1 ms
  tn1: 5 ms
  vnt: -55 mV
  dvnt: -30 mV

Other examples are in the models directory. To compile this model into a Python extension module, just run spykscc models/nakl.yml in the shell.

Important: although spyks will do basic dimensional analysis to ensure that your parameters, equations, and state variables all have compatible dimensions, it currently cannot make sure that your parameters are scaled correctly. Capacitances have to be in pF, voltages in mV, conductances in nS, and times in ms. So for example, although you ought to be able to put in 0.25 nF in the model descriptor above, you'll wind up with a 0.25 pF cell. Working on it.

To integrate the model in Python using a pre-determined injected current:

import numpy as np
import spyks.core as spk

Iinj = np.zeros(10000)
Iinj[2000:] = 50
dt = 0.05

pymodel = spk.load_model("models/nakl.yml")
nakl = spk.make_model(pymodel, forcing=Iinj, forcing_dt=dt, path="models")

initial_state = spk.to_array(pymodel['state'])
X = nakl.integrate(initial_state, step=dt)

If the inject current is not know ahead of time (e.g. for control problems), you can also integrate iteratively:

nakl = spk.make_model(pymodel, forcing=[0.0], forcing_dt=dt, path="models")
state = spk.to_array(pymodel['state'])
out = [state]
# this will ramp up the injected current but obviously this can be a more complex computation
for i in range(100):
	forcing = [float(i) * 5]
	nakl.update_forcing(forcing, dt)
	state = nakl.step(state, time=i * dt, step=dt)
	out.append(state)

Note that the step() method returns the new state, which has to be saved and then passed back for the next step . The integrator and system function only do runtime checking on the bounds of the forcing array.

Installation Notes

To compile models, you'll need a C++ compiler that's compliant with the C++11 or later standard and the boost libraries installed (specifically boost odeint)
If installing from source, use pip install . (or pip install -e . for a live/development install) rather than python setup.py install. pybind11 may not install its headers correctly otherwise. If you get errors about missing headers running spykscc, try reinstalling pip uninstall pybind11; pip install pybind11

melizalab/spyks

spyks

Installation Notes