#You will need to install the NEURON module for Python https://www.neuron.yale.edu/neuron/static/new_doc/programming/python.html

#you might need to set the path with export PYTHONPATH=$PYTHONPATH:$HOME/local/lib/python/site-packages first

#good tutorial for using neuron with python here: https://romaincaze.files.wordpress.com/2015/06/neuron_tuto.pdf

import neuron

import matplotlib

import subprocess

from neuron import load_mechanisms

import sys

#Check which version of Tkinter you have and use proper import command

if sys.version_info[0] < 3:

import Tkinter as tk

else:

import tkinter as tk

matplotlib.use("TkAgg") #matplot lib backend

from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg

import matplotlib.pyplot as plt

from matplotlib.figure import Figure

import numpy as np

LARGE_FONT=("Arial",12)

###Define the default biophysical parameters###

maxNa=.12#max sodium conductance through voltage gated sodium channels (uS)

maxK=.036#max potassium conductance through voltage gated potasium channels (uS)

maxLeak=.0003#The leak conductance (uS)

injcurrent1=.1#Default current to inject into the neuron (nA)

injcurrent2=0#If you want a second current injected after the first (nA)

delay1=100#how long to wait in the voltage trace to inject the first current (ms)

delay2=200#how long to wait in the voltage trace to inject the second current (ms)

dur1=100#duration of first current injection (ms)

dur2=500#duration of second current injection (ms)

NaRev=50#voltage gated sodium channel reversal potential (mV)

KRev=-77#voltage gated potassium channel reversal potential (mV)

LeakRev=-54.3#leak channel reversal potential (mV)

time=np.zeros(12002)#initialize a time variable

voltage=np.zeros(12002)#inititialize a voltage variable

cellnum=0

colors=['b','r','g','k','m']#this holds the colors that are used to plot various traces if the simulation is run multiple times

legendlist=list()#a list to build legend entries for voltage traces so the student can keep track of the parameters used to generate the result

def on_closing():

if messagebox.askokcancel("Quit", "Do you want to quit?"):

root.destroy()

#The cell class...builds a default cell that may be modified by user input

class cell(object):

self.soma.el_hh=self.LV

def runsimulation(legtext,amp1,dur1,start1):

plt.show()

class ui_window(tk.Tk):

frame.tkraise() #raise to front

class StartPage(tk.Frame):

self.setdefaults()

app=ui_window()

app.wm_title('NEURON Biophysics')

app.mainloop()