Geppetto integration sample scripts

electrofluid.py

import numpy
import pylab as pl
from matplotlib import pyplot as plt
import time

class muscle_simulation():

    #sample script inspired from https://github.com/openworm/Smoothed-Particle-Hydrodynamics/blob/integrated_electrophysiology/src/main_sim.py

    def __init__(self,increment=1.0):
        #create pre- and post- synaptic sections

        self.increment = increment
        self.pre = h.Section()
        self.post = h.Section()

        for sec in self.pre,self.post:
            sec.insert('hh')

        #inject current in the pre-synaptic section
        self.stim = h.IClamp(0.5, sec=self.pre)
        self.stim.amp = 70.0
        self.stim.delay = 1500.0
        self.stim.dur = 500.0

        #create a synapse in the pre-synaptic section
        self.syn = h.ExpSyn(0.5,sec=self.post)

        #connect the pre-synaptic section to the synapse object:
        self.nc = h.NetCon(self.pre(0.5)._ref_v, self.syn)
        self.nc.weight[0] = 10.0

        #let's do some manaical  experimentation of the most evil kind:
        self.calcium_level = 0
        self.vector['calcium_level']=[self.calcium_level]

        self.voltage_plot, = plt.plot([],[])
        #plt.show()

    def addition_rate(self):
        opening = abs(post_v+65)
        opening = (opening**2/(opening**2+opening))
        current = opening*(1-self.state.calcium_level)/100
        return current

    def removal_rate(self):
        opening = abs(20-post_v)
        opening = (opening**2/(opening**2+opening))
        current = opening*(self.calcium_level)/100
        return -current
    

    def run(self,do_plot = True):
    #run and return resting potential
        t_now = h.t
        self.calcium_level += self.addition_rate()+self.removal_rate()
        self.vector['calcium_level'].append(self.calcium_level)
        self.muscle_contraction = self.calcium_level

GEPPETTO.xml

<?xml version="1.0" encoding="UTF-8"?>
<tns:simulation xmlns:tns="http://www.openworm.org/simulationSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openworm.org/simulationSchema ../../src/main/resources/schema/simulationSchema.xsd ">
  <tns:configuration>
    <tns:outputFormat>RAW</tns:outputFormat>
  </tns:configuration>
  <tns:entities>
    <tns:entity>
      <tns:id>muscle_cell</tns:id>
      <tns:aspects>
        <tns:aspect>
          <tns:modelInterpreter>lemsModelInterpreter</tns:modelInterpreter>
            <tns:modelURL>https://dl.dropboxusercontent.com/u/7538688/GeppettoSimulations/SingleComponentHH/LEMS_NML2_Ex5_DetCell.xml?dl=1</tns:modelURL>
          <tns:simulator>jLemsSimulator</tns:simulator>
          <tns:id>example1</tns:id>
          <tns:group>group1</tns:group>
        </tns:aspect>
        <tns:aspect>
          <tns:modelInterpreter>lemsModelInterpreter</tns:modelInterpreter>
            <tns:modelURL>https://dl.dropboxusercontent.com/u/7538688/GeppettoSimulations/SingleComponentHH/LEMS_NML2_Ex5_DetCell.xml?dl=1</tns:modelURL>
          <tns:simulator>jLemsSimulator</tns:simulator>
          <tns:id>example1</tns:id>
          <tns:group>group1</tns:group>
        </tns:aspect>
        </tns:aspects>
        <tns:scripts>
          <tns:script>
            <tns:statesMap>
              <tns:element state="hhpop[0].v" var="pre_v"></tns:element>
              <tns:element state="hhpop[1].v" var="post_v"></tns:element>
              <tns:element state="hhpop[1].i" var="sync_i"></tns:element>
              <tns:element state="hhpop[0].bioPhys1.membraneProperties.caChans.ca.m.q" var="calcium_level"></tns:element>
              <tns:element state="muscle[0].contraction" var="muscle_contraction"></tns:element>
            </tns:statesMap>
            <tns:URL>https://dl.dropboxusercontent.com/u/7538688/electrofluid.py</tns:scriptURL>
          </tns:script>
        </tns:scripts>
      
    </tns:entity>
  <tns:entities>
  <tns:name>example1</tns:name>
</tns:simulation>

gistfile1.txt

1) timesteps need to have a minimum common denominator (e.g. 2ms, 4ms)
2) internal variables for the integration script
  a) geppetto defines an interface for a method that gets exceuted every time there is an integration
3) the user needs to specify the exchange of information clock
  
  timestep_simA = 2E-6 //from TimeConfiguration, unrelated to the script
  timestep_simB = 1E-3 //from TimeConfiguration, unrelated to the script
  "sampling" integer simA = 5 //from TimeConfiguration, unrelated to the script
  "sampling" integer simB = 2 //from TimeConfiguration, unrelated to the script

  timestep_script (by default the fastest clock) = 2s
    - should not be faster than the fastest clock
    - can be as slow as the user desires
    - all clocks have a minimum common denominator