Mitral cell activity gating by respiration and inhibition in an olfactory bulb NN (Short et al 2016)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:183300
To explore interactions between respiration, inhibition, and olfaction, experiments using light to active channel rhodopsin in sensory neurons expressing Olfactory Marker Protein were performed in mice and modeled in silico. This archive contains NEURON models that were run on parallel computers to explore the interactions between varying strengths of respiratory activity and olfactory sensory neuron input and the roles of periglomerular, granule, and external tufted cells in shaping mitral cell responses.
Reference:
1 . Short SM, Morse TM, McTavish TS, Shepherd GM, Verhagen JV (2016) Respiration Gates Sensory Input Responses in the Mitral Cell Layer of the Olfactory Bulb. PLoS One 11:e0168356 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron periglomerular GABA cell; Olfactory bulb main interneuron granule MC GABA cell; Olfactory bulb main tufted cell external;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Sensory processing; Sensory coding; Bursting; Oscillations; Olfaction;
Implementer(s): Morse, Tom [Tom.Morse at Yale.edu];
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron periglomerular GABA cell; Olfactory bulb main interneuron granule MC GABA cell;
Files displayed below are from the implementation
import Tkinter, Tkconstants, tkFileDialog

class TkFileDialogExample(Tkinter.Frame):

  def __init__(self, root):

    Tkinter.Frame.__init__(self, root)

    # options for buttons
    button_opt = {'fill': Tkconstants.BOTH, 'padx': 5, 'pady': 5}

    # define buttons
    Tkinter.Button(self, text='askopenfile', command=self.askopenfile).pack(**button_opt)
    Tkinter.Button(self, text='askopenfilename', command=self.askopenfilename).pack(**button_opt)
    Tkinter.Button(self, text='asksaveasfile', command=self.asksaveasfile).pack(**button_opt)
    Tkinter.Button(self, text='asksaveasfilename', command=self.asksaveasfilename).pack(**button_opt)
    Tkinter.Button(self, text='askdirectory', command=self.askdirectory).pack(**button_opt)

    # define options for opening or saving a file
    self.file_opt = options = {}
    options['defaultextension'] = '.txt'
    options['filetypes'] = [('all files', '.*'), ('text files', '.txt')]
    # options['initialdir'] = 'C:\\'
    options['initialdir'] = ''
    options['initialfile'] = 'myfile.txt'
    options['parent'] = root
    options['title'] = 'This is a title'

    # This is only available on the Macintosh, and only when Navigation Services are installed.
    #options['message'] = 'message'

    # if you use the multiple file version of the module functions this option is set automatically.
    #options['multiple'] = 1

    # defining options for opening a directory
    self.dir_opt = options = {}
    # options['initialdir'] = 'C:\\'
    options['initialdir'] = ''
    options['mustexist'] = False
    options['parent'] = root
    options['title'] = 'This is a title'

  def askopenfile(self):

    """Returns an opened file in read mode."""

    return tkFileDialog.askopenfile(mode='r', **self.file_opt)

  def askopenfilename(self):

    """Returns an opened file in read mode.
    This time the dialog just returns a filename and the file is opened by your own code.
    """

    # get filename
    filename = tkFileDialog.askopenfilename(**self.file_opt)

    # open file on your own
    if filename:
      return open(filename, 'r')

  def asksaveasfile(self):

    """Returns an opened file in write mode."""

    return tkFileDialog.asksaveasfile(mode='w', **self.file_opt)

  def asksaveasfilename(self):

    """Returns an opened file in write mode.
    This time the dialog just returns a filename and the file is opened by your own code.
    """

    # get filename
    filename = tkFileDialog.asksaveasfilename(**self.file_opt)

    # open file on your own
    if filename:
      return open(filename, 'w')

  def askdirectory(self):

    """Returns a selected directoryname."""

    return tkFileDialog.askdirectory(**self.dir_opt)

if __name__=='__main__':
  root = Tkinter.Tk()
  TkFileDialogExample(root).pack()
  root.mainloop()