IF lecture

.gitignore

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 /.quarto/
+.ipynb_checkpoints*
+Dont-Sync-2024*
+__pycache__*

.gitignore~

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+Don't-Sync/
+*.mp4
+*.ogv
+*.DS_Store
+*~

docs/IF.html

@@ -228,7 +228,7 @@
 }
 
 // Store cell data
-globalThis.qpyodideCellDetails = [{"id":1,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"import numpy as np\nimport matplotlib.pyplot as plt"},{"id":2,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"C=1.0\nI=1.0"},{"id":3,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"dt=0.01"},{"id":4,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"V = np.zeros([1000,1])\nnp.shape(V)"},{"id":5,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"V[0]=0.2"},{"id":6,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"for k in range(1,999):\n    V[k+1] = V[k] + dt*(I/C)"},{"id":7,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"plt.figure()\nplt.plot(V)\nplt.show()"},{"id":8,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"t = np.arange(0,len(V))*dt"},{"id":9,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"plt.figure()\nplt.plot(t,V)\nplt.xlabel('Time [s]')\nplt.ylabel('V')\nplt.show()"},{"id":10,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"import numpy as np\nimport matplotlib.pyplot as plt\n\nI   = 1                           #Set the parameter I.\nC   = 1                           #Set the parameter C.\ndt  = 0.01                        #Set the timestep.\nV   = np.zeros([1000,1])             #Initialize V.\nV[0]= 0.2;                        #Set the initial value of V.\n\nfor k in range(1,999):            #March forward in time,\n    V[k+1] = V[k] + dt*(I/C)      #... updating V along the way.\n\nt = np.arange(0,len(V))*dt        #Define the time axis.\n\nplt.figure()\nplt.plot(t,V)                         #Plot the results.\nplt.xlabel('Time [s]')\nplt.ylabel('Voltage [mV]')\nplt.show()"},{"id":11,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"Vth = 1;        #Define the voltage threshold.\nVreset = 0;     #Define the reset voltage.\n\nfor k in range(1,999):            #March forward in time,\n    V[k+1] = V[k] + dt*(I/C)      #Update the voltage,\n    ### ADD SOMETHING HERE??? --------------------------"},{"id":12,"options":{"out-height":"","fig-height":5,"warning":"true","fig-cap":"","dpi":72,"read-only":"false","results":"markup","output":"true","fig-width":7,"label":"","autorun":"","context":"interactive","message":"true","classes":"","comment":"","out-width":"700px"},"code":"### ADD YOUR CODE!"}];
+globalThis.qpyodideCellDetails = [{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":1,"code":"import numpy as np\nimport matplotlib.pyplot as plt"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":2,"code":"C=1.0\nI=1.0"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":3,"code":"dt=0.01"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":4,"code":"V = np.zeros([1000,1])\nnp.shape(V)"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":5,"code":"V[0]=0.2"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":6,"code":"for k in range(1,999):\n    V[k+1] = V[k] + dt*(I/C)"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":7,"code":"plt.figure()\nplt.plot(V)\nplt.show()"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":8,"code":"t = np.arange(0,len(V))*dt"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":9,"code":"plt.figure()\nplt.plot(t,V)\nplt.xlabel('Time [s]')\nplt.ylabel('V')\nplt.show()"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":10,"code":"import numpy as np\nimport matplotlib.pyplot as plt\n\nI   = 1                           #Set the parameter I.\nC   = 1                           #Set the parameter C.\ndt  = 0.01                        #Set the timestep.\nV   = np.zeros([1000,1])             #Initialize V.\nV[0]= 0.2;                        #Set the initial value of V.\n\nfor k in range(1,999):            #March forward in time,\n    V[k+1] = V[k] + dt*(I/C)      #... updating V along the way.\n\nt = np.arange(0,len(V))*dt        #Define the time axis.\n\nplt.figure()\nplt.plot(t,V)                         #Plot the results.\nplt.xlabel('Time [s]')\nplt.ylabel('Voltage [mV]')\nplt.show()"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":11,"code":"Vth = 1;        #Define the voltage threshold.\nVreset = 0;     #Define the reset voltage.\n\nfor k in range(1,999):            #March forward in time,\n    V[k+1] = V[k] + dt*(I/C)      #Update the voltage,\n    ### ADD SOMETHING HERE??? --------------------------"},{"options":{"dpi":72,"label":"","fig-width":7,"out-height":"","context":"interactive","fig-height":5,"out-width":"700px","fig-cap":"","classes":"","results":"markup","message":"true","comment":"","autorun":"","read-only":"false","output":"true","warning":"true"},"id":12,"code":"### ADD YOUR CODE!"}];
 
 
 </script>
@@ -782,27 +782,28 @@ <h1 data-number="6"><span class="header-section-number">6</span> I&amp;F CODE (v
 <section id="discussion" class="level1" data-number="7">
 <h1 data-number="7"><span class="header-section-number">7</span> Discussion</h1>
 <ol type="1">
-<li>Describe the main components of the IF model. Draw it (in some way).</li>
-<li>Describe the main components of the LIF model. Draw it (in some way).</li>
-<li>Describe the differences and similarities between the IF and LIF models.</li>
-<li>The IF model is meant to mimic a neurons activity. Describe what is realistic about the IF model? What is unrealistic?</li>
-<li>Describe the roles of the IF model parameters <code>Vreset</code> and <code>Vthreshold</code>.</li>
-<li>Consider the IF model. Sketch voltage (V) versus time (t) for a small input current, for a large input current.
+<li><p>Describe the main components of the <strong>IF</strong> model. Draw it (in some way).</p></li>
+<li><p>Describe the main components of the <strong>LIF</strong> model. Draw it (in some way).</p></li>
+<li><p>Describe the differences and similarities between the IF and LIF models.</p></li>
+<li><p>The IF model is meant to mimic a neurons activity. What is realistic about the IF model? What is unrealistic?</p></li>
+<li><p>Describe the roles of the IF model parameters <code>Vreset</code> and <code>Vthreshold</code>.</p></li>
+<li><p>Consider the IF model. Sketch voltage (V) versus time (t) for a small input current, for a large input current.</p>
 <ol type="1">
 <li>How does an increase in capacitance (C) impact the dynamics?</li>
 <li>Can you interpret this physically?</li>
 </ol></li>
+<li><p>Plot the f-I curve for the IF model.</p></li>
 </ol>
 <hr>
 </section>
 <section id="challenges" class="level1" data-number="8">
 <h1 data-number="8"><span class="header-section-number">8</span> Challenges</h1>
 <ol type="1">
-<li>Consider the <em>LIF</em> model. Plot (in Python) voltage (V) versus time (t) for a small input current, for a large input current.</li>
-<li>How does an increase in the capacitance (C) impact the dynamics of the LIF model?</li>
-<li>How does an increase in the resistance (R) impact the dynamics of the LIF model?</li>
-<li>Determine how the firing rate of the LIF model varies with input I. Plot the firing rate versus I (i.e., plot the “f-I curve”).</li>
-<li><strong>ADVANCED</strong>. Simulate the <a href="./Readings/Izhikevich_2003.pdf">Izhikevich neuron</a>. Provide examples of two different types of spiking activity.</li>
+<li><p>Consider the <strong>LIF</strong> model. Plot (in Python) voltage (V) versus time (t) for a small input current, for a large input current.</p></li>
+<li><p>Perform numerical simulations to determine how doubling the capacitance (C) impacts the firing rate of the LIF model. Based on your numerical simulations, does the firing rate increase or decrease? Provide a physical explanation for your results (i.e., how does the charge move around the circuit to impact the firing rate?) HINT: Capacitance represents the <em>capacity</em> of a cell to hold charge.</p></li>
+<li><p>Perform numerical simulations to determine how doubling the resistance (R) impacts the firing rate of the LIF model. Based on your numerical simulations, does the firing rate increase or decrease? Provide a physical explanation for your results (i.e., how does the charge move around the circuit to impact the firing rate?) HINT: Higher resistance makes it harder for charge to flow in or out of the cell.</p></li>
+<li><p>Determine how the firing rate of the LIF model varies with input I. Plot the firing rate versus I (i.e., plot the “f-I curve”).</p></li>
+<li><p><strong>ADVANCED</strong>. Simulate the <a href="./Readings/Izhikevich_2003.pdf">Izhikevich neuron</a>. Provide examples of two different types of spiking activity.</p></li>
 </ol>