Agenda

- Here is a very brief overview of the specific examples we'll work through:
	1. ex3.0	HH model.
			- Load and run
			- Show how to use matplotlib display
			- Change stimulus duration and ampl
			- Plot an extra field, like gNa

	2. ex4.1 	HH model on ball-and-stick, to show AP propgn
			- Show how to use display
				- rotate
				- zoom/pan with mouse
				- zoom/pan keys
				- replay
			- Change dend length
			- Change Na levels in dend to lose AP.

	3. ex9.0	Load and display arbitrary neuron morphology
			- Run with a bigger model like VHC
			- Add active spines to it. Look at them
			- Add random stim to active spines. Look at it.
			- Change spine density
			- Swap out cell model, show that spines appear in VHC.
			[- add active chans to soma and elsewhere ]
        3.5 ex9.3	spiral_spines
		        -Illustrates how to place spines in a spiral around the dendrite. 
                         For good measure the spines get bigger the further they are from the soma.

        
	4. ex6.0	Load chemical oscillator, single compt
                       
 			s ---a---> a  // s goes to a, catalyzed by a.
			s ---a---> b  // s goes to b, catalyzed by a.
			a ---b---> s  // a goes to s, catalyzed by b.
			b -------> s  // b is degraded irreversibly to s

	5. ex7.0	Load chemical oscillator, reac-diff
			- Run, rotate etc.
			- Point out 3 diffs with single compt: 
				- diffusion length
				- moogList and displayMoogli
				- initial conditions for osc.
			- Change initial conditions to start in middle.



	[ex7.4 travelling oscillator
			- Reminder on distribution of chem along dendrite.
			- Show what motor const does.


        
	ex8.4	3-D view of synaptically triggered CICR
			- Play with display
			- Scale dia up and down
			- Visualize just the elec and just the chem, comment
				out lines on moogList.
			- Walk through main blocks, esp adaptorList
			- Standard changes like making cell longer, more spines, etc.


        
        
	ex11.0	Presynaptic dynamics
			- Play with display
			- Note how presynaptic boutons are placed magically next to
				each spine, in the chemDistrib line.
			- Note how the adaptor converts the released glu into activation
				of postsyn receptor.
			- Note stochasticity flag. We can flip it.
			- Understand stimulus string to deliver burst of presyn inputs.



        
        
	ex12.0	Detection of synaptic input sequences as illustration of
			complex production level simulation.
			- Structure of model: 
			- Y cell (could be any shape)
				- complex patterned synaptic input + rand input.
				- 5 different cases on different parts of dend
			- Couple receptors to Ca influx -> chem pathways.
			- Chem pathways build up if sequence input.
			- Run it and see what it does.
	
	
	

When

Date: Monday, 27th June 2022 .
Time: 16.00-18.00 (UTC) / 21.30-23.30 (IST)

[repeat]
Date: Tuesday, 28th June 2022 .
Time: 06.00-7.30 (UTC) / 11.30-13.00(IST)