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Moose NCBS


Welcome to CNS*2022 Moose Session

Welcome to the MOOSE CNS tutorial June 2022 webpage.

Here is a brief overview of what we plan to do:

  - We plan to walk through the process of building multiscale models,
	starting with ephys, going on to chemical signaling, and
	culminating with some production multiscale models where 
	chemical and electrial signaling talk to each other.
- The examples we'll use are selected from among the Rdesigneur examples at
	in case you would like a preview.
- The key capability of Rdesigneur is to assemble quite complex models from
	standard formats, like NeuroML, SBML, .swc files, and so on. It also
	makes it easy to deliver stimuli and generate cool displays, all in
	just a few lines of Python.
- The entire contents of the tutorial are on a docker image. Installation 
	instructions and the link to the specific image are below.

Install and Running

We have provided docker images at bhallalab/pymoose.


- 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.


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

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


The tutorial be done online via Zoom.
Please register for the CNS*2022 satellite tutorials to receive the Zoom links.

Contact Us / Support

In case of any issues with installation or accessing the Zoom session, feel free to contact us at:
analkumar at ncbs dot res dot in
bhalla at ncbs dot res dot in
hrani at ncbs dot res dot in

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