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1		-XWiki.abonard
	1	+XWiki.jessicamitchell

Content

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	1	+Available tutorials:
1	1
	3	+=== [[Construction and Use of Models: Part 1. Elementary tools>>https://neuron.yale.edu/neuron/static/docs/elementarytools/outline.htm||rel=" noopener noreferrer" target="_blank"]] ===
2	2
3		-* ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
	5	+//Level: beginner//
4	4
5		-=== **Beginner** ===
	7	+A good beginner's tutorial. Introduces some of NEURON's basic GUI tools.
	8	+=== [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel=" noopener noreferrer" target="_blank"]] ===
6	6
7		-=== [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
	10	+//Level: beginner//
8	8
9		-**Level**: beginner(%%) **Type**: user documentation
	12	+=== [[1. Implement and test the computational model itself>>https://neuron.yale.edu/neuron/docs/1-implement-and-test-computational-model-itself-0||rel=" noopener noreferrer" target="_blank"]] ===
10	10
11		-After this tutorial, students will be able to replicate neurons using templates and connect these neurons together.
	14	+//Level: advanced//
	15	+
	16	+=== [[2. Run a "complete" simulation and save its results>>https://neuron.yale.edu/neuron/docs/2-run-complete-simulation-and-save-its-results||rel=" noopener noreferrer" target="_blank"]] ===
	17	+
	18	+//Level: advanced//
	19	+
	20	+=== [[3. Run a segmented simulation and save its results>>https://neuron.yale.edu/neuron/docs/3-run-segmented-simulation-and-save-its-results||rel=" noopener noreferrer" target="_blank"]] ===
	21	+
	22	+//Level: advanced//
	23	+
	24	+=== [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel=" noopener noreferrer" target="_blank"]] ===
	25	+
	26	+//Level: advanced//
	27	+
	28	+=== [[4. Reconstitute and verify the "complete" simulation results>>https://neuron.yale.edu/neuron/docs/4-reconstitute-and-verify-complete-simulation-results||rel=" noopener noreferrer" target="_blank"]] ===
	29	+
	30	+//Level: advanced//
	31	+
12	12	=== [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel=" noopener noreferrer" target="_blank"]] ===
13	13
14		-**Level**: beginner(%%) **Type**: user documentation
	34	+//Level: advanced//
15	15
16		-After this tutorial, students will be able to know how to create a single compartment neuron model with Hodgkin-Huxley conductances, how to run the simulator and how to display the simulation results
17	17	=== [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel=" noopener noreferrer" target="_blank"]] ===
18	18
19		-**Level**: beginner(%%) **Type**: user documentation
	38	+//Level: advanced//
20	20
21		-After this tutorial, students will be able to work with more advanced topics of building multi-compartmental neurons and using different types of graphs to display the results
22		-=== [[A NEURON Programming Tutorial - Part D>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
	40	+=== [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] ===
23	23
24		-**Level**: beginner(%%) **Type**: user documentation
	42	+//Level: advanced//
25	25
26		-After this tutorial, students will be able to add new membrane mechanisms to the simulator and incorporate them in our neurons.
	44	+=== [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] ===
27	27
	46	+//Level: advanced//
	47	+
	48	+=== [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel=" noopener noreferrer" target="_blank"]] ===
	49	+
	50	+//Level: advanced//
	51	+
	52	+=== [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel=" noopener noreferrer" target="_blank"]] ===
	53	+
	54	+//Level: advanced//
	55	+
	56	+=== [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel=" noopener noreferrer" target="_blank"]] ===
	57	+
	58	+//Level: advanced//
	59	+
	60	+=== [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel=" noopener noreferrer" target="_blank"]] ===
	61	+
	62	+//Level: advanced//
	63	+
	64	+=== [[Creating a channel from a kinetic scheme specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/kinetic/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	65	+
	66	+//Level: advanced//
	67	+
	68	+Here we will implement a new voltage-gated macroscopic current whose properties are described by a family of chemical reactions.
	69	+=== [[Creating a channel from an HH-style specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/hhstyle/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	70	+
	71	+//Level: advanced//
	72	+
	73	+Our goal is to implement a new voltage-gated macroscopic current whose properties are described by HH-style equations.
	74	+=== [[Creating a model of stochastic channel gating>>https://neuron.yale.edu/neuron/static/docs/chanlbild/stochastic/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	75	+
	76	+//Level: advanced//
	77	+
	78	+Given a Channel Builder that implements a deterministic channel specified by a kinetic scheme, we create a new one that implements stochastic gating.
	79	+=== [[Creating a stylized ("stick figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	80	+
	81	+//Level: advanced//
	82	+
	83	+Our goal is to build an extremely simplified model of a pyramidal cell.
	84	+=== [[Dealing with simulations that generate a lot of data>>https://neuron.yale.edu/neuron/docs/dealing-simulations-generate-lot-data||rel=" noopener noreferrer" target="_blank"]] ===
	85	+
	86	+//Level: advanced//
	87	+
	88	+=== [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] ===
	89	+
	90	+//Level: advanced//
	91	+
	92	+=== [[Example: restricting a reaction to part of a region>>https://neuron.yale.edu/neuron/docs/example-restricting-reaction-part-region||rel=" noopener noreferrer" target="_blank"]] ===
	93	+
	94	+//Level: advanced//
	95	+
	96	+=== [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel=" noopener noreferrer" target="_blank"]] ===
	97	+
	98	+//Level: advanced//
	99	+
	100	+=== [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
	101	+
	102	+//Level: advanced//
	103	+
	104	+=== [[How to generate independent random spike streams>>https://neuron.yale.edu/neuron/docs/how-generate-independent-random-spike-streams||rel=" noopener noreferrer" target="_blank"]] ===
	105	+
	106	+//Level: advanced//
	107	+
	108	+=== [[Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] ===
	109	+
	110	+//Level: advanced//
	111	+
	112	+=== [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	113	+
	114	+//Level: advanced//
	115	+
	116	+We use the CellBuilder to specify the spatial grid (nseg) and biophysical properties of a model based on detailed morphometric data.
	117	+=== [[mGluR example>>https://neuron.yale.edu/neuron/docs/mglur-example||rel=" noopener noreferrer" target="_blank"]] ===
	118	+
	119	+//Level: advanced//
	120	+
	121	+=== [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel=" noopener noreferrer" target="_blank"]] ===
	122	+
	123	+//Level: advanced//
	124	+
	125	+=== [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] ===
	126	+
	127	+//Level: advanced//
	128	+
	129	+This page provides a brief introduction to:
	130	+Python syntax
	131	+Variables
	132	+Lists and Dicts
	133	+For loops and iterators
	134	+Functions
	135	+Classes
	136	+Importing modules
	137	+Writing and reading files with Pickling.
	138	+=== [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel=" noopener noreferrer" target="_blank"]] ===
	139	+
	140	+//Level: advanced//
	141	+
	142	+=== [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel=" noopener noreferrer" target="_blank"]] ===
	143	+
	144	+//Level: advanced//
	145	+
	146	+=== [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel=" noopener noreferrer" target="_blank"]] ===
	147	+
	148	+//Level: advanced//
	149	+
	150	+=== [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel=" noopener noreferrer" target="_blank"]] ===
	151	+
	152	+//Level: advanced//
	153	+
	154	+=== [[Reaction-Diffusion: varying initial concentrations and parameters>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-varying-initial-concentrations-and-parameters||rel=" noopener noreferrer" target="_blank"]] ===
	155	+
	156	+//Level: advanced//
	157	+
	158	+=== [[Reading a morphometric data file and converting it to a NEURON model>>https://neuron.yale.edu/neuron/docs/import3d/read_data||rel=" noopener noreferrer" target="_blank"]] ===
	159	+
	160	+//Level: advanced//
	161	+
	162	+=== [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel=" noopener noreferrer" target="_blank"]] ===
	163	+
	164	+//Level: advanced//
	165	+
	166	+=== [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] ===
	167	+
	168	+//Level: advanced//
	169	+
	170	+The objectives of this part of the tutorial are to get familiar with basic operations of NEURON using Python. In this worksheet we will:
	171	+Create a passive cell membrane in NEURON.
	172	+Create a synaptic stimulus onto the neuron.
	173	+Modify parameters of the membrane and stimulus.
	174	+Visualize results with bokeh
	175	+=== [[Segmenting a simulation of a model cell>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel=" noopener noreferrer" target="_blank"]] ===
	176	+
	177	+//Level: advanced//
	178	+
	179	+=== [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel=" noopener noreferrer" target="_blank"]] ===
	180	+
	181	+//Level: advanced//
	182	+
	183	+=== [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel=" noopener noreferrer" target="_blank"]] ===
	184	+
	185	+//Level: advanced//
	186	+
	187	+=== [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	188	+
	189	+//Level: advanced//
	190	+
	191	+How to make one or more biophysical properties vary systematically with position in space.
	192	+=== [[The solution>>https://neuron.yale.edu/neuron/docs/solution||rel=" noopener noreferrer" target="_blank"]] ===
	193	+
	194	+//Level: advanced//
	195	+
	196	+=== [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	197	+
	198	+//Level: advanced//
	199	+
	200	+=== [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	201	+
	202	+//Level: advanced//
	203	+
	204	+=== [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	205	+
	206	+//Level: advanced//
	207	+
	208	+=== [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel=" noopener noreferrer" target="_blank"]] ===
	209	+
	210	+//Level: advanced//
	211	+
	212	+=== [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel=" noopener noreferrer" target="_blank"]] ===
	213	+
	214	+//Level: advanced//
	215	+
	216	+Reading a morphometric data file and converting it to a NEURON model
	217	+Exploring morphometric data and fixing problems
	218	+=== [[Using NEURON's Optimization Tools>>https://neuron.yale.edu/neuron/static/docs/optimiz/main.html||rel=" noopener noreferrer" target="_blank"]] ===
	219	+
	220	+//Level: advanced//
	221	+
	222	+