Rebuild models/08-spiking_neural_systems.jmd

markdown/models/08-spiking_neural_systems.md

@@ -85,21 +85,21 @@ cb = CallbackSet(current_step,threshold)
 ````
 DiffEqBase.CallbackSet{Tuple{},Tuple{DiffEqBase.DiscreteCallback{DiffEqCall
 backs.var"#61#64"{Array{Int64,1}},DiffEqCallbacks.var"#62#65"{Main.##WeaveS
-andBox#309.var"#1#2"},DiffEqCallbacks.var"#63#66"{typeof(DiffEqBase.INITIAL
-IZE_DEFAULT),Bool,Array{Int64,1},Main.##WeaveSandBox#309.var"#1#2"}},DiffEq
-Base.DiscreteCallback{typeof(Main.##WeaveSandBox#309.thr),typeof(Main.##Wea
-veSandBox#309.reset!),typeof(DiffEqBase.INITIALIZE_DEFAULT)}}}((), (DiffEqB
+andBox#337.var"#1#2"},DiffEqCallbacks.var"#63#66"{typeof(DiffEqBase.INITIAL
+IZE_DEFAULT),Bool,Array{Int64,1},Main.##WeaveSandBox#337.var"#1#2"}},DiffEq
+Base.DiscreteCallback{typeof(Main.##WeaveSandBox#337.thr),typeof(Main.##Wea
+veSandBox#337.reset!),typeof(DiffEqBase.INITIALIZE_DEFAULT)}}}((), (DiffEqB
 ase.DiscreteCallback{DiffEqCallbacks.var"#61#64"{Array{Int64,1}},DiffEqCall
-backs.var"#62#65"{Main.##WeaveSandBox#309.var"#1#2"},DiffEqCallbacks.var"#6
+backs.var"#62#65"{Main.##WeaveSandBox#337.var"#1#2"},DiffEqCallbacks.var"#6
 3#66"{typeof(DiffEqBase.INITIALIZE_DEFAULT),Bool,Array{Int64,1},Main.##Weav
-eSandBox#309.var"#1#2"}}(DiffEqCallbacks.var"#61#64"{Array{Int64,1}}([2, 15
-]), DiffEqCallbacks.var"#62#65"{Main.##WeaveSandBox#309.var"#1#2"}(Main.##W
-eaveSandBox#309.var"#1#2"()), DiffEqCallbacks.var"#63#66"{typeof(DiffEqBase
-.INITIALIZE_DEFAULT),Bool,Array{Int64,1},Main.##WeaveSandBox#309.var"#1#2"}
-(DiffEqBase.INITIALIZE_DEFAULT, true, [2, 15], Main.##WeaveSandBox#309.var"
+eSandBox#337.var"#1#2"}}(DiffEqCallbacks.var"#61#64"{Array{Int64,1}}([2, 15
+]), DiffEqCallbacks.var"#62#65"{Main.##WeaveSandBox#337.var"#1#2"}(Main.##W
+eaveSandBox#337.var"#1#2"()), DiffEqCallbacks.var"#63#66"{typeof(DiffEqBase
+.INITIALIZE_DEFAULT),Bool,Array{Int64,1},Main.##WeaveSandBox#337.var"#1#2"}
+(DiffEqBase.INITIALIZE_DEFAULT, true, [2, 15], Main.##WeaveSandBox#337.var"
 #1#2"()), Bool[1, 1]), DiffEqBase.DiscreteCallback{typeof(Main.##WeaveSandB
-ox#309.thr),typeof(Main.##WeaveSandBox#309.reset!),typeof(DiffEqBase.INITIA
-LIZE_DEFAULT)}(Main.##WeaveSandBox#309.thr, Main.##WeaveSandBox#309.reset!,
+ox#337.thr),typeof(Main.##WeaveSandBox#337.reset!),typeof(DiffEqBase.INITIA
+LIZE_DEFAULT)}(Main.##WeaveSandBox#337.thr, Main.##WeaveSandBox#337.reset!,
  DiffEqBase.INITIALIZE_DEFAULT, Bool[1, 1])))
 ````
 
@@ -139,7 +139,50 @@ sol = solve(prob)
 
 
 ````
-Error: UndefVarError: top not defined
+retcode: Success
+Interpolation: automatic order switching interpolation
+t: 153-element Array{Float64,1}:
+  0.0
+  9.999999999999999e-5
+  0.0010999999999999998
+  0.011099999999999997
+  0.11109999999999996
+  1.1110999999999995
+  2.0
+  2.0
+  2.6300346673750097
+  2.9226049547524595
+  ⋮
+ 38.34157935968204
+ 38.78215179003683
+ 38.78215179003683
+ 39.222724173706894
+ 39.222724173706894
+ 39.6632965982261
+ 39.6632965982261
+ 40.0
+ 40.0
+u: 153-element Array{Float64,1}:
+ -75.0
+ -75.0
+ -75.0
+ -75.0
+ -75.0
+ -75.0
+ -75.0
+ -75.0
+ -59.978080111690375
+ -57.32999167299642
+   ⋮
+ -75.0
+ -50.40489310815222
+ -75.0
+ -50.404894730067554
+ -75.0
+ -50.404893310891545
+ -75.0
+ -54.419318668318546
+ -75.0
 ````
 
 
@@ -154,11 +197,7 @@ plot(sol)
 ````
 
 
-````
-Error: UndefVarError: sol not defined
-````
-
-
+![](figures/08-spiking_neural_systems_5_1.png)
 
 
 
@@ -211,22 +250,22 @@ cb = CallbackSet(current_step,threshold)
 
 ````
 DiffEqBase.CallbackSet{Tuple{},Tuple{DiffEqBase.DiscreteCallback{DiffEqCall
-backs.var"#61#64"{Int64},DiffEqCallbacks.var"#62#65"{Main.##WeaveSandBox#30
-9.var"#3#4"},DiffEqCallbacks.var"#63#66"{typeof(DiffEqBase.INITIALIZE_DEFAU
-LT),Bool,Int64,Main.##WeaveSandBox#309.var"#3#4"}},DiffEqBase.DiscreteCallb
-ack{typeof(Main.##WeaveSandBox#309.thr),typeof(Main.##WeaveSandBox#309.rese
+backs.var"#61#64"{Int64},DiffEqCallbacks.var"#62#65"{Main.##WeaveSandBox#33
+7.var"#3#4"},DiffEqCallbacks.var"#63#66"{typeof(DiffEqBase.INITIALIZE_DEFAU
+LT),Bool,Int64,Main.##WeaveSandBox#337.var"#3#4"}},DiffEqBase.DiscreteCallb
+ack{typeof(Main.##WeaveSandBox#337.thr),typeof(Main.##WeaveSandBox#337.rese
 t!),typeof(DiffEqBase.INITIALIZE_DEFAULT)}}}((), (DiffEqBase.DiscreteCallba
 ck{DiffEqCallbacks.var"#61#64"{Int64},DiffEqCallbacks.var"#62#65"{Main.##We
-aveSandBox#309.var"#3#4"},DiffEqCallbacks.var"#63#66"{typeof(DiffEqBase.INI
-TIALIZE_DEFAULT),Bool,Int64,Main.##WeaveSandBox#309.var"#3#4"}}(DiffEqCallb
+aveSandBox#337.var"#3#4"},DiffEqCallbacks.var"#63#66"{typeof(DiffEqBase.INI
+TIALIZE_DEFAULT),Bool,Int64,Main.##WeaveSandBox#337.var"#3#4"}}(DiffEqCallb
 acks.var"#61#64"{Int64}(50), DiffEqCallbacks.var"#62#65"{Main.##WeaveSandBo
-x#309.var"#3#4"}(Main.##WeaveSandBox#309.var"#3#4"()), DiffEqCallbacks.var"
+x#337.var"#3#4"}(Main.##WeaveSandBox#337.var"#3#4"()), DiffEqCallbacks.var"
 #63#66"{typeof(DiffEqBase.INITIALIZE_DEFAULT),Bool,Int64,Main.##WeaveSandBo
-x#309.var"#3#4"}(DiffEqBase.INITIALIZE_DEFAULT, true, 50, Main.##WeaveSandB
-ox#309.var"#3#4"()), Bool[1, 1]), DiffEqBase.DiscreteCallback{typeof(Main.#
-#WeaveSandBox#309.thr),typeof(Main.##WeaveSandBox#309.reset!),typeof(DiffEq
-Base.INITIALIZE_DEFAULT)}(Main.##WeaveSandBox#309.thr, Main.##WeaveSandBox#
-309.reset!, DiffEqBase.INITIALIZE_DEFAULT, Bool[1, 1])))
+x#337.var"#3#4"}(DiffEqBase.INITIALIZE_DEFAULT, true, 50, Main.##WeaveSandB
+ox#337.var"#3#4"()), Bool[1, 1]), DiffEqBase.DiscreteCallback{typeof(Main.#
+#WeaveSandBox#337.thr),typeof(Main.##WeaveSandBox#337.reset!),typeof(DiffEq
+Base.INITIALIZE_DEFAULT)}(Main.##WeaveSandBox#337.thr, Main.##WeaveSandBox#
+337.reset!, DiffEqBase.INITIALIZE_DEFAULT, Bool[1, 1])))
 ````
 
 
@@ -260,11 +299,7 @@ plot(sol, vars=1)
 ````
 
 
-````
-Error: UndefVarError: top not defined
-````
-
-
+![](figures/08-spiking_neural_systems_9_1.png)
 
 
 
@@ -276,11 +311,7 @@ plot(sol, vars=2)
 ````
 
 
-````
-Error: UndefVarError: sol not defined
-````
-
-
+![](figures/08-spiking_neural_systems_10_1.png)
 
 
 
@@ -298,11 +329,7 @@ plot(sol, vars=1)
 ````
 
 
-````
-Error: UndefVarError: top not defined
-````
-
-
+![](figures/08-spiking_neural_systems_11_1.png)
 
 
 
@@ -388,11 +415,7 @@ plot(sol, vars=1)
 ````
 
 
-````
-Error: UndefVarError: top not defined
-````
-
-
+![](figures/08-spiking_neural_systems_14_1.png)
 
 
 
@@ -404,11 +427,7 @@ plot(sol, vars=[2,3,4], tspan=(105.0,130.0))
 ````
 
 
-````
-Error: UndefVarError: sol not defined
-````
-
-
+![](figures/08-spiking_neural_systems_15_1.png)
 
 
 
@@ -466,11 +485,7 @@ plot(sol, vars=1)
 ````
 
 
-````
-Error: UndefVarError: top not defined
-````
-
-
+![](figures/08-spiking_neural_systems_17_1.png)
 
 
 
@@ -486,11 +501,7 @@ plot!(sol, vars=1)
 ````
 
 
-````
-Error: UndefVarError: top not defined
-````
-
-
+![](figures/08-spiking_neural_systems_18_1.png)
 
 
 
@@ -534,23 +545,15 @@ plot(sol, vars=1)
 ````
 
 
-````
-Error: UndefVarError: top not defined
-````
-
-
+![](figures/08-spiking_neural_systems_19_1.png)
 
 ````julia
 
 plot(sol, vars=7)
 ````
 
 
-````
-Error: UndefVarError: sol not defined
-````
-
-
+![](figures/08-spiking_neural_systems_20_1.png)
 
 
 
@@ -562,11 +565,7 @@ plot(sol, vars=[5,6])
 ````
 
 
-````
-Error: UndefVarError: sol not defined
-````
-
-
+![](figures/08-spiking_neural_systems_21_1.png)
 
 
 
@@ -585,23 +584,15 @@ plot(sol, vars=7)
 ````
 
 
-````
-Error: UndefVarError: top not defined
-````
-
-
+![](figures/08-spiking_neural_systems_22_1.png)
 
 ````julia
 
 plot(sol, vars=[5,6])
 ````
 
 
-````
-Error: UndefVarError: sol not defined
-````
-
-
+![](figures/08-spiking_neural_systems_23_1.png)
 
 
 
@@ -620,27 +611,74 @@ plot(sol, vars=7)
 ````
 
 
-````
-Error: UndefVarError: top not defined
-````
-
-
+![](figures/08-spiking_neural_systems_24_1.png)
 
 ````julia
 
 plot(sol, vars=[5,6])
 ````
 
 
-````
-Error: UndefVarError: sol not defined
-````
-
-
+![](figures/08-spiking_neural_systems_25_1.png)
 
 
 
 Just changing those two time constants has changed the dynamics to short-term depression. This is still frequency dependent. Changing these parameters can generate a variety of different short-term dynamics.
 
 ## Summary
 That's it for now. Thanks for making it this far. If you want to learn more about neuronal dynamics, [this is a great resource](https://neuronaldynamics.epfl.ch/online/index.html). If you want to learn more about Julia check out the [official website](https://julialang.org/) and to learn more about the DifferentialEquations package you are in the right place, because this chapter is part of a [larger tutorial series about just that](https://github.com/SciML/SciMLTutorials.jl).
+
+
+## Appendix
+
+ This tutorial is part of the SciMLTutorials.jl repository, found at: <https://github.com/SciML/SciMLTutorials.jl>.
+ For more information on doing scientific machine learning (SciML) with open source software, check out <https://sciml.ai/>.
+
+To locally run this tutorial, do the following commands:
+```
+using SciMLTutorials
+SciMLTutorials.weave_file("models","08-spiking_neural_systems.jmd")
+```
+
+Computer Information:
+```
+Julia Version 1.4.2
+Commit 44fa15b150* (2020-05-23 18:35 UTC)
+Platform Info:
+  OS: Linux (x86_64-pc-linux-gnu)
+  CPU: Intel(R) Core(TM) i7-9700K CPU @ 3.60GHz
+  WORD_SIZE: 64
+  LIBM: libopenlibm
+  LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
+Environment:
+  JULIA_LOAD_PATH = /builds/JuliaGPU/DiffEqTutorials.jl:
+  JULIA_DEPOT_PATH = /builds/JuliaGPU/DiffEqTutorials.jl/.julia
+  JULIA_CUDA_MEMORY_LIMIT = 2147483648
+  JULIA_NUM_THREADS = 8
+
+```
+
+Package Information:
+
+```
+Status `/builds/JuliaGPU/DiffEqTutorials.jl/tutorials/models/Project.toml`
+[479239e8-5488-4da2-87a7-35f2df7eef83] Catalyst 5.0.0
+[459566f4-90b8-5000-8ac3-15dfb0a30def] DiffEqCallbacks 2.14.1
+[f3b72e0c-5b89-59e1-b016-84e28bfd966d] DiffEqDevTools 2.27.0
+[055956cb-9e8b-5191-98cc-73ae4a59e68a] DiffEqPhysics 3.6.0
+[0c46a032-eb83-5123-abaf-570d42b7fbaa] DifferentialEquations 6.15.0
+[31c24e10-a181-5473-b8eb-7969acd0382f] Distributions 0.23.12
+[587475ba-b771-5e3f-ad9e-33799f191a9c] Flux 0.11.1
+[f6369f11-7733-5829-9624-2563aa707210] ForwardDiff 0.10.12
+[23fbe1c1-3f47-55db-b15f-69d7ec21a316] Latexify 0.14.0
+[961ee093-0014-501f-94e3-6117800e7a78] ModelingToolkit 3.20.0
+[2774e3e8-f4cf-5e23-947b-6d7e65073b56] NLsolve 4.4.1
+[315f7962-48a3-4962-8226-d0f33b1235f0] NeuralPDE 2.3.0
+[429524aa-4258-5aef-a3af-852621145aeb] Optim 1.2.0
+[1dea7af3-3e70-54e6-95c3-0bf5283fa5ed] OrdinaryDiffEq 5.42.8
+[91a5bcdd-55d7-5caf-9e0b-520d859cae80] Plots 1.6.5
+[731186ca-8d62-57ce-b412-fbd966d074cd] RecursiveArrayTools 2.7.0
+[789caeaf-c7a9-5a7d-9973-96adeb23e2a0] StochasticDiffEq 6.26.0
+[37e2e46d-f89d-539d-b4ee-838fcccc9c8e] LinearAlgebra
+[2f01184e-e22b-5df5-ae63-d93ebab69eaf] SparseArrays
+```