Deploying to gh-pages from @ 9d25792 🚀

assets/pages/blox_connections/code/output/ex6.res

@@ -1,4 +1,4 @@
-Main.FD_SANDBOX_15604780526313532720.IzhNeuron(ModelingToolkit.ODESystem(0x0000000000001fe4, Symbolics.Equation[Differential(t)(V(t)) ~ 145 + jcn - u(t) + 5V(t) + 0.04(V(t)^2), Differential(t)(u(t)) ~ a*(-u(t) + b*V(t))], t, SymbolicUtils.BasicSymbolic{Real}[V(t), u(t), jcn], SymbolicUtils.BasicSymbolic{Real}[a, b, V_reset, d, θ], nothing, Dict{Any, Any}(:a => a, :b => b, :d => d, :V => V(t), :jcn => jcn, :u => u(t), :θ => θ, :V_reset => V_reset), Any[], Symbolics.Equation[], Base.RefValue{Vector{Symbolics.Num}}(Symbolics.Num[]), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), :izh, "", ModelingToolkit.ODESystem[], Dict{Any, Any}(a => 0.02, V_reset => -50, d => 2, u(t) => -13, V(t) => -65.0, b => 0.2, θ => 30), Dict{Any, Any}(), nothing, nothing, Symbolics.Equation[], nothing, nothing, nothing, ModelingToolkit.SymbolicContinuousCallback[], ModelingToolkit.SymbolicDiscreteCallback[condition: V(t) > θ
+Main.FD_SANDBOX_15604780526313532720.IzhNeuron(ModelingToolkit.ODESystem(0x0000000000001ff8, Symbolics.Equation[Differential(t)(V(t)) ~ 145 + jcn - u(t) + 5V(t) + 0.04(V(t)^2), Differential(t)(u(t)) ~ a*(-u(t) + b*V(t))], t, SymbolicUtils.BasicSymbolic{Real}[V(t), u(t), jcn], SymbolicUtils.BasicSymbolic{Real}[a, b, V_reset, d, θ], nothing, Dict{Any, Any}(:a => a, :b => b, :d => d, :V => V(t), :jcn => jcn, :u => u(t), :θ => θ, :V_reset => V_reset), Any[], Symbolics.Equation[], Base.RefValue{Vector{Symbolics.Num}}(Symbolics.Num[]), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), :izh, "", ModelingToolkit.ODESystem[], Dict{Any, Any}(a => 0.02, V_reset => -50, d => 2, u(t) => -13, V(t) => -65.0, b => 0.2, θ => 30), Dict{Any, Any}(), nothing, nothing, Symbolics.Equation[], nothing, nothing, nothing, ModelingToolkit.SymbolicContinuousCallback[], ModelingToolkit.SymbolicDiscreteCallback[condition: V(t) > θ
 affects:
   u(t) ~ d + u(t)
   V(t) ~ V_reset

assets/pages/learning/code/output/ex3.out

@@ -1,78 +1,78 @@
 Trial = 1, Category choice = 2, Response = Correct
 Trial = 2, Category choice = 1, Response = Correct
-Trial = 3, Category choice = 2, Response = False
-Trial = 4, Category choice = 1, Response = False
-Trial = 5, Category choice = 1, Response = Correct
+Trial = 3, Category choice = 1, Response = Correct
+Trial = 4, Category choice = 2, Response = Correct
+Trial = 5, Category choice = 2, Response = False
 Trial = 6, Category choice = 2, Response = Correct
-Trial = 7, Category choice = 1, Response = False
+Trial = 7, Category choice = 2, Response = Correct
 Trial = 8, Category choice = 1, Response = False
 Trial = 9, Category choice = 1, Response = False
-Trial = 10, Category choice = 2, Response = Correct
+Trial = 10, Category choice = 1, Response = False
 Trial = 11, Category choice = 1, Response = False
-Trial = 12, Category choice = 2, Response = Correct
+Trial = 12, Category choice = 1, Response = False
 Trial = 13, Category choice = 1, Response = Correct
 Trial = 14, Category choice = 2, Response = Correct
 Trial = 15, Category choice = 2, Response = False
 Trial = 16, Category choice = 2, Response = False
 Trial = 17, Category choice = 1, Response = Correct
 Trial = 18, Category choice = 2, Response = False
-Trial = 19, Category choice = 1, Response = Correct
-Trial = 20, Category choice = 2, Response = Correct
-Trial = 21, Category choice = 1, Response = Correct
-Trial = 22, Category choice = 1, Response = Correct
-Trial = 23, Category choice = 1, Response = Correct
+Trial = 19, Category choice = 2, Response = False
+Trial = 20, Category choice = 1, Response = False
+Trial = 21, Category choice = 2, Response = False
+Trial = 22, Category choice = 2, Response = False
+Trial = 23, Category choice = 2, Response = False
 Trial = 24, Category choice = 1, Response = False
-Trial = 25, Category choice = 2, Response = False
+Trial = 25, Category choice = 1, Response = Correct
 Trial = 26, Category choice = 1, Response = Correct
-Trial = 27, Category choice = 1, Response = Correct
+Trial = 27, Category choice = 2, Response = False
 Trial = 28, Category choice = 2, Response = False
 Trial = 29, Category choice = 1, Response = False
-Trial = 30, Category choice = 2, Response = False
+Trial = 30, Category choice = 1, Response = Correct
 Trial = 31, Category choice = 1, Response = False
-Trial = 32, Category choice = 2, Response = False
+Trial = 32, Category choice = 1, Response = Correct
 Trial = 33, Category choice = 1, Response = False
-Trial = 34, Category choice = 2, Response = Correct
-Trial = 35, Category choice = 1, Response = False
-Trial = 36, Category choice = 1, Response = Correct
+Trial = 34, Category choice = 1, Response = False
+Trial = 35, Category choice = 2, Response = Correct
+Trial = 36, Category choice = 2, Response = False
 Trial = 37, Category choice = 2, Response = False
 Trial = 38, Category choice = 1, Response = Correct
-Trial = 39, Category choice = 1, Response = False
+Trial = 39, Category choice = 2, Response = Correct
 Trial = 40, Category choice = 1, Response = Correct
-Trial = 41, Category choice = 2, Response = Correct
-Trial = 42, Category choice = 1, Response = Correct
+Trial = 41, Category choice = 1, Response = False
+Trial = 42, Category choice = 2, Response = False
 Trial = 43, Category choice = 1, Response = Correct
-Trial = 44, Category choice = 1, Response = False
+Trial = 44, Category choice = 2, Response = Correct
 Trial = 45, Category choice = 1, Response = Correct
-Trial = 46, Category choice = 2, Response = False
-Trial = 47, Category choice = 1, Response = Correct
-Trial = 48, Category choice = 1, Response = False
+Trial = 46, Category choice = 1, Response = Correct
+Trial = 47, Category choice = 2, Response = False
+Trial = 48, Category choice = 2, Response = Correct
 Trial = 49, Category choice = 2, Response = Correct
-Trial = 50, Category choice = 1, Response = False
+Trial = 50, Category choice = 2, Response = Correct
 Trial = 51, Category choice = 2, Response = False
-Trial = 52, Category choice = 1, Response = Correct
-Trial = 53, Category choice = 1, Response = False
+Trial = 52, Category choice = 2, Response = False
+Trial = 53, Category choice = 2, Response = Correct
 Trial = 54, Category choice = 1, Response = False
-Trial = 55, Category choice = 1, Response = False
-Trial = 56, Category choice = 2, Response = Correct
+Trial = 55, Category choice = 2, Response = Correct
+Trial = 56, Category choice = 1, Response = False
 Trial = 57, Category choice = 2, Response = False
-Trial = 58, Category choice = 1, Response = Correct
-Trial = 59, Category choice = 1, Response = Correct
-Trial = 60, Category choice = 2, Response = False
+Trial = 58, Category choice = 2, Response = False
+Trial = 59, Category choice = 2, Response = False
+Trial = 60, Category choice = 1, Response = Correct
 Trial = 61, Category choice = 1, Response = False
 Trial = 62, Category choice = 2, Response = Correct
 Trial = 63, Category choice = 1, Response = False
 Trial = 64, Category choice = 1, Response = Correct
-Trial = 65, Category choice = 1, Response = Correct
+Trial = 65, Category choice = 2, Response = False
 Trial = 66, Category choice = 2, Response = Correct
-Trial = 67, Category choice = 2, Response = False
-Trial = 68, Category choice = 1, Response = False
+Trial = 67, Category choice = 1, Response = Correct
+Trial = 68, Category choice = 2, Response = Correct
 Trial = 69, Category choice = 2, Response = Correct
 Trial = 70, Category choice = 1, Response = Correct
-Trial = 71, Category choice = 1, Response = Correct
-Trial = 72, Category choice = 1, Response = False
-Trial = 73, Category choice = 1, Response = False
-Trial = 74, Category choice = 2, Response = False
-Trial = 75, Category choice = 2, Response = False
+Trial = 71, Category choice = 2, Response = False
+Trial = 72, Category choice = 2, Response = Correct
+Trial = 73, Category choice = 2, Response = Correct
+Trial = 74, Category choice = 1, Response = Correct
+Trial = 75, Category choice = 1, Response = Correct
 Trial = 76, Category choice = 1, Response = False
 Trial = 77, Category choice = 1, Response = Correct
 Trial = 78, Category choice = 2, Response = False
@@ -85,16 +85,16 @@ Trial = 84, Category choice = 2, Response = Correct
 Trial = 85, Category choice = 2, Response = Correct
 Trial = 86, Category choice = 1, Response = Correct
 Trial = 87, Category choice = 2, Response = False
-Trial = 88, Category choice = 1, Response = Correct
-Trial = 89, Category choice = 2, Response = Correct
-Trial = 90, Category choice = 2, Response = False
+Trial = 88, Category choice = 2, Response = False
+Trial = 89, Category choice = 1, Response = False
+Trial = 90, Category choice = 1, Response = Correct
 Trial = 91, Category choice = 2, Response = Correct
 Trial = 92, Category choice = 2, Response = False
 Trial = 93, Category choice = 2, Response = Correct
 Trial = 94, Category choice = 2, Response = Correct
 Trial = 95, Category choice = 1, Response = Correct
-Trial = 96, Category choice = 2, Response = Correct
-Trial = 97, Category choice = 1, Response = False
-Trial = 98, Category choice = 1, Response = False
+Trial = 96, Category choice = 1, Response = False
+Trial = 97, Category choice = 2, Response = Correct
+Trial = 98, Category choice = 2, Response = Correct
 Trial = 99, Category choice = 2, Response = False
-Trial = 100, Category choice = 2, Response = False
+Trial = 100, Category choice = 1, Response = Correct

assets/pages/learning/code/output/ex3.res

@@ -1 +1 @@
-(trial = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100], correct = Bool[1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0], action = [2, 1, 2, 1, 1, 2, 1, 1, 1, 2, 1, 2, 1, 2, 2, 2, 1, 2, 1, 2, 1, 1, 1, 1, 2, 1, 1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 2, 1, 1, 2, 1, 2, 1, 1, 1, 1, 2, 2, 1, 1, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 1, 2, 1, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 2, 2])
+(trial = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100], correct = Bool[1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1], action = [2, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 1, 2, 2, 2, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 1, 1, 2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 2, 2, 2, 1, 1, 2, 1, 1, 2, 2, 1, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 2, 2, 2, 2, 1, 1, 2, 2, 2, 1])

notebooks/CS_circuit.ipynb

@@ -616,11 +616,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.4"
+   "version": "1.10.5"
   },
   "kernelspec": {
    "name": "julia-1.10",
-   "display_name": "Julia 1.10.4",
+   "display_name": "Julia 1.10.5",
    "language": "julia"
   }
  },

notebooks/DCM.ipynb

@@ -157,7 +157,7 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "@named simmodel = system_from_graph(g, split=false);"
+    "@named simmodel = system_from_graph(g, split=false)"
    ],
    "metadata": {},
    "execution_count": null
@@ -433,7 +433,7 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "@named fitmodel = system_from_graph(g, simplify=false);"
+    "@named fitmodel = system_from_graph(g, simplify=false)"
    ],
    "metadata": {},
    "execution_count": null
@@ -710,11 +710,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.4"
+   "version": "1.10.5"
   },
   "kernelspec": {
    "name": "julia-1.10",
-   "display_name": "Julia 1.10.4",
+   "display_name": "Julia 1.10.5",
    "language": "julia"
   }
  },

notebooks/PING_circuit.ipynb

@@ -339,11 +339,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.4"
+   "version": "1.10.5"
   },
   "kernelspec": {
    "name": "julia-1.10",
-   "display_name": "Julia 1.10.4",
+   "display_name": "Julia 1.10.5",
    "language": "julia"
   }
  },

notebooks/blox_connections.ipynb

@@ -103,7 +103,7 @@
    "source": [
     "@named ifn = IFNeuron() ## create an Integrate-and-Fire neuron, simpler than the `LIFNeuron`\n",
     "\n",
-    "connection_equations(lif, ifn, weight=1, connection_rule=\"basic\")"
+    "connection_equations(lif, ifn)"
    ],
    "metadata": {},
    "execution_count": null
@@ -119,15 +119,15 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "connection_rule(lif, ifn, weight=1, connection_rule=\"psp\")"
+    "connection_rule(lif, ifn)"
    ],
    "metadata": {},
    "execution_count": null
   },
   {
    "cell_type": "markdown",
    "source": [
-    "The `weight` and `connection_rule` are keyword arguments that can be ommitted. If we ommit them then we will get a message informing us about the default values that they take. The `connection_rule` argument applies to connections between `Neuron` types; `\"basic\"` is a simple weighted connection and `\"psp\"` applies a postsynaptic potential type of connection. The output of both `connection_equations` and `connection_rule` functions now seems very similar. However `connection_rule` will be more useful later on when we start using more complex Bloxs and connection rules that do more than just adding an equation and a symbolic weight."
+    "The output of both functions now seems very similar. However `connection_rule` will be more useful later on when we start using more complex Bloxs and connection rules."
    ],
    "metadata": {}
   },
@@ -146,7 +146,7 @@
    "cell_type": "code",
    "source": [
     "g = MetaDiGraph()\n",
-    "add_edge!(g, lif => ifn, weight=1) ## add connection with specific weight value\n",
+    "add_edge!(g, lif => ifn)\n",
     "\n",
     "@named sys = system_from_graph(g)\n",
     "prob = ODEProblem(sys, [], (0, 200.0))\n",
@@ -249,8 +249,8 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "connection_equations(izh, lif, weight=1, connection_rule=\"basic\") ## connection from izh to lif\n",
-    "connection_equations(lif, izh, weight=1, connection_rule=\"basic\") ## connection from lif to izh"
+    "connection_equations(izh, lif) ## connection from izh to lif\n",
+    "connection_equations(lif, izh) ## connection from lif to izh"
    ],
    "metadata": {},
    "execution_count": null
@@ -305,7 +305,7 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "connection_equations(lif, izh, weight=1, connection_rule=\"basic\")"
+    "connection_equations(lif, izh)"
    ],
    "metadata": {},
    "execution_count": null
@@ -517,11 +517,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.4"
+   "version": "1.10.5"
   },
   "kernelspec": {
    "name": "julia-1.10",
-   "display_name": "Julia 1.10.4",
+   "display_name": "Julia 1.10.5",
    "language": "julia"
   }
  },

notebooks/decision_making.ipynb

@@ -132,8 +132,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "## System construction & Simulation\n",
-    "We construct the graph with all connections and weights according to [1]. Please note that the `system_from_graph` call and the subsequent `ODEProblem` construction will take some minutes (probably 4-5, depending on your machine) as the system size is larger compared to other examples. The `graphdynamics=true` flag that we set in `system_from_graph` though will greatly enhance performance here."
+    "## System construction & Simulation"
    ],
    "metadata": {}
   },
@@ -262,11 +261,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.4"
+   "version": "1.10.5"
   },
   "kernelspec": {
    "name": "julia-1.10",
-   "display_name": "Julia 1.10.4",
+   "display_name": "Julia 1.10.5",
    "language": "julia"
   }
  },

notebooks/intro_diffeq.ipynb

@@ -601,11 +601,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.4"
+   "version": "1.10.5"
   },
   "kernelspec": {
    "name": "julia-1.10",
-   "display_name": "Julia 1.10.4",
+   "display_name": "Julia 1.10.5",
    "language": "julia"
   }
  },

notebooks/intro_plot.ipynb

@@ -334,11 +334,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.4"
+   "version": "1.10.5"
   },
   "kernelspec": {
    "name": "julia-1.10",
-   "display_name": "Julia 1.10.4",
+   "display_name": "Julia 1.10.5",
    "language": "julia"
   }
  },

notebooks/learning.ipynb

@@ -372,11 +372,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.4"
+   "version": "1.10.5"
   },
   "kernelspec": {
    "name": "julia-1.10",
-   "display_name": "Julia 1.10.4",
+   "display_name": "Julia 1.10.5",
    "language": "julia"
   }
  },