Merge pull request #835 from SciML/docs

Add acausal modeling tutorial

Author: ChrisRackauckas

docs/make.jl

@@ -12,6 +12,7 @@ makedocs(
         "Home" => "index.md",
         "Tutorials" => Any[
             "tutorials/ode_modeling.md",
+            "tutorials/acausal_components.md",
             "tutorials/higher_order.md",
             "tutorials/nonlinear.md",
             "tutorials/modelingtoolkitize.md",

docs/src/basics/Composition.md

@@ -1,4 +1,4 @@
-# [Composing Models and Building Reusable Components](@ref components)
+# [Composing Models and Building Reusable Components](@id components)
 
 The symbolic models of ModelingToolkit can be composed together to
 easily build large models. The composition is lazy and only instantiated

docs/src/index.md

@@ -60,16 +60,28 @@ is built on, consult the
 - Chemical Reactions
 - Optimal Control
 
+## Model Import Formats
+
+- [CellMLToolkit.jl](https://github.com/SciML/CellMLToolkit.jl): Import [CellML](https://www.cellml.org/) models into ModelingToolkit
+    - Repository of more than a thousand pre-made models
+    - Focus on biomedical models in areas such as: Calcium Dynamics,
+      Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms,
+      Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation,
+      Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws,
+      Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD,
+      Protein Modules, Signal Transduction, and Synthetic Biology.
+- [SbmlInterface.jl](https://github.com/paulflang/SbmlInterface.jl): Import [SBML](http://sbml.org/Main_Page) models into ModelingToolkit
+    - Uses the robust libsbml library for parsing and transforming the SBML
+- [ReactionNetworkImporters.jl](https://github.com/isaacsas/ReactionNetworkImporters.jl): Import various models into ModelingToolkit
+    - Supports the BioNetGen `.net` file
+    - Supports importing networks specified by stoichiometric matrices
+
 ## Extension Libraries
 
 Because ModelingToolkit.jl is the core foundation of a equation-based modeling
 ecosystem, there is a large set of libraries adding features to this system.
 Below is an incomplete list of extension libraries one may want to be aware of:
 
-- [StructuralTransformations.jl](https://github.com/JuliaComputing/StructuralTransformations.jl): Various transformations of models into structurally better versions for improved numerical simulation
-    - Pantelides algortihm for index reduction of DAEs
-    - Tearing of `ODESystem`s and `NonolinearSystem`s to reduce the numerical
-      cost of handling large implicit systems via Newton methods
 - [Catalyst.jl](https://github.com/SciML/Catalyst.jl): Symbolic representations of chemical reactions
     - Symbolically build and represent large systems of chemical reactions
     - Generate code for ODEs, SDEs, continuous-time Markov Chains, and more
@@ -87,22 +99,6 @@ Below is an incomplete list of extension libraries one may want to be aware of:
     - Diffusion limited rates. Sensitivity analysis for all reactors.
     - Flux diagrams with molecular images (if molecular information is provided).
 
-## Model Import Formats
-
-- [CellMLToolkit.jl](https://github.com/SciML/CellMLToolkit.jl): Import [CellML](https://www.cellml.org/) models into ModelingToolkit
-    - Repository of more than a thousand pre-made models
-    - Focus on biomedical models in areas such as: Calcium Dynamics,
-      Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms,
-      Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation,
-      Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws,
-      Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD,
-      Protein Modules, Signal Transduction, and Synthetic Biology.
-- [SbmlInterface.jl](https://github.com/paulflang/SbmlInterface.jl): Import [SBML](http://sbml.org/Main_Page) models into ModelingToolkit
-    - Uses the robust libsbml library for parsing and transforming the SBML
-- [ReactionNetworkImporters.jl](https://github.com/isaacsas/ReactionNetworkImporters.jl): Import various models into ModelingToolkit
-    - Supports the BioNetGen `.net` file
-    - Supports importing networks specified by stoichiometric matrices
-
 ## Compatible Numerical Solvers
 
 All of the symbolic systems have a direct conversion to a numerical system which