up

docs/pages.jl

@@ -1,61 +1,61 @@
 pages = Any[
     "Home" => "index.md",
     "Introduction to Catalyst" => Any[
-        #"introduction_to_catalyst/catalyst_for_new_julia_users.md",
+        "introduction_to_catalyst/catalyst_for_new_julia_users.md",
         # "introduction_to_catalyst/introduction_to_catalyst.md"
         # Advanced introduction.
     ],
     "Model Creation and Properties" => Any[
-        #"model_creation/dsl_basics.md",
-        #"model_creation/dsl_advanced.md",
+        "model_creation/dsl_basics.md",
+        "model_creation/dsl_advanced.md",
         #"model_creation/programmatic_CRN_construction.md",
         #"model_creation/compositional_modeling.md",
         #"model_creation/constraint_equations.md",
         # Events.
         #"model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
         # Loading and writing models to files.
-        #"model_creation/model_visualisation.md",
+        "model_creation/model_visualisation.md",
         #"model_creation/network_analysis.md",
-        #"model_creation/chemistry_related_functionality.md",
+        "model_creation/chemistry_related_functionality.md",
         "Model creation examples" => Any[
-            #"model_creation/examples/basic_CRN_library.md",
-            #"model_creation/examples/programmatic_generative_linear_pathway.md",
+            "model_creation/examples/basic_CRN_library.md",
+            "model_creation/examples/programmatic_generative_linear_pathway.md",
             #"model_creation/examples/hodgkin_huxley_equation.md",
             #"model_creation/examples/smoluchowski_coagulation_equation.md"
         ]
     ],
     "Model simulation" => Any[
-        #"model_simulation/simulation_introduction.md",
+        "model_simulation/simulation_introduction.md",
         # Simulation introduction.
-        #"model_simulation/simulation_plotting.md",
-        #"model_simulation/simulation_structure_interfacing.md",
-        #"model_simulation/ensemble_simulations.md",
+        "model_simulation/simulation_plotting.md",
+        "model_simulation/simulation_structure_interfacing.md",
+        "model_simulation/ensemble_simulations.md",
         # Stochastic simulation statistical analysis.
-        #"model_simulation/ode_simulation_performance.md",
+        "model_simulation/ode_simulation_performance.md",
         # ODE Performance considerations/advice.
         # SDE Performance considerations/advice.
         # Jump Performance considerations/advice.
         # Finite state projection
     ],
     "Steady state analysis" => Any[
-        #"steady_state_functionality/homotopy_continuation.md",
-        #"steady_state_functionality/nonlinear_solve.md",
-        #"steady_state_functionality/steady_state_stability_computation.md",        
-        #"steady_state_functionality/bifurcation_diagrams.md",
-        #"steady_state_functionality/dynamical_systems.md"
+        "steady_state_functionality/homotopy_continuation.md",
+        "steady_state_functionality/nonlinear_solve.md",
+        "steady_state_functionality/steady_state_stability_computation.md",        
+        "steady_state_functionality/bifurcation_diagrams.md",
+        "steady_state_functionality/dynamical_systems.md"
     ],
     "Inverse Problems" => Any[
         # Inverse problems introduction.
-        #"inverse_problems/optimization_ode_param_fitting.md",
+        "inverse_problems/optimization_ode_param_fitting.md",
         # "inverse_problems/petab_ode_param_fitting.md",
         # ODE parameter fitting using Turing.
         # SDE/Jump fitting.
-        #"inverse_problems/behaviour_optimisation.md",
-        #"inverse_problems/structural_identifiability.md",
+        "inverse_problems/behaviour_optimisation.md",
+        "inverse_problems/structural_identifiability.md",
         # Practical identifiability.
-        #"inverse_problems/global_sensitivity_analysis.md",
+        "inverse_problems/global_sensitivity_analysis.md",
         "Inverse problem examples" => Any[
-            #"inverse_problems/examples/ode_fitting_oscillation.md"
+            "inverse_problems/examples/ode_fitting_oscillation.md"
         ]
     ],
     "Spatial modelling" => Any[