From b1e601bcee4ab786aace4c3584b83f5e7181c04c Mon Sep 17 00:00:00 2001
From: Torkel Loman <torkel.loman@gmail.com>
Date: Sun, 17 Nov 2024 14:43:23 +0000
Subject: [PATCH 1/2] init

---
 .../math_models_intro.md                      |  2 +-
 docs/src/model_creation/dsl_advanced.md       | 34 +++++++++++++++++++
 docs/src/model_creation/dsl_basics.md         |  2 +-
 3 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/docs/src/introduction_to_catalyst/math_models_intro.md b/docs/src/introduction_to_catalyst/math_models_intro.md
index 0a2647a799..59a619a5f5 100644
--- a/docs/src/introduction_to_catalyst/math_models_intro.md
+++ b/docs/src/introduction_to_catalyst/math_models_intro.md
@@ -73,7 +73,7 @@ while the jump process propensity function is
 a(\mathbf{X}(t)) = k A (A-1) B.
 ```
 
-## Reaction Rate Equation (RRE) ODE Models
+## [Reaction Rate Equation (RRE) ODE Models](@id math_models_in_catalyst_rre_odes)
 The RRE ODE models Catalyst creates for a general system correspond to the coupled system of ODEs given by
 ```math
 \frac{d X_m}{dt} =\sum_{k=1}^K \nu_m^k a_k(\mathbf{X}(t),t), \quad m = 1,\dots,M.
diff --git a/docs/src/model_creation/dsl_advanced.md b/docs/src/model_creation/dsl_advanced.md
index ce4cb43f7f..31f92732f2 100644
--- a/docs/src/model_creation/dsl_advanced.md
+++ b/docs/src/model_creation/dsl_advanced.md
@@ -540,3 +540,37 @@ nothing # hide
 
 !!! note
     When using interpolation, expressions like `2$spec` won't work; the multiplication symbol must be explicitly included like `2*$spec`.
+
+## [Disabling mass action for reactions](@id dsl_advanced_options_disable_ma)
+
+As [described previously](@ref math_models_in_catalyst_rre_odes), Catalyst uses *mass action kinetics* to generate ODEs from reactions. Here, each reaction generates a term for each of its reactants, which consists of the reaction's rate, substrates, and the reactant's stoichiometry. E.g. the following reaction:
+```@example dsl_advanced_disable_ma
+using Catalyst # hide
+rn = @reaction_network begin
+  k, X --> ∅
+end
+```
+generates a single term $-k*[X]$:
+```@example dsl_advanced_disable_ma
+using Latexify
+latexify(rn; form = :ode)
+```
+
+It is possible to remove the substrate contribution by using any of the following non-filled arrows when declaring the reaction: `<=`, `⇐`, `⟽`, `=>`, `⇒`, `⟾`, `⇔`, `⟺`. This means that the reaction
+```@example faq7
+rn = @reaction_network begin
+  k, X => ∅
+end
+latexify(rn; form = :ode)
+```
+will occur at rate $d[X]/dt = -k$ (which might become a problem since $[X]$ will be degraded at a constant rate even when very small or equal to 0). This functionality allows the user to fully customise the ODEs generated by their models. 
+
+Note, stoichiometric coefficients are still included, i.e. the reaction
+```@example faq7
+rn = @reaction_network begin
+  k, 2*X ⇒ ∅
+end
+latexify(rn; form = :ode)
+```
+has rate $d[X]/dt = -2 k$.
+
diff --git a/docs/src/model_creation/dsl_basics.md b/docs/src/model_creation/dsl_basics.md
index 409e3b1f95..b1b5e6d889 100644
--- a/docs/src/model_creation/dsl_basics.md
+++ b/docs/src/model_creation/dsl_basics.md
@@ -373,4 +373,4 @@ It should be noted that the following symbols are *not permitted* to be used as
 - `∅` ([used for production/degradation reactions](@ref dsl_description_symbols_empty_set)).
 - `im` (used in Julia to represent [complex numbers](https://docs.julialang.org/en/v1/manual/complex-and-rational-numbers/#Complex-Numbers)).
 - `nothing` (used in Julia to denote [nothing](https://docs.julialang.org/en/v1/base/constants/#Core.nothing)).
-- `Γ` (used by Catalyst to represent conserved quantities).
+- `Γ` (used by Catalyst to represent [conserved quantities](@ref constraint_equations)).

From facee97caecac568ddd6f7317748538d58e40096 Mon Sep 17 00:00:00 2001
From: Torkel Loman <torkel.loman@gmail.com>
Date: Sun, 17 Nov 2024 15:12:09 +0000
Subject: [PATCH 2/2] doc code fix

---
 docs/src/model_creation/dsl_advanced.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/src/model_creation/dsl_advanced.md b/docs/src/model_creation/dsl_advanced.md
index 31f92732f2..c59c4ba21e 100644
--- a/docs/src/model_creation/dsl_advanced.md
+++ b/docs/src/model_creation/dsl_advanced.md
@@ -557,7 +557,7 @@ latexify(rn; form = :ode)
 ```
 
 It is possible to remove the substrate contribution by using any of the following non-filled arrows when declaring the reaction: `<=`, `⇐`, `⟽`, `=>`, `⇒`, `⟾`, `⇔`, `⟺`. This means that the reaction
-```@example faq7
+```@example dsl_advanced_disable_ma
 rn = @reaction_network begin
   k, X => ∅
 end
@@ -566,7 +566,7 @@ latexify(rn; form = :ode)
 will occur at rate $d[X]/dt = -k$ (which might become a problem since $[X]$ will be degraded at a constant rate even when very small or equal to 0). This functionality allows the user to fully customise the ODEs generated by their models. 
 
 Note, stoichiometric coefficients are still included, i.e. the reaction
-```@example faq7
+```@example dsl_advanced_disable_ma
 rn = @reaction_network begin
   k, 2*X ⇒ ∅
 end