diff --git a/aliases.pl b/aliases.pl
index d5dd6c565910d428b9622e743c0fba2512f29118..fddbd50bed3c0ef5bf45df31537de29abb27bffd 100644
--- a/aliases.pl
+++ b/aliases.pl
@@ -30,7 +30,7 @@ add_equivalence_class_list(EquivalenceClassList) :-
   ;
     list_to_equals(EquivalenceClassList, EquivalenceClass),
     add_item(alias, EquivalenceClassList, alias(EquivalenceClass)),
-    simplify_all_rules
+    simplify_all_reactions
   ).
 
 
diff --git a/aliases.plt b/aliases.plt
index 3a852a2306ab0ee92fc7a45f937df674c4d6d273..47ee22e642b47b44b5ecc0d18a427569a8bbd42b 100644
--- a/aliases.plt
+++ b/aliases.plt
@@ -2,10 +2,10 @@
 
 :- begin_tests(aliases).
 
-test('alias', [true(Rules == [2 * a => c])]) :-
+test('alias', [true(Reactions == [2 * a => c])]) :-
   clear_model,
-  add_rule(a + b => c),
+  add_reaction(a + b => c),
   command(alias(a = b)),
-  all_items([model: current_model, kind: rule], Rules).
+  all_items([model: current_model, kind: reaction], Reactions).
 
 :- end_tests(aliases).
diff --git a/conservation_laws.pl b/conservation_laws.pl
index cf7e0aa4c593c9da1c086c0d82d1ba2d281e995b..31ba2c8e0e8255792012f11507610b02b2259242 100644
--- a/conservation_laws.pl
+++ b/conservation_laws.pl
@@ -30,7 +30,7 @@ add_conservation(Conservation) :-
     these checks are not complete, even a failure will be accepted with a
     warning.'
   ),
-  rule_editor:solution_to_list(Conservation, C),
+  solution_to_list(Conservation, C),
   add_item(conservation, C).
 
 
@@ -38,7 +38,7 @@ delete_conservation(Conservation) :-
   biocham_command,
   type(Conservation, solution),
   doc('removes the given mass conservation law.'),
-  rule_editor:solution_to_list(Conservation, C),
+  solution_to_list(Conservation, C),
   find_item([model: current_model, id: Id, type: conservation, item: C]),
   delete_item(Id).
 
diff --git a/initial_state.plt b/initial_state.plt
index ccfcec87496910a93cde977f912a5921e3278a41..6795e29b4e109036fb91e6f95414bd8748cd64a9 100644
--- a/initial_state.plt
+++ b/initial_state.plt
@@ -33,7 +33,7 @@ test(
   [true(InitialState == [present(a), absent(b)])]
 ) :-
   clear_model,
-  add_rule(a => b),
+  add_reaction(a => b),
   command(present(a)),
   make_absent_not_present,
   all_items([model: current_model, kind: initial_state], InitialState).
@@ -43,7 +43,7 @@ test(
   [true(InitialState == [absent(a), present(b)])]
 ) :-
   clear_model,
-  add_rule(a => b),
+  add_reaction(a => b),
   command(absent(a)),
   make_present_not_absent,
   all_items([model: current_model, kind: initial_state], InitialState).
diff --git a/models.plt b/models.plt
index a3092b5897eea7054959056c75b5f44a273e637b..96caa06886995aa91b9ad2184eaa43a6566bc491 100644
--- a/models.plt
+++ b/models.plt
@@ -3,13 +3,13 @@
 :- begin_tests(models).
 
 
-test('new_model', [true(Rules == [])]) :-
+test('new_model', [true(Reactions == [])]) :-
   new_model,
   single_model(Id0),
-  add_rule(a => b),
+  add_reaction(a => b),
   new_model,
   single_model(Id1),
-  all_items([model: current_model, kind: rule], Rules),
+  all_items([model: current_model, kind: reaction], Reactions),
   delete_item(Id0),
   delete_item(Id1).
 
diff --git a/nusmv.plt b/nusmv.plt
index 7a1fba219bee13932c2a9609c257a7b5e877cc9d..bb2eabcbaff83733ac76a9025884143110946aa4 100644
--- a/nusmv.plt
+++ b/nusmv.plt
@@ -4,8 +4,8 @@
 
 test('nusmv') :-
   clear_model,
-  add_rule(a => b),
-  add_rule(a + b => c),
+  add_reaction(a => b),
+  add_reaction(a + b => c),
   command(present(a)),
   command(absent(c)),
   export_nusmv('unittest').
diff --git a/rule_editor.pl b/reaction_editor.pl
similarity index 81%
rename from rule_editor.pl
rename to reaction_editor.pl
index d311839feca18980894c405ebc53306d69707ac8..309585d2012eff4f49cedacd2ee585cca69eea92 100644
--- a/rule_editor.pl
+++ b/reaction_editor.pl
@@ -1,40 +1,41 @@
 :- module(
-  rule_editor,
+  reaction_editor,
   [
-    add_rule/1,
-    list_rules/0,
-    rule/4,
-    simplify_all_rules/0,
-    enumerate_molecules/1
+    add_reaction/1,
+    list_reactions/0,
+    reaction/4,
+    simplify_all_reactions/0,
+    enumerate_molecules/1,
+    solution_to_list/2
   ]
 ).
 
-add_rule(Reaction) :-
+add_reaction(Reaction) :-
   biocham_command,
   type(Reaction, reaction),
-  doc('adds reaction rules to the current set of rules.'),
-  simplify_rule(Reaction, SimplifiedReaction),
-  add_item(rule, SimplifiedReaction).
+  doc('adds reaction rules to the current set of reactions.'),
+  simplify_reaction(Reaction, SimplifiedReaction),
+  add_item(reaction, SimplifiedReaction).
 
 
-list_rules :-
+list_reactions :-
   biocham_command,
-  doc('lists the current set of rules.'),
-  list_items([model: current_model, kind: rule]).
+  doc('lists the current set of reactions.'),
+  list_items([model: current_model, kind: reaction]).
 
 
-simplify_all_rules :-
+simplify_all_reactions :-
   \+ (
-    item([model: current_model, kind: rule, id: Id, item: Rule]),
+    item([model: current_model, kind: reaction, id: Id, item: Reaction]),
     \+ (
       delete_item(Id),
-      simplify_rule(Rule, SimplifiedRule),
-      add_item(rule, SimplifiedRule)
+      simplify_reaction(Reaction, SimplifiedReaction),
+      add_item(reaction, SimplifiedReaction)
     )
   ).
 
 
-rule(Item, Kinetics, Reactants, Products, Reversible) :-
+reaction(Item, Kinetics, Reactants, Products, Reversible) :-
   (
     Item = (Kinetics for Body)
   ->
@@ -68,8 +69,8 @@ rule(Item, Kinetics, Reactants, Products, Reversible) :-
   append(CatalystMolecules, LeftMolecules, Reactants),
   append(CatalystMolecules, RightMolecules, Products).
 
-rule(Item, Kinetics, Reactants, Products) :-
-  rule(Item, PairKinetics, LeftMolecules, RightMolecules, Reversible),
+reaction(Item, Kinetics, Reactants, Products) :-
+  reaction(Item, PairKinetics, LeftMolecules, RightMolecules, Reversible),
   (
     Reversible = yes
   ->
@@ -139,16 +140,16 @@ coefficient_object(1 * Object, Object) :-
 coefficient_object(CoefficientObject, CoefficientObject).
 
 
-simplify_rule(Rule, SimplifiedRule) :-
-  rule(Rule, Kinetics, LeftMolecules, RightMolecules, Reversible),
+simplify_reaction(Reaction, SimplifiedReaction) :-
+  reaction(Reaction, Kinetics, LeftMolecules, RightMolecules, Reversible),
   simplify_kinetics(Kinetics, KineticsSimplified),
   simplify_solution(LeftMolecules, LeftMoleculesSimplified),
   simplify_solution(RightMolecules, RightMoleculesSimplified),
   simplify_catalyst(
     LeftMoleculesSimplified, RightMoleculesSimplified, Left, Catalyst, Right
   ),
-  build_rule(
-    KineticsSimplified, Left, Catalyst, Right, Reversible, SimplifiedRule
+  build_reaction(
+    KineticsSimplified, Left, Catalyst, Right, Reversible, SimplifiedReaction
   ).
 
 
@@ -225,13 +226,13 @@ simplify_catalyst([Head | Tail], Right, NewLeft, Catalyst, NewRight) :-
   ).
 
 
-build_rule(Kinetics, Left, Catalyst, Right, Reversible, Rule) :-
+build_reaction(Kinetics, Left, Catalyst, Right, Reversible, Reaction) :-
   (
     Kinetics = 'MA'(1)
   ->
-    Rule = Body
+    Reaction = Body
   ;
-    Rule = (Kinetics for Body)
+    Reaction = (Kinetics for Body)
   ),
   list_to_solution(Left, LeftSolution),
   list_to_solution(Catalyst, CatalystSolution),
@@ -266,8 +267,8 @@ enumerate_molecules(Molecules) :-
 
 
 enumerate_molecule(Molecule) :-
-  item([model: current_model, kind: rule, item: Item]),
-  rule(Item, _Kinetics, Reactants, Products, _Reversible),
+  item([model: current_model, kind: reaction, item: Item]),
+  reaction(Item, _Kinetics, Reactants, Products, _Reversible),
   (
     member(_ * Molecule, Reactants)
   ;
diff --git a/reaction_editor.plt b/reaction_editor.plt
new file mode 100644
index 0000000000000000000000000000000000000000..c3d32135eeb035f70c8d031bc4f16faecfafd9cd
--- /dev/null
+++ b/reaction_editor.plt
@@ -0,0 +1,18 @@
+:- use_module(library(plunit)).
+
+
+:- begin_tests(reaction_editor).
+
+
+test('compound', [true(Reactions == [2 * a + 2 * b => 2 * 'a-b'])]) :-
+  clear_model,
+  command(add_reaction(2 * a + 2 * b => 2 * a-b)),
+  all_items([model: current_model, kind: reaction], Reactions).
+
+test('catalyst', [true(Reactions == [2 * b <=[ a + c ]=> b])]) :-
+  clear_model,
+  add_reaction(a + b + c <=[ b ]=> a + c),
+  all_items([model: current_model, kind: reaction], Reactions).
+
+
+:- end_tests(reaction_editor).
diff --git a/rule_editor.plt b/rule_editor.plt
deleted file mode 100644
index 6cd572c9f6a7bef301917729186febd5811c52aa..0000000000000000000000000000000000000000
--- a/rule_editor.plt
+++ /dev/null
@@ -1,18 +0,0 @@
-:- use_module(library(plunit)).
-
-
-:- begin_tests(rule_editor).
-
-
-test('compound', [true(Rules == [2 * a + 2 * b => 2 * 'a-b'])]) :-
-  clear_model,
-  command(add_rule(2 * a + 2 * b => 2 * a-b)),
-  all_items([model: current_model, kind: rule], Rules).
-
-test('catalyst', [true(Rules == [2 * b <=[ a + c ]=> b])]) :-
-  clear_model,
-  add_rule(a + b + c <=[ b ]=> a + c),
-  all_items([model: current_model, kind: rule], Rules).
-
-
-:- end_tests(rule_editor).
diff --git a/toc.org b/toc.org
index 8b975a7c01b9b96129a9933909d3917451adca9a..98192120826f80ab2b1d9e5ef7e89eb02d0ad4cc 100644
--- a/toc.org
+++ b/toc.org
@@ -32,9 +32,9 @@
 *** Graphics files
 *** Other files
 - nusmv.pl
-** Listing and editing rules and events
-*** Rules
-- rule_editor.pl
+** Listing and editing reactions and events
+*** Reactions
+- reaction_editor.pl
 - ode.pl
 *** Events
 - events.pl