araignee du soir espoir

biocham_jupyter/guinbextension/src/config/workflows/commands.py

@@ -166,6 +166,8 @@ commands = [
     "new_model",
     "new_ode_system",
     "numerical_simulation",
+    "ode_function",
+    "ode_parameter",
     "ode_system",
     "option",
     "pac_learning",

rate_independence.pl

@@ -181,7 +181,7 @@ writeln('--------- iterate ---------'), list_model,
   simplify(Inputs, Outputs).
   
 
-% Elimination of trivial reactions with products same as reactants
+% Elimination of trivial reactions with products=reactants
 trivial_reaction:-
   item([kind:reaction, id: Id, item: Reaction]),
   reaction(Reaction, _Kinetics, Reactants, _Inhibitors, Reactants),
@@ -236,6 +236,7 @@ simpl(M):-
 % Todo: accept reversible reactions with syntax <=>
 
 % Elimination of M in 2 loops a 1<=>3 M (4<)=>2 b rewritten a (<)=> b
+% WOULD NEED TO BE GENERALIZED TO alpha <=> beta <=> gamma in alpha<=>gamma FOR ELIMINATING ISOLATED beta
 simpl(M):-
   reactions_with_reactant([M], [Reaction1, Reaction2]), 
   reactions_with_product([M], [Reaction3 | Reactions]),

rate_independence_test.bc

@@ -7,29 +7,33 @@ list_model.
 test_rate_independence_inputs_sinks.
 prolog('writeln("ANSWER YES: max = sum-min")'). prolog('writeln("============")').
 
+
 clear_model.
 a => b.
 b => c.
 c => b + d.
 list_model.
 test_rate_independence_inputs_sinks.
-prolog('writeln("ANSWER YES: loop leakage")'). prolog('writeln("============")').
+prolog('writeln("ANSWER YES: loop leakage with and-fork")'). prolog('writeln("============")').
+
 
 clear_model.
+input=>a.
 a => b.
 b => c.
-c => b.
-c => d.
+c => a + d.
 list_model.
 test_rate_independence_inputs_sinks.
-prolog('writeln("ANSWER YES: loop leakage")'). prolog('writeln("============")').
+prolog('writeln("ANSWER YES: loop leakage with and-fork")'). prolog('writeln("============")').
 
 clear_model.
-a+b=>b. 
-b+c=>d.
+a => b.
+b => c.
+c => a.
+c => d.
 list_model.
 test_rate_independence_inputs_sinks.
-prolog('writeln("ANSWER YES: irrelevant fork")'). prolog('writeln("============")').
+prolog('writeln("ANSWER YES: loop leakage with or-fork")'). prolog('writeln("============")').
 
 
 clear_model.
@@ -38,7 +42,16 @@ b => a.
 b => c.
 list_model.
 test_rate_independence_inputs_sinks. %
-prolog('writeln("ANSWER YES: loop leakage")'). prolog('writeln("============")').
+prolog('writeln("ANSWER YES: loop leakage with or-fork")'). prolog('writeln("============")').
+
+
+clear_model.
+a+b=>c+d.
+c+d=>a+b.
+c+d=>e.
+list_model.
+test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: composite loop leakage with or-fork")'). prolog('writeln("============")').
 
 
 clear_model.
@@ -49,7 +62,35 @@ e=>c+d.
 e=>f+g.
 list_model.
 test_rate_independence_inputs_sinks.
-prolog('writeln("ANSWER YES: composite loop leakage")'). prolog('writeln("============")').
+prolog('writeln("ANSWER YES: composite loop leakage with or-fork")'). prolog('writeln("============")').
+
+
+
+clear_model.
+a+b=>c+d.
+c+d=>a+b.
+c+d=>e.
+e=>c+f.
+list_model.
+test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: composite loop leakage with and-fork")'). prolog('writeln("============")').
+
+
+clear_model.
+a=>b+c.
+b=>d.
+c=>d.
+list_model.
+test_rate_independence_inputs_sinks. % yes
+prolog('writeln("ANSWER YES: closing and-fork with or-join")'). prolog('writeln("============")').
+
+
+clear_model.
+a=>b+c.
+b+c=>d.
+list_model.
+test_rate_independence_inputs_sinks. % yes
+prolog('writeln("ANSWER NO: closing and-fork with and-join")'). prolog('writeln("============")').
 
 
 clear_model.
@@ -62,6 +103,15 @@ test_rate_independence_inputs_sinks. % yes
 prolog('writeln("ANSWER YES: closing or-fork with or-join")'). prolog('writeln("============")').
 
 
+clear_model.
+a=>b.
+a=>c.
+b+c=>d.
+list_model.
+test_rate_independence_inputs_sinks. % yes
+prolog('writeln("ANSWER NO: closing or-fork with and-join")'). prolog('writeln("============")').
+
+
 clear_model.
 MA(k1) for A => B.
 MA(k2) for A + B => C.
@@ -70,7 +120,6 @@ test_rate_independence_inputs_sinks. % no
 prolog('writeln("ANSWER NO: closing or-fork with and-join")'). prolog('writeln("============")').
 
 
-% loop and fork
 clear_model.
 MA(1) for A=>B.
 MA(2) for B=>C.
@@ -82,21 +131,22 @@ prolog('writeln("ANSWER NO: parasite loop and fork")'). prolog('writeln("=======
 
 
 clear_model.
+input=>a.
 MA(k1) for a => b.
 MA(k2) for b => a.
 MA(k3) for b => c.
 MA(k4) for c => b.
 list_model.
-test_rate_independence({a},{c}). % no
-prolog('writeln("ANSWER NO: loop equilibrium output")'). prolog('writeln("============")').
+test_rate_independence_inputs_sinks. % no
+prolog('writeln("ANSWER NO: output in loop equilibriuem")'). prolog('writeln("============")').
 
 
 clear_model.
 MA(k1) for a+b => b.
 MA(k2) for b+c=>d.
 list_model.
-test_rate_independence({a},{c}). % no
-prolog('writeln("ANSWER NO")'). prolog('writeln("============")').
+test_rate_independence_inputs_sinks. % no
+prolog('writeln("ANSWER YES: irrelevant input")'). prolog('writeln("============")').