Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Lifeware
biocham
Commits
2ff72798
Commit
2ff72798
authored
Apr 21, 2020
by
FAGES Francois
Browse files
araignee du soir espoir
parent
be10e62f
Changes
3
Hide whitespace changes
Inline
Side-by-side
biocham_jupyter/guinbextension/src/config/workflows/commands.py
View file @
2ff72798
...
...
@@ -166,6 +166,8 @@ commands = [
"new_model"
,
"new_ode_system"
,
"numerical_simulation"
,
"ode_function"
,
"ode_parameter"
,
"ode_system"
,
"option"
,
"pac_learning"
,
...
...
rate_independence.pl
View file @
2ff72798
...
...
@@ -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
View file @
2ff72798
...
...
@@ -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 equilibriu
e
m")'). 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("============")').
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment