Commit 4a9647e9 authored by FAGES Francois's avatar FAGES Francois
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doc

parent 06d0eab4
......@@ -40,7 +40,7 @@
:- use_module(reaction_rules).
:- doc('Firt-Order Linear Time Logic with linear constraints over the reals, FO-LTL(Rlin), can be used to specify semi-qualitative semi-quantitative constraints on the dynamical behavior of the system, in a much more flexible manner than by curves to fit \\cite{RBFS11tcs}. The syntax of FO-LTL(Rlin) formulas is given below together with some useful abbreviations \\cite{FT14book}:').
:- doc('Firt-Order Linear Time Logic with linear constraints over the reals, FO-LTL(Rlin), can be used to specify semi-qualitative semi-quantitative constraints on the dynamical behavior of the system, in a much more flexible manner than by curves to fit \\cite{RBFS11tcs}. The syntax of FO-LTL(Rlin) formulas is given below with some useful abbreviations \\cite{FT14book}:').
:- doc('The \\texttt{foltl_magnitude} option (default 5) is the multiplicative factor used for the strong comparison operators \\texttt{<<} and \\texttt{>>} over positive numbers, \\texttt{A<<B} means \\texttt{5*A<B}.').
......
......@@ -53,16 +53,17 @@ Rq: The distinction between pivp_string and pivp_list is not always obvious.
:- doc('The Turing completeness of continuous CRNs \\cite{FLBP17cmsb} states that any computable function over the reals can be computed by a CRN over a finite set of molecular species. Biocham uses the proof of that result to compile any computable real function presented as the solution of a polynomial differential equation system into a finite CRN.').
:- doc('The restriction to reactions with at most two reactants is an option.').
:- doc('The lazy introduction of molecular species for negative real values is another option.').
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Main Tools of the module %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
:- doc('The option for binomial reduction restricts the synthesis of reactions with at most two reactants (the default is not).').
:- initial(option(binomial_reduction: no)).
:- doc('Another option is the lazy introduction of molecular species for negative real values (the default is yes).').
:- initial(option(lazy_negatives: yes)).
%! compile_from_expression(+Expr, +Output)
......@@ -81,19 +82,19 @@ compile_from_expression(Expr, Output) :-
type(Expr, arithmetic_expression),
type(Output, name),
doc('
creates a biochemical reaction network such that Output = Expr(t).
creates a biochemical reaction network such that Output = Expr(time).
'),
option(
binomial_reduction,
yesno,
_Reduction,
'Determine if the binomial reduction has to be performed'
'Determine if the binomial reduction for synthesizing reactions with at most two reactants has to be performed'
),
option(
lazy_negatives,
yesno,
_Lazyness,
'Switch between a brutal or a lazy negation'
'Switch between systematic and lazy introduction of molecular species for negative values'
),
expression_to_PIVP(Expr, PIVP),
PIVP = [N, _PODE, _IC],
......@@ -118,19 +119,21 @@ compile_from_expression(Expr, Input, Output) :-
type(Input, name),
type(Output, name),
doc('
creates a biochemical reaction network such that Output = Expr(Input).
creates a biochemical reaction network to compute the function Output = Expr(Input).'),
doc('
The Input species is initialized with the value of a special parameter named input, and is degraded by the computation.
'),
option(
binomial_reduction,
yesno,
_Reduction,
'Determine if the binomial reduction has to be performed'
'Determine if the binomial reduction for synthesizing reactions with at most two reactants has to be performed'
),
option(
lazy_negatives,
yesno,
_Lazyness,
'Switch between a brutal or a lazy negation'
'Switch between systematic and lazy introduction of molecular species for negative values'
),
expression_to_PIVP(Expr, PIVP),
PIVP = [N, _PODE, _IC],
......
......@@ -13,8 +13,14 @@
:- use_module(library(clpfd)).
:- doc('Tropical algebra can be used to reason about orders of magnitude of molecular concentrations, kinetic parameters and reactions rates.
The solutions to tropical equilibration problems provide candidates for regimes exhibiting fast-slow dynamics leading to model reductions \\cite{SFR14amb}.').
:- doc('Tropical algebra can be used to reason about orders of magnitude of molecular concentrations, kinetic parameters and reactions rates.').
:- doc('While steady state analysis consists in finding the roots of the differential functions associated to all or some molecular species in a CRN,
tropical equilibration consists in finding when the positive and negative preponderant terms of the differential functions have the same order of magnitude
(i.e. same integer logarithm).').
:- doc('The solutions to tropical equilibration problems provide candidates for regimes exhibiting fast-slow dynamics leading to model reductions
based on quasi-steady states or reactions in quasi-equilibrium \\cite{SFR14amb}.').
% store monomials of -inf degree
......
......@@ -141,10 +141,10 @@ logarithmic_dose_response(Dose, Value1, Value2):-
:- doc('\\begin{example}This example shows the dose-response diagrams of the MAPK model of Huang and Ferrell in BiomModels revealing the amplifier and analog-digital converter functions
of this network at the second and third level of the cascade. ').
:- biocham_silent(clear_model).
:- biocham('load_sbml(library:examples/mapk/BIOMD0000000009.xml)').
:- biocham('load_sbml(library:biomodels/BIOMD0000000009.xml)').
:- biocham('option(time:100, show:{P_KKK,PP_KK,PP_K})').
:- biocham('dose_response(E1,1e-6,1e-4)').
:- biocham('logarithmic_dose_response(E1,1e-6,1e-4)').
%:- biocham('logarithmic_dose_response(E1,1e-6,1e-4)').
:- doc('\\end{example}').
......@@ -235,26 +235,37 @@ logarithmic_bifurcations(Dose, Value1, Value2):-
clear_variation(Dose).
:- doc('\\begin{example}This example shows a memory effect (and erroneous dose-response diagrams) in the MAPK network when using too short simulation times.
:- doc('\\begin{example}This example of the MAPK network shows a memory effect in one single level of two phosphorylation cycles.
The hysteresis corresponds to the existence of two stable states in the rate equation.
\\clearmodel
\\trace{
biocham: load_sbml(library:examples/mapk/BIOMD0000000009.xml).
biocham: option(time:100,show:{PP_KK,PP_K}).
biocham: dose_response(E1,1e-6,1e-4).
biocham: bifurcations(E1,1e-6,1e-4).
biocham: bifurcations(E1,1e-6,1e-4,time:1000000).
biocham: load_sbml(library:biomodels/BIOMD0000000026.xml).
biocham: dose_response(MAPKK, 0, 100, time:1e4, show:Mpp).
biocham: bifurcations(MAPKK, 0, 100, time:1e4, show:Mpp).
}
\\end{example}').
%:- doc('\\begin{example}This example shows a memory effect (and erroneous dose-response diagrams) in the MAPK network when using too short simulation times.
%\\clearmodel
%\\trace{
%biocham: load_sbml(library:examples/mapk/BIOMD0000000009.xml).
%biocham: option(time:100,show:{PP_KK,PP_K}).
%biocham: dose_response(E1,1e-6,1e-4).
%biocham: bifurcations(E1,1e-6,1e-4).
%biocham: bifurcations(E1,1e-6,1e-4,time:1000000).
%}
%\\end{example}').
:- doc('\\begin{example}
\\clearmodel
\\trace{
biocham: load(library:examples/cell_cycle/Qu_et_al_2003.bc).
biocham: change_parameter_to_variable(k1).
biocham: list_model.
biocham: dose_response(k1,1,1000,time:200,show:CycB-CDK~{p1}).
}
\\end{example}').
%:- doc('\\begin{example}
%\\clearmodel
%\\trace{
%biocham: load(library:examples/cell_cycle/Qu_et_al_2003.bc).
%biocham: change_parameter_to_variable(k1).
%biocham: list_model.
%biocham: dose_response(k1,1,1000,time:200,show:CycB-CDK~{p1}).
%}
%\\end{example}').
......@@ -89,6 +89,11 @@ wgpac_well_formed(Y :: B) :-
object(Y),
wgpac_box_free(B, Y).
:- doc('The option fast rate (defaulting to 1000) is intended to define a high rate constant for reactions faster than the other reactions.
It is used \\begin{itemize}\\item in the reactions for computing the results of the sum and product GPAC blocks,
\\item and in the annihilation reactions between the molecular species for the positive and negative values of a real valued variable. \\end{itemize}
').
:- initial(option(fast_rate: 1000)).
......@@ -97,11 +102,7 @@ compile_wgpac(WgpacSet) :-
type(WgpacSet, {wgpac}),
doc('compiles a set of weak GPAC circuits into a reaction network.'),
set_counter(fresh, 0),
option(fast_rate, arithmetic_expression, Rate, '
This reaction constant (defaulting to 1000) is intended to be a high rate constant.
It is used in the reactions for computing the results of the sum and product GPAC blocks,
and in the annihilation reactions between the positive and negative values of a real valued variable.
'),
option(fast_rate, arithmetic_expression, Rate, ''),
set_parameter(fast, Rate),
\+ (
member(Wgpac, WgpacSet),
......
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