Merge branch 'release/4.5.1'

Makefile

@@ -53,7 +53,8 @@ KERNEL_DIR=$(JUPYTER_DIR)/kernel/biocham_kernel
 WORKFLOWS_DIR=$(JUPYTER_DIR)/guinbextension/src/config/workflows
 
 # NOTEBOOKS=$(shell find . -type f -name '*.ipynb' -print)
-NOTEBOOKS=library/examples/C2-19-Biochemical-Programming/TD1_lotka_volterra.ipynb library/examples/doctor_in_the_cell/diagnosis.ipynb
+NOTEBOOKS=library/examples/C2-19-Biochemical-Programming/TD1_lotka_volterra.ipynb library/examples/C2-19-Biochemical-Programming/TD2_enzyme_kinetics.ipynb library/examples/C2-19-Biochemical-Programming/TD4_genetic_switch.ipynb library/examples/C2-19-Biochemical-Programming/TD5_protein_switch.ipynb library/examples/C2-19-Biochemical-Programming/TD6_oscillators.ipynb library/examples/C2-19-Biochemical-Programming/TD7_switches.ipynb library/examples/C2-19-Biochemical-Programming/TD7_rate_independence.ipynb library/examples/C2-19-Biochemical-Programming/TD8_mapk_signalling.ipynb
+
 REFDIR=nbrefs
 
 all: biocham biocham_debug quick doc/index.html pldoc install_kernel install_gui

about.pl

@@ -8,7 +8,7 @@
     about/0
   ]).
 
-version('4.4.15').
+version('4.5.1').
 
 copyright(
   'Copyright (C) 2003-2020 Inria, EPI Lifeware, Saclay-Île de France, France'

aliases.pl

@@ -11,6 +11,7 @@
   ]
 ).
 
+:- use_module(doc).
 
 :- devdoc('\\section{Commands}').
 

arithmetic_rules.pl

@@ -6,9 +6,13 @@
     additive_normal_form/2,
     always_negative/1,
     always_positive/1,
+    determine_sign/2,
     normalize_number/2,
     is_null/1,
-    modulo/3
+    zero_like/1,
+    modulo/3,
+    is_numeric/2,
+    is_numeric/1
   ]).
 
 % Insert here for separate compilation and linting
@@ -270,29 +274,41 @@ extract_coefficient(+ CA, C, A) :-
   extract_coefficient(CA, C, A),
   !.
 
-extract_coefficient(A * B, A, B) :-
-  number(A),
-  !.
-
-extract_coefficient(A / B, A, 1 / B) :-
-  number(A),
-  !.
-
-extract_coefficient(A * B, B, A) :-
-  number(B),
-  !.
-
-extract_coefficient(A / B, BInv, A) :-
-  number(B),
+extract_coefficient(A * B, SubCoeff, Others) :-
+  extract_coefficient(A, ACoeff, AOthers),
+  extract_coefficient(B, BCoeff, BOthers),
   !,
-  BInv is 1 / B.
+  (
+    AOthers = 1
+  ->
+    Others = BOthers
+  ;
+    BOthers = 1
+  ->
+    Others = AOthers
+  ;
+    Others = AOthers*BOthers
+  ),
+  SubCoeff is ACoeff*BCoeff.
 
-extract_coefficient(CA * B, C, A * B) :-
-  extract_coefficient(CA, C, A),
-  !.
+extract_coefficient(A / B, SubCoeff, Others) :-
+  extract_coefficient(A, ACoeff, AOthers),
+  extract_coefficient(B, BCoeff, BOthers),
+  !,
+  (
+    AOthers = 1
+  ->
+    Others = BOthers
+  ;
+    BOthers = 1
+  ->
+    Others = AOthers
+  ;
+    Others = AOthers/BOthers
+  ),
+  SubCoeff is ACoeff/BCoeff.
 
-extract_coefficient(A * CB, C, A * B) :-
-  extract_coefficient(CB, C, B).
+extract_coefficient(A, 1, A).
 
 
 extract_powers(sqrt(Expr), Power, Sub) :-
@@ -637,6 +653,11 @@ rewrite_additive_normal_form(A * (B * C), D * C) :-
 rewrite_additive_normal_form(A * (B * C), B * (A * C)) :-
   number(B).
 
+rewrite_additive_normal_form((A * B) / C, D * B) :-
+  number(A),
+  number(C),
+  D is A/C.
+
 rewrite_additive_normal_form((A * B) / C, A * (B / C)) :-
   number(A).
 
@@ -665,105 +686,132 @@ arithmetic_operation(- _).
 
 arithmetic_operation(_ ^ _).
 
-always_negative(A) :-
-  rewrite(rewrite_simplify, A, B),
-  B \= A,
-  !,
-  always_negative(B).
-
-always_negative(A) :-
-  number(A),
-  !,
-  A =< 0.
-
-always_negative(- A) :-
-  always_positive(A).
-
-always_negative(A + B) :-
-  always_negative(A),
-  always_negative(B).
 
-always_negative(A - B) :-
-  always_negative(A),
-  always_positive(B).
+%! always_negative(+Expr)
+%! always_positive(+Expr)
+%
+% Check if Expr is assure to be always negative/positive, fail if it can change sign
+% or if it is impossible to decide
 
-always_negative(A * B) :-
-  always_negative(A),
-  always_positive(B).
+always_negative(Expr) :-
+  determine_sign(Expr, zero);
+  determine_sign(Expr, neg).
 
-always_negative(0 * _) :-
-  !.
+always_positive(Expr) :-
+  determine_sign(Expr, zero);
+  determine_sign(Expr, pos).
 
-always_negative(A * B) :-
-  always_positive(A),
-  always_negative(B).
 
-always_negative(A / B) :-
-  always_negative(A),
-  always_positive(B).
+%! determine_sign(+Expr, -Sign)
+%
+% Try to infer the sign of Expr, Sign will be unified to: neg/pos/zero/dnk (do not know)
 
-always_negative(A / B) :-
-  always_positive(A),
-  always_negative(B).
+% TODO : Verify if it needs rewriting
+%always_negative(A) :-
+%  rewrite(rewrite_simplify, A, B),
+%  B \= A,
+%  !,
+%  always_negative(B).
 
+determine_sign(A, zero) :-
+  is_null(A),
+  !.
 
-always_positive(A) :-
-  rewrite(rewrite_simplify, A, B),
-  B \= A,
+determine_sign(Expr, Sign) :-
+  is_numeric(Expr, A),
   !,
-  always_positive(B).
+  (
+    A = 0
+  ->
+    Sign = zero
+  ;
+    A < 0
+  ->
+    Sign = neg
+  ;
+    Sign = pos
+  ).
 
-always_positive(A) :-
-  number(A),
+determine_sign(- A, NSign) :-
+  determine_sign(A, Sign),
   !,
-  A >= 0.
-
-always_positive(A):- % assumed for concentrations, parameters
-    atom(A),
-    !.
-
-always_positive(- A) :-
-  always_negative(A).
+  (
+    Sign = pos
+  ->
+    NSign = neg
+  ;
+    Sign = neg
+  ->
+    NSign = pos
+  ;
+    NSign = Sign
+  ).
 
-always_positive(_A ^ B) :-
-  number(B),
+determine_sign(A + B, Sign) :-
+  !,
   (
-    modulo(B, 2, 0)
+    determine_sign(A, SignAB),
+    determine_sign(B, SignAB)
   ->
-    true
+    Sign = SignAB
+  ;
+    Sign = dnk
   ).
 
-always_positive(A ^ _B) :-
-  always_positive(A).
+determine_sign(A - B, Sign) :-
+  !,
+  determine_sign(A + (- B), Sign).
 
-always_positive(A + B) :-
-  always_positive(A),
-  always_positive(B).
+determine_sign(A * B, Sign) :-
+  !,
+  determine_sign(A, SignA),
+  determine_sign(B, SignB),
+  (
+    (SignA = zero ; SignB = zero)
+  ->
+    Sign = zero
+  ;
+    (SignA = dnk ; SignB = dnk)
+  ->
+    Sign = dnk
+  ;
+    SignA = SignB
+  ->
+    Sign = pos
+  ;
+    Sign = neg
+  ).
 
-always_positive(A - B) :-
-  always_positive(A),
-  always_negative(B).
+determine_sign(A / B, Sign) :-
+  !,
+  (
+    is_null(B)
+  ->
+    throw(error(division_by_zero, arithmetic_rules_determine_sign))
+  ;
+    true
+  ),
+  determine_sign(A * B, Sign).
 
-always_positive(0 * _) :-
+determine_sign(A, pos) :- % concentrations and parameters are assumed positive
+  atom(A),
   !.
 
-always_positive(A * B) :-
-  always_negative(A),
-  always_negative(B).
+determine_sign(_A ^ B, pos) :-
+  is_integer(B, Value),
+  (
+    modulo(Value, 2, 0)
+  ->
+    !,
+    true
+  ).
 
-always_positive(A * B) :-
-  always_positive(A),
-  always_positive(B).
+determine_sign(A ^ _B, Sign) :-
+  determine_sign(A, Sign).
 
-always_positive(A / B) :-
-  always_positive(A),
-  always_positive(B).
+determine_sign(exp(_A), pos).
 
-always_positive(A / B) :-
-  always_negative(A),
-  always_negative(B).
 
-always_positive(exp(_A)).
 
 normalize_number(N, Norm) :-
   (
@@ -796,6 +844,14 @@ is_null_sr(_A^(-_N)) :- !, false.
 is_null_sr(A^_N) :- is_null_sr(A).
 
 
+%! zero_like(+Expr)
+%
+% A more drastic version of is_null
+
+zero_like(0).
+zero_like(0.0).
+
+
 %! modulo(+A, +B)
 %
 % compute C is mod(A,B) but fail instead of raising an error when A or B are not integer
@@ -807,4 +863,48 @@ modulo(A, B, C) :-
     fail
   ).
 
+%! is_numeric(+Expr, -Value)
+%! is_numeric(+Expr)
+%
+% determine if an expression is a simple numeric value (eventualy with parameters)
+
+is_numeric(N) :- is_numeric(N, _V).
+
+is_numeric(N, Value) :-
+  item([kind:parameter, key:N, item:parameter(N = Value)]),
+  !.
+
+is_numeric(N, Value) :-
+  % needed for parameters attached to ode system
+  get_current_ode_system(Id),
+  item([parent:Id, kind:parameter, item:par(N = Value)]),
+  !.
+
+is_numeric(N, N) :-
+  number(N).
+
+is_numeric(A + B, Vab) :- !,
+  is_numeric(A, Va),
+  is_numeric(B, Vb),
+  Vab is Va+Vb.
+is_numeric(A - B, Vab) :- !,
+  is_numeric(A, Va),
+  is_numeric(B, Vb),
+  Vab is Va - Vb.
+is_numeric(-(A), Vma) :- !,
+  is_numeric(A, Va),
+  Vma is -Va.
+is_numeric(A*B, Vab) :- !,
+  is_numeric(A, Va),
+  is_numeric(B, Vb),
+  Vab is Va*Vb.
+is_numeric(A^N, Van) :- !,
+  is_numeric(N, Vn),
+  is_numeric(A, Va),
+  Van is Va^Vn.
+is_numeric(A/N, Van) :- !,
+  is_numeric(N, Vn),
+  is_numeric(A, Va),
+  Van is Va/Vn.
+
 

arithmetic_rules.plt

@@ -2,6 +2,10 @@
 
 :- begin_tests(arithmetic_rules, [setup((clear_model, reset_options))]).
 
+test('simplify1', []) :-
+  simplify(a+2*a, 3*a),
+  simplify(-1*a/b+2*a/b, a/b).
+
 test('distribute1', [true(Out == a * a + a * b + c)]) :-
   distribute(a * (a + b) + c, Out).
 
@@ -9,6 +13,17 @@ test('distribute2', []) :-
   distribute((a+b)^2, a*a+a*b+(b*a+b*b)),
   distribute((a+b)^ -2, (a+b)^ -2).
 
+test('determine_sign', []) :-
+  parameter([k1 = 2, k2 = 3]),
+  determine_sign((a+1)^2, pos),
+  determine_sign((a-1)^3, dnk),
+  determine_sign(-exp(a), neg),
+  determine_sign(a/(a+1), pos),
+  determine_sign((2+a)*0, zero),
+  determine_sign((x-1)^k1, pos),
+  determine_sign((x-1)^k2, dnk).
+
+
 test('is_null', []) :-
   is_null(a*0*1/2),
   \+(is_null(a*b/0)).

binder/Dockerfile

-FROM registry.gitlab.inria.fr/lifeware/biocham:v4.4.15
+FROM registry.gitlab.inria.fr/lifeware/biocham:v4.5.1

biocham_jupyter/guinbextension/package.json

 {
   "name": "gui",
-  "version": "4.4.15",
+  "version": "4.5.1",
   "description": "biocham gui in jupyter notebook",
   "main": "src/index.js",
   "scripts": {
@@ -26,21 +26,21 @@
     "babel-loader": "^8.0.0",
     "classnames": "^2.2.6",
     "clean-webpack-plugin": "^0.1.19",
+    "css-loader": "^0.28.10",
+    "file-loader": "^1.1.11",
     "html-webpack-plugin": "^3.2.0",
+    "jest": "^23.6.0",
+    "jsdoc": "^3.5.5",
+    "lodash": "^4.17.11",
     "react-test-renderer": "^16.6.0",
     "redux-devtools-extension": "^2.13.8",
     "redux-logger": "^3.0.6",
     "style-loader": "^0.20.3",
     "ttf-loader": "^1.0.2",
     "url-loader": "^1.1.2",
-    "css-loader": "^0.28.10",
-    "file-loader": "^1.1.11",
     "webpack": "^4.22.0",
     "webpack-bundle-analyzer": "^3.3.2",
-    "webpack-cli": "^3.1.1",
-    "jest": "^23.6.0",
-    "jsdoc": "^3.5.5",
-    "lodash": "^4.17.11"
+    "webpack-cli": "^3.1.1"
   },
   "dependencies": {
     "@material-ui/core": "^3.1.0",

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

@@ -101,6 +101,7 @@ commands = [
     "hybrid_static_simulation",
     "import_ode",
     "import_reactions_from_graph",
+    "infer_hidden_molecules",
     "influence_graph",
     "influence_hypergraph",
     "influence_model",
@@ -184,6 +185,7 @@ commands = [
     "place",
     "plot",
     "polynomial_ODE",
+    "polynomize_ode",
     "present",
     "prolog",
     "quadratic_reduction_ODE",

biocham_jupyter/kernel/biocham_kernel/__init__.py

 """Example magic"""
-__version__ = '4.4.15'
+__version__ = '4.5.1'

biochamlib.sh

+#!/usr/bin/bash
+
+# quadratization
+swipl --goal=main --stand_alone=true -DSWIPL_LINKER_FLAGS="-static" -DSWIPL_SHARED_LIB=OFF\
+  --foreign=save -o quadratization -c biochamlib_quadratization.pl
+
+# ODE2SBML
+swipl --goal=main --stand_alone=true -DSWIPL_LINKER_FLAGS="-static" -DSWIPL_SHARED_LIB=OFF\
+  --foreign=save -o ODE2SBML -c biochamlib_ode2sbml.pl

biochamlib_ode2sbml.pl

+#!/usr/bin/prolog
+/*
+ * The prolog script to create the stand-alone saved state for conversion of an ODE to an
+ * SBML file. 
+ * Coder: M. Hemery
+ */
+
+% Loading libraries
+:- use_module(aliases).
+:- use_module(arithmetic_rules).
+:- use_module(biocham).
+:- use_module(counters).
+:- use_module(doc).
+:- use_module(filename).
+:- use_module(formal_derivation).
+:- use_module(functions).
+:- use_module(initial_state).
+:- use_module(kinetics).
+:- use_module(models).
+:- use_module(molecules).
+:- use_module(namespace).
+:- use_module(objects). 
+:- use_module(ode). 
+:- use_module(parameters). 
+:- use_module(reaction_editor). 
+:- use_module(reaction_rules). 
+:- use_module(sbml_files). 
+:- use_module(toplevel).
+:- use_module(types).
+:- use_module(util).
+:- use_module(xpp_parser).
+
+set_my_option(Option, Value) :-
+  change_item([], option, Option, option(Option: Value)).
+
+% parse_arguments(+Arguments, -Input)
+%
+% Handle the various option of the standalone:
+% -i: input file
+
+parse_arguments([], none).
+
+parse_arguments(['-i', Input| Argv], Input) :-
+  parse_arguments(Argv, _I).
+
+parse_arguments(['--help'| _Argv], _I, _M, _T) :-
+  print_help.
+
+% print_help
+
+print_help :-
+  format("help~n", []),
+  halt.
+
+% main(+argv)
+
+main(Argv) :-
+  (Argv = [] -> print_help ; true),
+  % Handling naming and options
+  parse_arguments(Argv, Input),
+  file_name_extension(InputBase, 'ode', Input),
+  file_name_extension(InputBase, 'sbml', Output),
+  format("Input: ~w~nOutput: ~w~n", [Input, Output]),
+  % Initialization (see biocham:initialize)
+  set_prolog_flag(allow_variable_name_as_functor, true),
+  set_counter(list_item_counter, 0),
+  set_counter(item_id, 0),
+  set_counter(model, 0),
+  set_counter(molecule_id, 0),
+  set_counter(parameter_id, 1),
+  nb_setval(ode_viewer, inline),
+  nb_setval(current_models, []),
+  new_model,
+  set_my_option(import_reactions_with_inhibitors, yes),
+  % Main procedure
+  read_xpp(Input),
+  list_ode,
+  add_reactions_from_ode_system,
+  export_sbml(Output).
+
+

biochamlib_quadratization.pl

+#!/usr/bin/prolog
+/*
+ * The prolog script to create the stand-alone saved state for quadratization, it reads
+ * and returns an .ode file.
+ * Coder: M. Hemery
+ */
+
+% Loading libraries
+:- use_module(arithmetic_rules).
+:- use_module(biocham).
+:- use_module(counters).
+:- use_module(doc).
+:- use_module(kinetics).
+:- use_module(models).
+:- use_module(namespace).
+:- use_module(ode). 
+:- use_module(quadratic_reduction). 
+:- use_module(sat). 
+:- use_module(toplevel).
+:- use_module(types).
+:- use_module(util).
+:- use_module(xpp_parser).
+
+set_my_option(Option, Value) :-
+  change_item([], option, Option, option(Option: Value)).
+
+% parse_arguments(+Arguments, -Input, -Method, -Timeout)
+%
+% Handle the various option of the standalone:
+% --method: method used to perform the reduction
+% --timeout: timeout for sat call
+% --help: print help and quit
+% -i: input file
+
+parse_arguments([], none, sat_species, 120).
+
+parse_arguments(['--method', Method| Argv], Input, Method, Timeout) :-