Commit 45004842 authored by FAGES Francois's avatar FAGES Francois

demo Doctor in the cell

parent a3860d16
......@@ -216,7 +216,7 @@ generate_ctl(Formula):-
generate_ctl:-
biocham_command,
doc('adds to the CTL specification all reachable , reachable steady, reachable stable, checkpoint2, and oscil formulas on all molecules.'),
doc('adds to the CTL specification all reachable stable, reachable steady, reachable, checkpoint2, and oscil formulas on all molecules (using this order of enumeration for performing subsumption checks).'),
generate_ctl(reachable(stable(wildcard))),
generate_ctl(reachable(steady(wildcard))),
generate_ctl(reachable(wildcard)),
......@@ -229,7 +229,7 @@ generate_ctl:-
generate_ctl_not:-
biocham_command,
doc('adds to the CTL specification all reachable , reachable not, reachable steady, reachable steady not, reachable stable, reachable stable not, checkpoint2, and oscil formulas on all molecules.'),
doc('adds to the CTL specification all reachable stable , reachable stable not, reachable steady, reachable steady not, reachable, reachable not, checkpoint2, and oscil formulas on all molecules.'),
generate_ctl(reachable(stable(wildcard))),
generate_ctl(reachable(stable(not(wildcard)))),
generate_ctl(reachable(steady(wildcard))),
......
parameter(k1= 1.15157e-5).
parameter(k2=24).
parameter(k3=7.77313e-006).
parameter(k4=1).
parameter(k5=240).
parameter(k6=2.91492e-009).
parameter(k7=0.0009).
parameter(k8=0.009).
parameter(k9=5.82985e-008).
parameter(k10=15).
parameter(k11=150).
parameter(k12=10000).
parameter(k13=9.50049e-012).
parameter(k14=0.033).
parameter(k15=1.08824e-006).
parameter(k16=0.07).
parameter(k17=0.7).
parameter(k18=0.33).
parameter(k19=1.8077e-006).
parameter(k20=40).
parameter(k21=9.71641e-009).
parameter(k22=20).
parameter(k23=200).
parameter(k24=400).
parameter(k25=5e-3).
parameter(k26=1e-2).
% Transmembrane inputs
MA(k25) for glucoseext => glucose.
MA(k26) for acetoneext => acetone.
% Glucose pathway to NADH
MA(k19) for G_1DH + NAD => Cia1.
MA(k20) for Cia1 => G_1DH + NAD.
MA(k21) for Cia1 + glucose => Cib1.
MA(k22) for Cib1 => Cia1 + glucose.
MA(k23) for Cib1 => Cfa1 + NADH.
MA(k24) for Cfa1 => G_1DH + gluconolacrone.
% Acetone pathway to Resorufin by consuming NADH
MA(k13) for ADH + NADH => Cia2.
MA(k14) for Cia2 => ADH + NADH.
MA(k15) for Cia2 + acetone => Cib2.
MA(k16) for Cib2 => Cia2 + acetone.
MA(k17) for Cib2 => Cfa2 + NAD.
MA(k18) for Cfa2 => ADH + isopropanol.
MA(k1) for HRP + H_2O_2 => Cia5.
MA(k2) for Cia5 => HRP + H_2O_2.
MA(k3) for Cia5 + resazurin => Cib5.
MA(k4) for Cib5 => Cia5 + resazurin.
MA(k5) for Cib5 => HRP + resorufin.
MA(k6) for HRP2 + NADH => Cf4.
MA(k7) for Cf4 => HRP2 + NADH.
MA(k8) for Cf4 => HRP2 + NADN.
MA(k9) for AO + isopropanol => Cf3.
MA(k10) for Cf3 => AO + isopropanol.
MA(k11) for Cf3 => Cio3 + H_2O_2.
MA(k12) for Cio3 => AO + HRP2.
present(glucose, 0).
present(gluconolacrone, 0).
present(G_1DH, c).
present(acetone, 0).
present(isopropanol, 0).
present(ADH, a).
present(NADH, 31533).
present(NAD, 1576691971).
present(resazurin, 315338394).
present(resorufin, 0).
present(HRP, 6565).
present(H_2O_2, 0).
present(AO, b).
present(NADN, 0).
present(HRP2, 6565).
%present(Cfa5, 0).
present(Cia5, 0).
present(Cib5, 0).
present(Cf4, 0).
present(Cf3, 0).
present(Cio3, 0).
present(Cfa2, 0).
present(Cia2, 0).
present(Cib2, 0).
present(Cfa1, 0).
present(Cia1, 0).
parameter(b=175012).
parameter(c=2232595).
parameter(a=92078816).
%option(show_molecules:{NADN, acetone, glucose, resorufin, NADH}).
option(time:3600).
This diff is collapsed.
......@@ -212,7 +212,7 @@ list_current_models :-
list_model :-
biocham_command,
doc('lists the contents of the current Biocham model.'),
doc('lists the current Biocham model: reactions, influences, initial state, parameters, events, functions, LTL patterns, options.'),
list_model_reactions,
list_model_influences,
list_model_initial_state,
......
......@@ -945,7 +945,7 @@ check_multistability_graph :-
),
get_current_graph(GraphId),
get_attribute(GraphId, swaps_used=Swaps),
write('There is no multistationarity, no positive circuit\n'),
write('There is no multiple steady states with non-zero values, no positive circuit\n'),
(
identity_swap(Swaps)
->
......@@ -989,7 +989,7 @@ check_multistability_graph :-
;
true
),
write('There may be multistationarity, positive circuit detected.'),
write('There may be non-degenerate multistationarity, positive circuit detected.'),
debug(multistability, "~nDone in ~ws", [Diff_time]),
write('\n')
)
......
......@@ -14,13 +14,13 @@ test('acyclic_multi_graph') :-
test('multistability_fail') :-
with_output_to(atom(Output), check_multistability),
sub_atom(Output, 0, _, _, 'There may be multistationarity, positive circuit detected').
sub_atom(Output, 0, _, _, 'There may be non-degenerate multistationarity, positive circuit detected').
test('multistability_success') :-
with_output_to(
atom(Output),
with_option(test_transpositions: yes, check_multistability)
),
sub_atom(Output, 0, _, _, 'There is no multistationarity, no positive circuit').
sub_atom(Output, 0, _, _, 'There is no multiple steady states with non-zero values, no positive circuit').
:- end_tests(multistability).
......@@ -1066,7 +1066,7 @@ print_ode_system_as_latex :-
format('\\begin{align*}\n'),
forall(
item([parent: Id, kind: initial_concentration, item: init(X = E)]),
format('~w_0 &= ~w\\\\\n', [X, E])
format('{~w}_0 &= ~w\\\\\n', [X, E])
),
forall(
item([parent: Id, kind: parameter, item: par(K = V)]),
......
......@@ -79,8 +79,8 @@ test(
test(
'export_ode_as_latex',
[true(Lines == [
'\\begin{align*}', 'b_0 &= 0\\\\',
'a_0 &= 1\\\\', 'k &= 2\\\\',
'\\begin{align*}', '{b}_0 &= 0\\\\',
'{a}_0 &= 1\\\\', 'k &= 2\\\\',
'\\frac{db}{dt} &= k*a\\\\',
'\\frac{da}{dt} &= - (k*a)\\\\',
'\\end{align*}'
......
......@@ -3625,7 +3625,7 @@ condition_to_PIVP( OdeSystem, C, Post ) :-% {{{
% constants{{{
constant( true, 1.5 ).
constant( false, 0 ).
constant( fast, 10000 ).
constant( fast, F ):- get_option(fast_rate, F).
constant( tempPrefix, temp ).
constant( preNull, null ).
constant( counter, counter ).
......
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