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Commit ceec83a2 authored by FAGES Francois's avatar FAGES Francois

notebooks C2-19 added as tests

parent eb8dd30d
......@@ -53,7 +53,7 @@ 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/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 library/examples/C2-19-Biochemical-Programming/TD9_doctor_in_the_cell.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 library/examples/C2-19-Biochemical-Programming/TD9_doctor_in_the_cell.ipynb library/examples/doctor_in_the_cell/diagnosis.ipynb
REFDIR=nbrefs
all: biocham biocham_debug quick doc/index.html pldoc install_kernel install_gui
......
license GNU GPL 2, http://lifeware.inria.fr/biocham4/
k1*E*S for E+S=>C.
k2*C for C=>E+S.
k3*C for C=>E+P.
present(E,e).
present(S,s).
absent(C).
absent(P).
parameter(
k1 = 4000000.0,
k2 = 25,
k3 = 15,
e = 1.0e-8,
s = 1.0e-5
).
<img src="graph0.png" alt="Simulation results">
<img src="graph1.png" alt="Simulation results">
<img src="ode.tex" alt="Simulation results">
C+E
C+P+S
2 complex invariant(s)
<img src="plot-0.csv" alt="Simulation results">
<img src="plot-1.csv" alt="Simulation results">
<img src="plot-2.csv" alt="Simulation results">
<img src="plot-3.csv" alt="Simulation results">
<img src="graph2.png" alt="Simulation results">
k1*E*S for E+S=>C.
k2*C for C=>E+S.
k3*C for C=>E+P.
Vm*A/(Km+A) for A=>B.
present(E,e).
present(S,s).
absent(C).
absent(P).
present(A,s).
absent(B).
parameter(
k1 = 4000000.0,
k2 = 25,
k3 = 15,
e = 1.0e-8,
s = 1.0e-5
).
function(
Vm = k3*e,
Km = (k2+k3)/k1
).
<img src="ode.tex" alt="Simulation results">
<img src="plot-4.csv" alt="Simulation results">
k1*E*S for E+S=>C.
k2*C for C=>E+S.
k3*C for C=>E+P.
Vm*A/(Km+A) for A=>B.
present(E,e).
present(S,s).
absent(C).
absent(P).
present(A,s).
absent(B).
parameter(
k1 = 4000000.0,
k2 = 25,
k3 = 15,
e = 1.0e-8,
s = 1.0e-5
).
function(
Vm = k3*e,
Km = (k2+k3)/k1
).
<img src="plot-5.csv" alt="Simulation results">
<img src="plot-6.csv" alt="Simulation results">
<img src="plot-7.csv" alt="Simulation results">
license GNU GPL 2, http://lifeware.inria.fr/biocham4/
<img src="graph0.png" alt="Simulation results">
DNA+DNAX1+DNAX2
1 complex invariant(s)
<img src="graph1.png" alt="Simulation results">
<img src="plot-0.csv" alt="Simulation results">
<img src="plot-1.csv" alt="Simulation results">
reachable(stable(DNAX1))
reachable(stable(DNAX2))
reachable(stable(not DNA))
reachable(steady(DNA))
reachable(steady(X1))
reachable(steady(X2))
reachable(steady(not X1))
reachable(steady(not X2))
oscil(X1)
oscil(X2)
AG(x)
EG(x)
EU(not f,f/\EU(f,not f/\EU(not f,f/\EU(f,not f/\EU(not f,f)))))/\EG(EF(f)/\EF(not f))
Trace:
present({DNA, DNAX1}).
reachable(stable(not X1)) is false
reachable(stable(DNAX1))
reachable(stable(DNAX2))
reachable(stable(not DNA))
reachable(stable(not X1))
reachable(stable(not X2))
reachable(stable(not DNAX1))
reachable(stable(not DNAX2))
reachable(steady(DNA))
reachable(steady(X1))
reachable(steady(X2))
checkpoint2(DNA,X1)
checkpoint2(DNA,X2)
checkpoint2(DNA,DNAX1)
checkpoint2(X1,DNAX1)
checkpoint2(DNA,DNAX2)
checkpoint2(X2,DNAX2)
checkpoint2(not X2,X1)
checkpoint2(not DNAX1,X1)
checkpoint2(not DNAX2,X1)
checkpoint2(not X1,X2)
checkpoint2(not DNAX1,X2)
checkpoint2(not DNAX2,X2)
checkpoint2(not X1,DNAX1)
checkpoint2(not X2,DNAX1)
checkpoint2(not DNAX2,DNAX1)
checkpoint2(not X1,DNAX2)
checkpoint2(not X2,DNAX2)
checkpoint2(not DNAX1,DNAX2)
checkpoint2(not X1,not DNA)
checkpoint2(not X2,not DNA)
checkpoint2(not DNAX1,not DNA)
checkpoint2(not DNAX2,not DNA)
oscil(X1)
oscil(X2)
<img src="plot-2.csv" alt="Simulation results">
<img src="plot-3.csv" alt="Simulation results">
<img src="plot-4.csv" alt="Simulation results">
There is no multiple steady states with non-zero values, no positive circuit
(using change of sign for species : X2 X1 DNA )
license GNU GPL 2, http://lifeware.inria.fr/biocham4/
k1*M*MAPKK for M+MAPKK=>M_MAPKK.
k_1*M_MAPKK for M_MAPKK=>M+MAPKK.
k2*M_MAPKK for M_MAPKK=>MAPKK+Mp.
k3*Mp*MAPKK for MAPKK+Mp=>Mp_MAPKK.
k_3*Mp_MAPKK for Mp_MAPKK=>MAPKK+Mp.
k4*Mp_MAPKK for Mp_MAPKK=>MAPKK+Mpp.
h1*Mpp*MKP3 for MKP3+Mpp=>Mpp_MKP3.
h_1*Mpp_MKP3 for Mpp_MKP3=>MKP3+Mpp.
h2*Mpp_MKP3 for Mpp_MKP3=>Mp_MKP3_dep.
h3*Mp_MKP3_dep/uVol for Mp_MKP3_dep=>MKP3+Mp.
h_3*Mp*MKP3/uVol for MKP3+Mp=>Mp_MKP3_dep.
h4*Mp*MKP3 for MKP3+Mp=>Mp_MKP3.
h_4*Mp_MKP3 for Mp_MKP3=>MKP3+Mp.
h5*Mp_MKP3 for Mp_MKP3=>M_MKP3.
h6*M_MKP3 for M_MKP3=>M+MKP3.
h_6*M*MKP3 for M+MKP3=>M_MKP3.
present(M,500.0).
present(Mp,0.0).
present(Mpp,0.0).
present(MAPKK,50.0).
present(MKP3,100.0).
present(M_MAPKK,0.0).
present(Mp_MAPKK,0.0).
present(Mpp_MKP3,0.0).
present(Mp_MKP3_dep,0.0).
present(Mp_MKP3,0.0).
present(M_MKP3,0.0).
parameter(
uVol = 1.0,
k1 = 0.02,
k_1 = 1.0,
k2 = 0.01,
k3 = 0.032,
k_3 = 1.0,
k4 = 15.0,
h1 = 0.045,
h_1 = 1.0,
h2 = 0.092,
h3 = 1.0,
h_3 = 0.01,
h4 = 0.01,
h_4 = 1.0,
h5 = 0.5,
h6 = 0.086,
h_6 = 0.0011
).
M+M_MAPKK+M_MKP3+Mp+Mp_MAPKK+Mp_MKP3+Mp_MKP3_dep+Mpp+Mpp_MKP3
MAPKK+M_MAPKK+Mp_MAPKK
MKP3+M_MKP3+Mp_MKP3+Mp_MKP3_dep+Mpp_MKP3
3 complex invariant(s)
<img src="graph0.png" alt="Simulation results">
There may be non-degenerate multistationarity, positive circuit detected.
<img src="ode.tex" alt="Simulation results">
<img src="plot-0.csv" alt="Simulation results">
<img src="plot-1.csv" alt="Simulation results">
<img src="plot-2.csv" alt="Simulation results">
<img src="plot-3.csv" alt="Simulation results">
license GNU GPL 2, http://lifeware.inria.fr/biocham4/
fast*[x2]*[y] for x2+y=>x1+x2+y.
fast*[x1] for x1=>_.
MA(1) for x1=>x0+x1.
MA(1) for x0=>x0+y.
present(x2,-1).
present(y,1).
parameter(
fast = 1000
).
<img src="ode.tex" alt="Simulation results">
<img src="plot-0.csv" alt="Simulation results">
<img src="plot-1.csv" alt="Simulation results">
MA(fast) for costime_m+costime_p=>_.
MA(fast) for A_m+A_p=>_.
MA(1.0) for A_p=>A_p+costime_p.
MA(1.0) for A_m=>A_m+costime_m.
MA(1.0) for costime_m=>A_p+costime_m.
MA(1.0) for costime_p=>A_m+costime_p.
present(costime_p,1).
parameter(
fast = 1000
).
No complex invariant found
<img src="ode.tex" alt="Simulation results">
<img src="plot-2.csv" alt="Simulation results">
<img src="plot-3.csv" alt="Simulation results">
<img src="plot-4.csv" alt="Simulation results">
<img src="plot-5.csv" alt="Simulation results">
<img src="plot-6.csv" alt="Simulation results">
MA(fast) for costime1_m+costime1_p=>_.
MA(fast) for C_m+C_p=>_.
MA(fast) for B_m+B_p=>_.
MA(1.0) for B_p=>B_p+C_p+costime1_p.
MA(1.0) for B_m=>B_m+C_m+costime1_m.
MA(1.0) for C_m=>B_p+C_m.
MA(1.0) for C_p=>B_m+C_p.
present(costime1_p,2).
present(C_p,1).
present(A,1).
parameter(
fast = 1000
).
<img src="plot-7.csv" alt="Simulation results">
<img src="plot-8.csv" alt="Simulation results">
MA(fast) for cosx_m+cosx_p=>_.
MA(fast) for A_m+A_p=>_.
MA(1.0) for A_p+x=>A_p+cosx_p+x.
MA(1.0) for A_m+x=>A_m+cosx_m+x.
MA(1.0) for cosx_m+x=>A_p+cosx_m+x.
MA(1.0) for cosx_p+x=>A_m+cosx_p+x.
MA(1.0) for x=>_.
present(cosx_p,1).
present(x,input).
parameter(
fast = 1000,
input = 4
).
<img src="graph0.png" alt="Simulation results">
<img src="graph1.png" alt="Simulation results">
<img src="ode.tex" alt="Simulation results">
<img src="plot-9.csv" alt="Simulation results">
v=0.653644
t>1.00391
1.000000
MA(fast) for cosx_m+cosx_p=>_.
MA(fast) for A_m+A_p=>_.
MA(k_2) for A_p+x=>A_p+cosx_p+x.
MA(k_3) for A_m+x=>A_m+cosx_m+x.
MA(k_4) for cosx_m+x=>A_p+cosx_m+x.
MA(k_5) for cosx_p+x=>A_m+cosx_p+x.
MA(k_6) for x=>_.
present(x,input).
present(cosx_p,k_1).
parameter(
fast = 1000,
input = 4,
k_1 = 1,
k_2 = 1.0,
k_3 = 1.0,
k_4 = 1.0,
k_5 = 1.0,
k_6 = 1.0
).
<img src="plot-10.csv" alt="Simulation results">
<img src="plot-11.csv" alt="Simulation results">
v=43
<img src="plot-12.csv" alt="Simulation results">
license GNU GPL 2, http://lifeware.inria.fr/biocham4/
<img src="graph0.png" alt="Simulation results">
<img src="ode.tex" alt="Simulation results">
<img src="plot-0.csv" alt="Simulation results">
v=1
license GNU GPL 2, http://lifeware.inria.fr/biocham4/
<img src="ode.tex" alt="Simulation results">
<img src="plot-0.csv" alt="Simulation results">
<img src="ode.tex" alt="Simulation results">
<img src="plot-1.csv" alt="Simulation results">
<img src="ode.tex" alt="Simulation results">
<img src="plot-2.csv" alt="Simulation results">
<img src="ode.tex" alt="Simulation results">
<img src="plot-3.csv" alt="Simulation results">
<img src="plot-4.csv" alt="Simulation results">
<img src="plot-5.csv" alt="Simulation results">
MA(1) for S=>2*S.
MA(1) for 2*S=>S.
MA(1) for _=>HT.
MA(1) for 2*HT=>HT.
MA(1) for _=>T.
1/(1+T^2) for '/T'=>AT.
MA(1) for 2*NH1=>NH1.
MA(1) for 2*NH1=>H1+2*NH1.
MA(2) for T+2*NH2=>NH2+T.
MA(2) for T+2*NH2=>H2+T+2*NH2.
MA(5) for 2*NH5+4*T=>NH5+4*T.
MA(5) for 2*NH5+4*T=>H5+2*NH5+4*T.
present(S,0.5).
present(NH1,1).
present(NH2,1).
present(NH5,1).
<img src="ode.tex" alt="Simulation results">
<img src="plot-6.csv" alt="Simulation results">
<img src="plot-7.csv" alt="Simulation results">
This diff is collapsed.
license GNU GPL 2, http://lifeware.inria.fr/biocham4/
MA(k25) for glucoseext=>glucose.
MA(k26) for acetoneext=>acetone.
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.
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(G_1DH,c).
present(ADH,a).
present(NADH,31533).
present(NAD,1576691971).
present(resazurin,315338394).
present(HRP,6565).
present(AO,b).
present(HRP2,6565).
present(glucoseext,d).
present(acetoneext,e).
parameter(
k1 = 1.15157e-5,
k2 = 24,
k3 = 7.77313e-6,
k4 = 1,
k5 = 240,
k6 = 2.91492e-9,
k7 = 0.0009,
k8 = 0.009,
k9 = 5.82985e-8,
k10 = 15,
k11 = 150,
k12 = 10000,
k13 = 9.50049e-12,
k14 = 0.033,
k15 = 1.08824e-6,
k16 = 0.07,
k17 = 0.7,
k18 = 0.33,
k19 = 1.8077e-6,
k20 = 40,
k21 = 9.71641e-9,
k22 = 20,
k23 = 200,
k24 = 400,
k25 = 0.005,
k26 = 0.01,
a = 92078816,
b = 175012,
c = 2232595,
d = 300000000.0,
e = 300000000.0
).
<img src="graph0.png" alt="Simulation results">
<img src="graph1.png" alt="Simulation results">
Cfa1+Cib1+gluconolacrone+glucose+glucoseext
Cf3+Cf4+Cfa2+Cia2+Cia5+Cib1+Cib2+Cib5+H_2O_2+NADH+NADN+glucose+glucoseext+isopropanol+resorufin
Cfa1+Cia1+Cib1+G_1DH
Cfa1+Cia1+Cib1+Cib2+NAD+acetone+acetoneext+gluconolacrone
Cf4+Cia1+Cia2+Cib1+Cib2+NAD+NADH+NADN
ADH+Cfa2+Cia2+Cib2
Cf3+Cf4+Cfa2+Cib2+Cio3+HRP2+acetone+acetoneext+isopropanol
Cf3+Cfa2+Cia5+Cib2+Cib5+H_2O_2+acetone+acetoneext+isopropanol+resorufin
AO+Cf3+Cio3
Cia5+Cib5+HRP
Cib5+resazurin+resorufin
Cf3+Cfa2+Cia2+Cib1+Cib2+Cio3+HRP2+NADH+NADN+glucose+glucoseext+isopropanol+2*Cf4
12 complex invariant(s)
<img src="ode.tex" alt="Simulation results">
<img src="plot-0.csv" alt="Simulation results">
m=0/\M=67383000
G(x>=y)/\F(x<=y)
T>287.057
0.946074
<img src="plot-1.csv" alt="Simulation results">
T>88.2305
acetone_p*glucose_p for acetone_p+glucose_p=>acetone_p+glucose_p+resorufin_p.
acetone_n*glucose_n for acetone_n+glucose_n=>acetone_n+glucose_n+resorufin_p.
MA(1) for resorufin_p=>_.
acetone_p*glucose_n for acetone_p+glucose_n=>acetone_p+glucose_n+resorufin_n.
acetone_n*glucose_p for acetone_n+glucose_p=>acetone_n+glucose_p+resorufin_n.
MA(1) for resorufin_n=>_.
fast*resorufin_p*resorufin_n for resorufin_n+resorufin_p=>_.
MA(1) for _=>temp2_p.
MA(1) for acetone_n=>acetone_n+temp2_p.
MA(1) for temp2_p=>_.
MA(1) for acetone_p=>acetone_p+temp2_n.
MA(1) for temp2_n=>_.
fast*temp2_p*temp2_n for temp2_n+temp2_p=>_.
glucose_p*temp2_p for glucose_p+temp2_p=>NADH_p+glucose_p+temp2_p.
glucose_n*temp2_n for glucose_n+temp2_n=>NADH_p+glucose_n+temp2_n.
MA(1) for NADH_p=>_.
glucose_p*temp2_n for glucose_p+temp2_n=>NADH_n+glucose_p+temp2_n.
glucose_n*temp2_p for glucose_n+temp2_p=>NADH_n+glucose_n+temp2_p.
MA(1) for NADH_n=>_.
fast*NADH_p*NADH_n for NADH_n+NADH_p=>_.
present(temp0_p,0).
present(temp0_n,0).
present(temp1_p,0).
present(temp1_n,0).
present(resorufin_p,0).
present(resorufin_n,0).
present(glucose_p,0).
present(glucose_n,0).
present(acetone_p,0).
present(acetone_n,0).
present(temp2_p,0).
present(temp2_n,0).
present(NADH_p,0).
present(NADH_n,0).
parameter(
fast = 10
).
<img src="graph2.png" alt="Simulation results">
<img src="ode.tex" alt="Simulation results">
<img src="plot-2.csv" alt="Simulation results">
<img src="plot-3.csv" alt="Simulation results">
......@@ -127,7 +127,10 @@ check_ctl :-
:- biocham(check_ctl).
:- doc('\\end{example}').
:- doc('A Linear Time Logic (LTL) formula contains no path quantifier. The syntax of LTL formulae is given in the next chapter for the more general setting of First-Order LTL (FO-LTL) formulae with numerical constraints.
Here a boolean LTL formula is true if it is satisfied by all paths and all boolean initial states.
This can be changed by double negation with the option \\texttt{boolean_initial_states: some} to verify that there exists an initial state and a path satisfying the formula.
Unlike CTL, the path quantifier cannot be decoupled from the quantifier on the initial state.').
check_ltl(Query) :-
biocham_command,
doc('
......@@ -148,9 +151,6 @@ check_ltl(Query) :-
format('~w is ~w\n', [Query, Result]).
:- doc('An LTL formula is true if it is satisfied by all paths and all initial states.
This can be changed by double negation with the option \\texttt{boolean_initial_states: some} to verify that there exists an initial state and a path satisfying the formula.
Unlike CTL, the path quantifier cannot be decoupled from the quantifier on the initial state.').
:- doc('\\begin{example}\n').
:- biocham_silent(clear_model).
:- biocham(present(a)).
......
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