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add benchmarks for SIAN and COMBOS
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@sumiya11
sumiya11 committed Oct 8, 2023
1 parent d56de7a commit 621a6ac
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Showing 38 changed files with 398 additions and 9 deletions.
12 changes: 12 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/Akt_pathway
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dx1/dt = -reaction,1,k1*x9 + reaction,1,k2*x9 - x1*EGFR,turnover + EGFR,turnover*u1;
dx2/dt = -reaction,4,k1*x2 + reaction,9,k1*x9 - x2*x4*reaction,2,k1 + reaction,3,k1*x3 + x3*reaction,2,k2;
dx3/dt = x2*x4*reaction,2,k1 - reaction,3,k1*x3 - x3*reaction,2,k2;
dx4/dt = x5*reaction,7,k1 - x2*x4*reaction,2,k1 + x3*reaction,2,k2;
dx5/dt = -x5*reaction,7,k1 - x5*reaction,5,k1*x6 + reaction,6,k1*x7 + reaction,3,k1*x3 + x7*reaction,5,k2;
dx6/dt = x8*reaction,8,k1 - x5*reaction,5,k1*x6 + x7*reaction,5,k2;
dx7/dt = x5*reaction,5,k1*x6 - reaction,6,k1*x7 - x7*reaction,5,k2;
dx8/dt = -x8*reaction,8,k1 + reaction,6,k1*x7;
dx9/dt = reaction,1,k1*x9 - reaction,9,k1*x9 - reaction,1,k2*x9;
y1 = x2*a1 + a1*x3;
y2 = a2*x5 + a2*x7;
y3 = x8*a3
5 changes: 5 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/Bilirubin2_io
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dx1/dt = -k01*x1 - k31*x1 - k21*x1 + k12*x2 + x3*k13 + u1 - x1*k41 + x4*k14;
dx2/dt = k21*x1 - k12*x2;
dx3/dt = k31*x1 - x3*k13;
dx4/dt = x1*k41 - x4*k14;
y1 = x1
6 changes: 6 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/Biohydrogenation
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dx1/dt = (-k5*x1) / (k6 + x1);
dx2/dt = (k5*k8*x1 + k5*x3*x1 + k5*x2*x1 - k6*x2*k7 - x2*k7*x1) / (k8*k6 + k8*x1 + k6*x3 + k6*x2 + x3*x1 + x2*x1);
dx3/dt = (-k8*k9*k10*x3 + k8*k9*x3^2 - k9*k10*x3^2 - k9*k10*x3*x2 + k9*x3^3 + k9*x3^2*x2 + k10*x2*k7) / (k8*k10 + k10*x3 + k10*x2);
dx4/dt = (k9*k10*x3 - k9*x3^2) / (k10);
y1 = x1;
y2 = x2
6 changes: 6 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/CGV1990
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dx1/dt = -k3*x1 - x1*k7 + k4*x2 + u1;
dx2/dt = (5*k5*x4*V36*x2 - 5*k5*S*V36^2*x2 - k5*R*x2*V3^2 + k5*x2*x3*V3 + k3*x1*V3 + x4*k6*V3 - k4*x2*V3 + k6*x3*V3) / (V3);
dx3/dt = k5*R*x2*V3 - k5*x2*x3 - k6*x3;
dx4/dt = (-5*k5*x4*V36*x2 + 5*k5*S*V36^2*x2 - x4*k6*V3) / (V3);
dx5/dt = x1*k7;
y1 = x5
7 changes: 7 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/HIV
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dx1/dt = lm - x1*d - x1*x3*beta;
dx2/dt = x1*x3*beta - a*x2;
dx3/dt = k*x2 - x3*u;
dx4/dt = -b*x4 + c*x4*x1*x2 - c*x4*q*x2;
dx5/dt = c*x4*q*x2 - h*x5;
y1 = x4;
y2 = x5
40 changes: 40 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/HighDimNonLin
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dx1/dt = (-p1*km*x1 - p1*x1^2 + km*u1 - x1*vm + x1*u1) / (km + x1);
dx2/dt = -p2*x2 + p1*x1;
dx3/dt = p2*x2 - x3*p3;
dx4/dt = x3*p3 - x4*p4;
dx5/dt = -p5*x5 + x4*p4;
dx6/dt = -p6*x6 + p5*x5;
dx7/dt = -p7*x7 + p6*x6;
dx8/dt = p7*x7 - p8*x8;
dx9/dt = -x9*p9 + p8*x8;
dx10/dt = x9*p9 - x10*p10;
dx11/dt = x10*p10 - x11*p11;
dx12/dt = x11*p11 - p12*x12;
dx13/dt = -x13*p13 + p12*x12;
dx14/dt = x13*p13 - p14*x14;
dx15/dt = -p15*x15 + p14*x14;
dx16/dt = p15*x15 - x16*p16;
dx17/dt = -p17*x17 + x16*p16;
dx18/dt = -p18*x18 + p17*x17;
dx19/dt = -x19*p19 + p18*x18;
dx20/dt = -p20*x20 + x19*p19;
y1 = x1;
y2 = x2;
y3 = x3;
y4 = x4;
y5 = x5;
y6 = x6;
y7 = x7;
y8 = x8;
y9 = x9;
y10 = x10;
y11 = x11;
y12 = x12;
y13 = x13;
y14 = x14;
y15 = x15;
y16 = x16;
y17 = x17;
y18 = x18;
y19 = x19;
y20 = x20
17 changes: 17 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/MAPK_5o
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dx1/dt = x6*gamma1100 + gamma1000*x5 + x4*gamma0100 + b00*x1 - x9*x7*a00;
dx2/dt = c0001*x1 + x6*gamma1101 - x8*alpha01*x10 + x4*beta01 - x7*x10*a01 + x2*b01;
dx3/dt = -a10*x7*x11 + x6*gamma1110 - x8*alpha10*x11 + x3*b10 + beta10*x5 + c0010*x1;
dx4/dt = x6*beta11 - x8*alpha11*x12 + x3*c1011 + c0111*x2 + c0011*x1;
dx5/dt = -c0001*x1 - b00*x1 + x9*x7*a00 - c0011*x1 - c0010*x1;
dx6/dt = -c0111*x2 + x7*x10*a01 - x2*b01;
dx7/dt = a10*x7*x11 - x3*b10 - x3*c1011;
dx8/dt = x8*alpha01*x10 - x4*beta01 - x4*gamma0100;
dx9/dt = x8*alpha10*x11 - gamma1000*x5 - beta10*x5;
dx10/dt = -x6*beta11 - x6*gamma1100 - x6*gamma1101 - x6*gamma1110 + x8*alpha11*x12;
dx11/dt = c0001*x1 - a10*x7*x11 + x3*b10 + x3*c1011 + b00*x1 + c0111*x2 - x9*x7*a00 - x7*x10*a01 + c0011*x1 + c0010*x1 + x2*b01;
dx12/dt = x6*beta11 + x6*gamma1100 + x6*gamma1101 + x6*gamma1110 - x8*alpha10*x11 - x8*alpha11*x12 - x8*alpha01*x10 + gamma1000*x5 + x4*beta01 + x4*gamma0100 + beta10*x5;
y1 = x8;
y2 = x9;
y3 = x10;
y4 = x11;
y5 = x12
18 changes: 18 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/MAPK_6o
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dx1/dt = x6*gamma1100 + gamma1000*x5 + x4*gamma0100 + b00*x1 - x9*x7*a00;
dx2/dt = c0001*x1 + x6*gamma1101 - x8*alpha01*x10 + x4*beta01 - x7*x10*a01 + x2*b01;
dx3/dt = -a10*x7*x11 + x6*gamma1110 - x8*alpha10*x11 + x3*b10 + beta10*x5 + c0010*x1;
dx4/dt = x6*beta11 - x8*alpha11*x12 + x3*c1011 + c0111*x2 + c0011*x1;
dx5/dt = -c0001*x1 - b00*x1 + x9*x7*a00 - c0011*x1 - c0010*x1;
dx6/dt = -c0111*x2 + x7*x10*a01 - x2*b01;
dx7/dt = a10*x7*x11 - x3*b10 - x3*c1011;
dx8/dt = x8*alpha01*x10 - x4*beta01 - x4*gamma0100;
dx9/dt = x8*alpha10*x11 - gamma1000*x5 - beta10*x5;
dx10/dt = -x6*beta11 - x6*gamma1100 - x6*gamma1101 - x6*gamma1110 + x8*alpha11*x12;
dx11/dt = c0001*x1 - a10*x7*x11 + x3*b10 + x3*c1011 + b00*x1 + c0111*x2 - x9*x7*a00 - x7*x10*a01 + c0011*x1 + c0010*x1 + x2*b01;
dx12/dt = x6*beta11 + x6*gamma1100 + x6*gamma1101 + x6*gamma1110 - x8*alpha10*x11 - x8*alpha11*x12 - x8*alpha01*x10 + gamma1000*x5 + x4*beta01 + x4*gamma0100 + beta10*x5;
y1 = x7;
y2 = x8;
y3 = x9;
y4 = x10;
y5 = x11;
y6 = x12
6 changes: 6 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/PK1
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dx1/dt = u1 - k2*x1 - k1*x1;
dx2/dt = k5*x4 - k3*x2 - k6*x2 + k1*x1 - k7*x2;
dx3/dt = k3*x2 - k4*x3 + k2*x1;
dx4/dt = -k5*x4 + k6*x2;
y1 = s2*x2;
y2 = s3*x3
5 changes: 5 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/PK2
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dx1/dt = (-ka*n*x1 - ka*kc*a1*x1 + ka*kc*a1*x2 - ka*a1*x1^2 + ka*a1*x1*x2 - kc*a1*x1*x3 + kc*a1*x2*x3) / (ka*kc + ka*x1 + kc*x3);
dx2/dt = a2*x1 - a2*x2;
dx3/dt = (ka*kc*b1*x4 - ka*kc*b1*x3 + ka*b1*x1*x4 - ka*b1*x1*x3 - n*kc*x3 + kc*b1*x4*x3 - kc*b1*x3^2) / (ka*kc + ka*x1 + kc*x3);
dx4/dt = -b2*x4 + b2*x3;
y1 = x1
20 changes: 20 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/QY
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dx1/dt = x2;
dx2/dt = x3;
dx3/dt = x4;
dx4/dt = x5;
dx5/dt = (-siga1*x1^2*beta,SI*phi*M*Mar*Ks^2*siga2^2 + siga1*x1^2*beta,SI*M*Mar*Ks^2*siga2^2 - siga1*x1^2*phi*M^2*Mar*Ks^2*siga2*beta,SA + siga1*x1^2*phi*M^2*Ks^2*siga2^2*beta,SA + siga1*x1^2*M^2*Mar*Ks^2*siga2*beta,SA - siga1*x1*x2*beta,SI*phi*M*Mar*Ks^2*siga2 - 2*siga1*x1*x2*beta,SI*phi*M*Mar*Ks*siga2^2 - siga1*x1*x2*beta,SI*phi*M*Ks^2*siga2^2 - siga1*x1*x2*beta,SI*phi*Mar*Ks^2*siga2^2 + siga1*x1*x2*beta,SI*M*Mar*Ks^2*siga2 + 2*siga1*x1*x2*beta,SI*M*Mar*Ks*siga2^2 + siga1*x1*x2*beta,SI*M*Ks^2*siga2^2 + siga1*x1*x2*beta,SI*Mar*Ks^2*siga2^2 - siga1*x1*x2*phi*M^2*Mar*Ks^2*beta,SA - 2*siga1*x1*x2*phi*M^2*Mar*Ks*siga2*beta,SA + siga1*x1*x2*phi*M^2*Ks^2*siga2*beta,SA + 2*siga1*x1*x2*phi*M^2*Ks*siga2^2*beta,SA - 2*siga1*x1*x2*phi*M*Mar*Ks^2*siga2*beta,SA + 2*siga1*x1*x2*phi*M*Ks^2*siga2^2*beta,SA + siga1*x1*x2*M^2*Mar*Ks^2*beta,SA + 2*siga1*x1*x2*M^2*Mar*Ks*siga2*beta,SA + siga1*x1*x2*M^2*Ks^2*siga2*beta,SA + 2*siga1*x1*x2*M*Mar*Ks^2*siga2*beta,SA - siga1*x1*beta,SI*x4*phi*Mar*Ks*siga2 + siga1*x1*beta,SI*x4*Mar*Ks*siga2 - siga1*x1*beta,SI*phi*M*x3*Mar*Ks*siga2 - siga1*x1*beta,SI*phi*M*x3*Ks*siga2^2 - siga1*x1*beta,SI*phi*x3*Mar*Ks^2*siga2 - siga1*x1*beta,SI*phi*x3*Mar*Ks*siga2^2 + siga1*x1*beta,SI*M*x3*Mar*Ks*siga2 +
siga1*x1*beta,SI*M*x3*Ks*siga2^2 + siga1*x1*beta,SI*x3*Mar*Ks^2*siga2 + siga1*x1*beta,SI*x3*Mar*Ks*siga2^2 - siga1*x1*x4*phi*M*Mar*Ks*beta,SA + siga1*x1*x4*phi*M*Ks*siga2*beta,SA + siga1*x1*x4*M*Mar*Ks*beta,SA + siga1*x1*x4*M*Ks*siga2*beta,SA - siga1*x1*phi*M^2*x3*Mar*Ks*beta,SA + siga1*x1*phi*M^2*x3*Ks*siga2*beta,SA - siga1*x1*phi*M^2*Mar*x6*Ks*siga2^2 - siga1*x1*phi*M^2*Ks*beta*siga2^2 - siga1*x1*phi*M*x3*Mar*Ks^2*beta,SA - 2*siga1*x1*phi*M*x3*Mar*Ks*siga2*beta,SA + siga1*x1*phi*M*x3*Ks^2*siga2*beta,SA + 2*siga1*x1*phi*M*x3*Ks*siga2^2*beta,SA + siga1*x1*M^2*x3*Mar*Ks*beta,SA + siga1*x1*M^2*x3*Ks*siga2*beta,SA + siga1*x1*M^2*Mar*x6*Ks*siga2^2 + siga1*x1*M^2*Ks*beta*siga2^2 + siga1*x1*M*x3*Mar*Ks^2*beta,SA + 2*siga1*x1*M*x3*Mar*Ks*siga2*beta,SA + siga1*x1*M*x3*Ks^2*siga2*beta,SA - siga1*x2^2*beta,SI*phi*M*Mar*Ks*siga2 - siga1*x2^2*beta,SI*phi*M*Mar*siga2^2 - siga1*x2^2*beta,SI*phi*M*Ks^2*siga2 - siga1*x2^2*beta,SI*phi*M*Ks*siga2^2 - siga1*x2^2*beta,SI*phi*Mar*Ks*siga2^2 - siga1*x2^2*beta,SI*phi*Ks^2*siga2^2 + siga1*x2^2*beta,SI*M*Mar*Ks*siga2 + siga1*x2^2*beta,SI*M*Mar*siga2^2 + siga1*x2^2*beta,SI*M*Ks^2*siga2 + siga1*x2^2*beta,SI*M*Ks*siga2^2 + siga1*x2^2*beta,SI*Mar*Ks*siga2^2 + siga1*x2^2*beta,SI*Ks^2*siga2^2
- siga1*x2^2*phi*M^2*Mar*Ks*beta,SA - siga1*x2^2*phi*M^2*Mar*siga2*beta,SA +
siga1*x2^2*phi*M^2*Ks*siga2*beta,SA + siga1*x2^2*phi*M^2*siga2^2*beta,SA - siga1*x2^2*phi*M*Mar*Ks^2*beta,SA - 2*siga1*x2^2*phi*M*Mar*Ks*siga2*beta,SA + siga1*x2^2*phi*M*Ks^2*siga2*beta,SA + 2*siga1*x2^2*phi*M*Ks*siga2^2*beta,SA -
siga1*x2^2*phi*Mar*Ks^2*siga2*beta,SA + siga1*x2^2*phi*Ks^2*siga2^2*beta,SA + siga1*x2^2*M^2*Mar*Ks*beta,SA + siga1*x2^2*M^2*Mar*siga2*beta,SA + siga1*x2^2*M^2*Ks^2*beta,SA + siga1*x2^2*M^2*Ks*siga2*beta,SA + siga1*x2^2*M*Mar*Ks^2*beta,SA + 2*siga1*x2^2*M*Mar*Ks*siga2*beta,SA + siga1*x2^2*M*Ks^2*siga2*beta,SA + siga1*x2^2*Mar*Ks^2*siga2*beta,SA - siga1*x2*beta,SI*x4*phi*Mar*siga2 -
siga1*x2*beta,SI*x4*phi*Ks*siga2 + siga1*x2*beta,SI*x4*Mar*siga2 + siga1*x2*beta,SI*x4*Ks*siga2 - siga1*x2*beta,SI*phi*M*x3*Mar*siga2 - 2*siga1*x2*beta,SI*phi*M*x3*Ks*siga2 - siga1*x2*beta,SI*phi*M*x3*siga2^2 - siga1*x2*beta,SI*phi*x3*Mar*Ks*siga2 - siga1*x2*beta,SI*phi*x3*Mar*siga2^2 - siga1*x2*beta,SI*phi*x3*Ks^2*siga2 - 2*siga1*x2*beta,SI*phi*x3*Ks*siga2^2 + siga1*x2*beta,SI*M*x3*Mar*siga2 + 2*siga1*x2*beta,SI*M*x3*Ks*siga2 + siga1*x2*beta,SI*M*x3*siga2^2 + siga1*x2*beta,SI*x3*Mar*Ks*siga2 + siga1*x2*beta,SI*x3*Mar*siga2^2 + siga1*x2*beta,SI*x3*Ks^2*siga2 + 2*siga1*x2*beta,SI*x3*Ks*siga2^2 - siga1*x2*x4*phi*M*Mar*beta,SA + siga1*x2*x4*phi*M*siga2*beta,SA - siga1*x2*x4*phi*Mar*Ks*beta,SA + siga1*x2*x4*phi*Ks*siga2*beta,SA + siga1*x2*x4*M*Mar*beta,SA + 2*siga1*x2*x4*M*Ks*beta,SA + siga1*x2*x4*M*siga2*beta,SA + siga1*x2*x4*Mar*Ks*beta,SA + siga1*x2*x4*Ks*siga2*beta,SA - siga1*x2*phi*M^2*x3*Mar*beta,SA + siga1*x2*phi*M^2*x3*siga2*beta,SA - siga1*x2*phi*M^2*Mar*x6*Ks*siga2 - siga1*x2*phi*M^2*Mar*x6*siga2^2 - siga1*x2*phi*M^2*Ks*beta*siga2 - siga1*x2*phi*M^2*Ks*siga2^2 - siga1*x2*phi*M^2*beta*siga2^2 - 3*siga1*x2*phi*M*x3*Mar*Ks*beta,SA - 2*siga1*x2*phi*M*x3*Mar*siga2*beta,SA + 3*siga1*x2*phi*M*x3*Ks*siga2*beta,SA + 2*siga1*x2*phi*M*x3*siga2^2*beta,SA - siga1*x2*phi*M*Mar*x6*Ks*siga2^2 - siga1*x2*phi*M*Ks*beta*siga2^2 - siga1*x2*phi*x3*Mar*Ks^2*beta,SA - 2*siga1*x2*phi*x3*Mar*Ks*siga2*beta,SA + siga1*x2*phi*x3*Ks^2*siga2*beta,SA + 2*siga1*x2*phi*x3*Ks*siga2^2*beta,SA + siga1*x2*M^2*x3*Mar*beta,SA + 2*siga1*x2*M^2*x3*Ks*beta,SA + siga1*x2*M^2*x3*siga2*beta,SA + siga1*x2*M^2*Mar*x6*Ks*siga2 + siga1*x2*M^2*Mar*x6*siga2^2 + siga1*x2*M^2*Ks*beta*siga2 + siga1*x2*M^2*Ks*siga2^2 + siga1*x2*M^2*beta*siga2^2 + 3*siga1*x2*M*x3*Mar*Ks*beta,SA + 2*siga1*x2*M*x3*Mar*siga2*beta,SA + 2*siga1*x2*M*x3*Ks^2*beta,SA + 3*siga1*x2*M*x3*Ks*siga2*beta,SA + siga1*x2*M*Mar*x6*Ks*siga2^2 + siga1*x2*M*Ks*beta*siga2^2 + siga1*x2*x3*Mar*Ks^2*beta,SA + 2*siga1*x2*x3*Mar*Ks*siga2*beta,SA + siga1*x2*x3*Ks^2*siga2*beta,SA - siga1*beta,SI*x4*phi*x3*siga2 + siga1*beta,SI*x4*x3*siga2 - siga1*beta,SI*phi*M*x3^2*siga2 - siga1*beta,SI*phi*x3^2*Ks*siga2 - siga1*beta,SI*phi*x3^2*siga2^2 + siga1*beta,SI*M*x3^2*siga2 + siga1*beta,SI*x3^2*Ks*siga2 + siga1*beta,SI*x3^2*siga2^2 + siga1*x4^2*beta,SA - siga1*x4*phi*M^2*siga2 - siga1*x4*phi*M*Mar*x6*siga2 - siga1*x4*phi*M*Ks*siga2 - siga1*x4*phi*M*beta*siga2 - siga1*x4*phi*M*siga2^2 - siga1*x4*phi*x3*Mar*beta,SA + siga1*x4*phi*x3*siga2*beta,SA + siga1*x4*M^2*siga2 + 2*siga1*x4*M*x3*beta,SA + siga1*x4*M*Mar*x6*siga2 + siga1*x4*M*Ks*siga2 + siga1*x4*M*beta*siga2 + siga1*x4*M*siga2^2 + siga1*x4*x3*Mar*beta,SA + 2*siga1*x4*x3*Ks*beta,SA + siga1*x4*x3*siga2*beta,SA - siga1*phi*M^2*x3*Mar*x6*siga2 - siga1*phi*M^2*x3*Ks*siga2 - siga1*phi*M^2*x3*beta*siga2 - siga1*phi*M^2*x3*siga2^2 - siga1*phi*M*x5*siga2 - siga1*phi*M*x3^2*Mar*beta,SA + siga1*phi*M*x3^2*siga2*beta,SA - siga1*phi*M*x3*Mar*x6*Ks*siga2 - siga1*phi*M*x3*Mar*x6*siga2^2 - siga1*phi*M*x3*Ks*beta*siga2 - siga1*phi*M*x3*Ks*siga2^2 - siga1*phi*M*x3*beta*siga2^2 - siga1*phi*x3^2*Mar*Ks*beta,SA - siga1*phi*x3^2*Mar*siga2*beta,SA + siga1*phi*x3^2*Ks*siga2*beta,SA + siga1*phi*x3^2*siga2^2*beta,SA + siga1*M^2*x3^2*beta,SA + siga1*M^2*x3*Mar*x6*siga2 + siga1*M^2*x3*Ks*siga2 + siga1*M^2*x3*beta*siga2 + siga1*M^2*x3*siga2^2 + siga1*M*x5*siga2 + siga1*M*x3^2*Mar*beta,SA + 2*siga1*M*x3^2*Ks*beta,SA + siga1*M*x3^2*siga2*beta,SA + siga1*M*x3*Mar*x6*Ks*siga2 + siga1*M*x3*Mar*x6*siga2^2 + siga1*M*x3*Ks*beta*siga2 + siga1*M*x3*Ks*siga2^2 + siga1*M*x3*beta*siga2^2 + siga1*x3^2*Mar*Ks*beta,SA + siga1*x3^2*Mar*siga2*beta,SA + siga1*x3^2*Ks^2*beta,SA + siga1*x3^2*Ks*siga2*beta,SA - x1*x2*beta,SI*phi*M*Mar*Ks^2*siga2^2 + x1*x2*beta,SI*M*Mar*Ks^2*siga2^2 - x1*x2*phi*M^2*Mar*Ks^2*siga2*beta,SA + x1*x2*phi*M^2*Ks^2*siga2^2*beta,SA + x1*x2*M^2*Mar*Ks^2*siga2*beta,SA - x1*beta,SI*x4*phi*M*Mar*Ks*siga2 - x1*beta,SI*x4*phi*Mar*Ks^2*siga2 - x1*beta,SI*x4*phi*Mar*Ks*siga2^2 + x1*beta,SI*x4*M*Mar*Ks*siga2 + x1*beta,SI*x4*Mar*Ks^2*siga2 + x1*beta,SI*x4*Mar*Ks*siga2^2 - x1*beta,SI*phi*alpa*Mar*Ks*siga2 - x1*beta,SI*phi*M*x3*Mar*Ks^2*siga2 - x1*beta,SI*phi*M*x3*Mar*Ks*siga2^2 - x1*beta,SI*phi*x5*Mar*Ks*siga2 - x1*beta,SI*phi*x3*Mar*Ks^2*siga2^2 + x1*beta,SI*alpa*Mar*Ks*siga2 + x1*beta,SI*M*x3*Mar*Ks^2*siga2 + x1*beta,SI*M*x3*Mar*Ks*siga2^2 + x1*beta,SI*x5*Mar*Ks*siga2 + x1*beta,SI*x3*Mar*Ks^2*siga2^2 - x1*x4*phi*M^2*Mar*Ks*beta,SA + x1*x4*phi*M^2*Ks*siga2*beta,SA - x1*x4*phi*M*Mar*Ks^2*beta,SA - x1*x4*phi*M*Mar*Ks*siga2*beta,SA + x1*x4*phi*M*Ks^2*siga2*beta,SA + x1*x4*phi*M*Ks*siga2^2*beta,SA + x1*x4*M^2*Mar*Ks*beta,SA + x1*x4*M*Mar*Ks^2*beta,SA + x1*x4*M*Mar*Ks*siga2*beta,SA - x1*phi*alpa*M*Mar*Ks*beta,SA + x1*phi*alpa*M*Ks*siga2*beta,SA - x1*phi*M^2*x3*Mar*Ks^2*beta,SA - x1*phi*M^2*x3*Mar*Ks*siga2*beta,SA + x1*phi*M^2*x3*Ks^2*siga2*beta,SA +
x1*phi*M^2*x3*Ks*siga2^2*beta,SA - x1*phi*M*x5*Mar*Ks*beta,SA + x1*phi*M*x5*Ks*siga2*beta,SA - x1*phi*M*x3*Mar*Ks^2*siga2*beta,SA + x1*phi*M*x3*Ks^2*siga2^2*beta,SA + x1*alpa*M*Mar*Ks*beta,SA + x1*M^2*x3*Mar*Ks^2*beta,SA + x1*M^2*x3*Mar*Ks*siga2*beta,SA + x1*M*x5*Mar*Ks*beta,SA + x1*M*x3*Mar*Ks^2*siga2*beta,SA - x2^2*beta,SI*phi*M*Mar*Ks*siga2^2 - x2^2*beta,SI*phi*M*Ks^2*siga2^2 + x2^2*beta,SI*M*Mar*Ks*siga2^2 + x2^2*beta,SI*M*Ks^2*siga2^2 - x2^2*phi*M^2*Mar*Ks*siga2*beta,SA + x2^2*phi*M^2*Ks*siga2^2*beta,SA - x2^2*phi*M*Mar*Ks^2*siga2*beta,SA + x2^2*phi*M*Ks^2*siga2^2*beta,SA + x2^2*M^2*Mar*Ks*siga2*beta,SA
+ x2^2*M^2*Ks^2*siga2*beta,SA + x2^2*M*Mar*Ks^2*siga2*beta,SA - x2*beta,SI*x4*phi*M*Mar*siga2 - x2*beta,SI*x4*phi*M*Ks*siga2 - x2*beta,SI*x4*phi*Mar*Ks*siga2 - x2*beta,SI*x4*phi*Mar*siga2^2 - x2*beta,SI*x4*phi*Ks^2*siga2 - x2*beta,SI*x4*phi*Ks*siga2^2 + x2*beta,SI*x4*M*Mar*siga2 + x2*beta,SI*x4*M*Ks*siga2 + x2*beta,SI*x4*Mar*Ks*siga2 + x2*beta,SI*x4*Mar*siga2^2 + x2*beta,SI*x4*Ks^2*siga2 + x2*beta,SI*x4*Ks*siga2^2 - x2*beta,SI*phi*alpa*Mar*siga2 - x2*beta,SI*phi*alpa*Ks*siga2 - x2*beta,SI*phi*M*x3*Mar*Ks*siga2 - x2*beta,SI*phi*M*x3*Mar*siga2^2 - x2*beta,SI*phi*M*x3*Ks^2*siga2 - 2*x2*beta,SI*phi*M*x3*Ks*siga2^2 - x2*beta,SI*phi*x5*Mar*siga2 - x2*beta,SI*phi*x5*Ks*siga2 - x2*beta,SI*phi*x3*Mar*Ks*siga2^2 - x2*beta,SI*phi*x3*Ks^2*siga2^2 + x2*beta,SI*alpa*Mar*siga2 + x2*beta,SI*alpa*Ks*siga2 + x2*beta,SI*M*x3*Mar*Ks*siga2 + x2*beta,SI*M*x3*Mar*siga2^2 + x2*beta,SI*M*x3*Ks^2*siga2 + 2*x2*beta,SI*M*x3*Ks*siga2^2 + x2*beta,SI*x5*Mar*siga2 + x2*beta,SI*x5*Ks*siga2 + x2*beta,SI*x3*Mar*Ks*siga2^2 + x2*beta,SI*x3*Ks^2*siga2^2 - x2*x4*phi*M^2*Mar*beta,SA + x2*x4*phi*M^2*siga2*beta,SA - 2*x2*x4*phi*M*Mar*Ks*beta,SA - x2*x4*phi*M*Mar*siga2*beta,SA +
2*x2*x4*phi*M*Ks*siga2*beta,SA + x2*x4*phi*M*siga2^2*beta,SA - x2*x4*phi*Mar*Ks^2*beta,SA - x2*x4*phi*Mar*Ks*siga2*beta,SA + x2*x4*phi*Ks^2*siga2*beta,SA
+ x2*x4*phi*Ks*siga2^2*beta,SA + x2*x4*M^2*Mar*beta,SA + x2*x4*M^2*Ks*beta,SA + 2*x2*x4*M*Mar*Ks*beta,SA + x2*x4*M*Mar*siga2*beta,SA + x2*x4*M*Ks^2*beta,SA + 2*x2*x4*M*Ks*siga2*beta,SA + x2*x4*Mar*Ks^2*beta,SA + x2*x4*Mar*Ks*siga2*beta,SA - x2*phi*alpa*M*Mar*beta,SA + x2*phi*alpa*M*siga2*beta,SA - x2*phi*alpa*Mar*Ks*beta,SA + x2*phi*alpa*Ks*siga2*beta,SA - x2*phi*M^2*x3*Mar*Ks*beta,SA - x2*phi*M^2*x3*Mar*siga2*beta,SA + x2*phi*M^2*x3*Ks*siga2*beta,SA + x2*phi*M^2*x3*siga2^2*beta,SA - x2*phi*M^2*Mar*x6*Ks*siga2^2 - x2*phi*M^2*Ks*beta*siga2^2 - x2*phi*M*x5*Mar*beta,SA + x2*phi*M*x5*siga2*beta,SA - x2*phi*M*x3*Mar*Ks^2*beta,SA - 3*x2*phi*M*x3*Mar*Ks*siga2*beta,SA + x2*phi*M*x3*Ks^2*siga2*beta,SA + 3*x2*phi*M*x3*Ks*siga2^2*beta,SA - x2*phi*x5*Mar*Ks*beta,SA + x2*phi*x5*Ks*siga2*beta,SA - x2*phi*x3*Mar*Ks^2*siga2*beta,SA + x2*phi*x3*Ks^2*siga2^2*beta,SA + x2*alpa*M*Mar*beta,SA + x2*alpa*M*Ks*beta,SA + x2*alpa*Mar*Ks*beta,SA + x2*M^2*x3*Mar*Ks*beta,SA + x2*M^2*x3*Mar*siga2*beta,SA + x2*M^2*x3*Ks^2*beta,SA + 2*x2*M^2*x3*Ks*siga2*beta,SA + x2*M^2*Mar*x6*Ks*siga2^2 + x2*M^2*Ks*beta*siga2^2 + x2*M*x5*Mar*beta,SA + x2*M*x5*Ks*beta,SA + x2*M*x3*Mar*Ks^2*beta,SA + 3*x2*M*x3*Mar*Ks*siga2*beta,SA + 2*x2*M*x3*Ks^2*siga2*beta,SA
+ x2*x5*Mar*Ks*beta,SA + x2*x3*Mar*Ks^2*siga2*beta,SA - beta,SI*x4*phi*M*x3*siga2 - beta,SI*x4*phi*x3*Ks*siga2 - beta,SI*x4*phi*x3*siga2^2 + beta,SI*x4*M*x3*siga2 + beta,SI*x4*x3*Ks*siga2 + beta,SI*x4*x3*siga2^2 - beta,SI*phi*alpa*x3*siga2 - beta,SI*phi*M*x3^2*Ks*siga2 - beta,SI*phi*M*x3^2*siga2^2 - beta,SI*phi*x5*x3*siga2 - beta,SI*phi*x3^2*Ks*siga2^2 + beta,SI*alpa*x3*siga2 + beta,SI*M*x3^2*Ks*siga2 + beta,SI*M*x3^2*siga2^2 + beta,SI*x5*x3*siga2 + beta,SI*x3^2*Ks*siga2^2 + x4^2*M*beta,SA + x4^2*Ks*beta,SA + x4^2*siga2*beta,SA - x4*phi*M^2*Mar*x6*siga2 - x4*phi*M^2*Ks*siga2 - x4*phi*M^2*beta*siga2 - x4*phi*M^2*siga2^2 - x4*phi*M*x3*Mar*beta,SA + x4*phi*M*x3*siga2*beta,SA - x4*phi*M*Mar*x6*Ks*siga2 - x4*phi*M*Mar*x6*siga2^2 - x4*phi*M*Ks*beta*siga2 - x4*phi*M*Ks*siga2^2 - x4*phi*M*beta*siga2^2 - x4*phi*x3*Mar*Ks*beta,SA - x4*phi*x3*Mar*siga2*beta,SA + x4*phi*x3*Ks*siga2*beta,SA + x4*phi*x3*siga2^2*beta,SA + x4*alpa*beta,SA + x4*M^2*x3*beta,SA + x4*M^2*Mar*x6*siga2 + x4*M^2*Ks*siga2 + x4*M^2*beta*siga2 + x4*M^2*siga2^2 + x4*M*x3*Mar*beta,SA + 3*x4*M*x3*Ks*beta,SA + 2*x4*M*x3*siga2*beta,SA + x4*M*Mar*x6*Ks*siga2 + x4*M*Mar*x6*siga2^2 + x4*M*Ks*beta*siga2 + x4*M*Ks*siga2^2 + x4*M*beta*siga2^2 + x4*x5*beta,SA + x4*x3*Mar*Ks*beta,SA + x4*x3*Mar*siga2*beta,SA + x4*x3*Ks^2*beta,SA + 2*x4*x3*Ks*siga2*beta,SA - phi*alpa*M*Mar*x6*siga2 - phi*alpa*M*beta*siga2 - phi*alpa*x3*Mar*beta,SA + phi*alpa*x3*siga2*beta,SA - phi*M^2*x5*siga2 - phi*M^2*x3*Mar*x6*Ks*siga2 - phi*M^2*x3*Mar*x6*siga2^2 - phi*M^2*x3*Ks*beta*siga2 - phi*M^2*x3*Ks*siga2^2 - phi*M^2*x3*beta*siga2^2 - phi*M*x5*Mar*x6*siga2 - phi*M*x5*Ks*siga2 - phi*M*x5*beta*siga2 - phi*M*x5*siga2^2 - phi*M*x3^2*Mar*Ks*beta,SA -
phi*M*x3^2*Mar*siga2*beta,SA + phi*M*x3^2*Ks*siga2*beta,SA + phi*M*x3^2*siga2^2*beta,SA - phi*M*x3*Mar*x6*Ks*siga2^2 - phi*M*x3*Ks*beta*siga2^2 - phi*x5*x3*Mar*beta,SA + phi*x5*x3*siga2*beta,SA - phi*x3^2*Mar*Ks*siga2*beta,SA + phi*x3^2*Ks*siga2^2*beta,SA + alpa*M*x3*beta,SA + alpa*M*Mar*x6*siga2 + alpa*M*beta*siga2 + alpa*x3*Mar*beta,SA + alpa*x3*Ks*beta,SA + M^2*x5*siga2 + M^2*x3^2*Ks*beta,SA + M^2*x3^2*siga2*beta,SA + M^2*x3*Mar*x6*Ks*siga2 + M^2*x3*Mar*x6*siga2^2 + M^2*x3*Ks*beta*siga2 + M^2*x3*Ks*siga2^2 + M^2*x3*beta*siga2^2 +
M*x5*x3*beta,SA + M*x5*Mar*x6*siga2 + M*x5*Ks*siga2 + M*x5*beta*siga2 + M*x5*siga2^2 + M*x3^2*Mar*Ks*beta,SA + M*x3^2*Mar*siga2*beta,SA + M*x3^2*Ks^2*beta,SA + 2*M*x3^2*Ks*siga2*beta,SA + M*x3*Mar*x6*Ks*siga2^2 + M*x3*Ks*beta*siga2^2 + x5*x3*Mar*beta,SA + x5*x3*Ks*beta,SA + x3^2*Mar*Ks*siga2*beta,SA + x3^2*Ks^2*siga2*beta,SA) / (phi*M*siga2 - M*siga2);
dx6/dt = (-x1*beta,SI*phi*Mar*Ks*siga2 + x1*beta,SI*Mar*Ks*siga2 - x1*phi*M*Mar*Ks*beta,SA + x1*phi*M*Ks*siga2*beta,SA + x1*M*Mar*Ks*beta,SA - x2*beta,SI*phi*Mar*siga2 - x2*beta,SI*phi*Ks*siga2 + x2*beta,SI*Mar*siga2 + x2*beta,SI*Ks*siga2 - x2*phi*M*Mar*beta,SA + x2*phi*M*siga2*beta,SA - x2*phi*Mar*Ks*beta,SA + x2*phi*Ks*siga2*beta,SA + x2*M*Mar*beta,SA + x2*M*Ks*beta,SA + x2*Mar*Ks*beta,SA - beta,SI*phi*x3*siga2 + beta,SI*x3*siga2 + x4*beta,SA - phi*M*Mar*x6*siga2 - phi*M*beta*siga2 - phi*x3*Mar*beta,SA + phi*x3*siga2*beta,SA + M*x3*beta,SA + M*Mar*x6*siga2 + M*beta*siga2 + x3*Mar*beta,SA + x3*Ks*beta,SA) /
(phi*M*siga2 - M*siga2);
y1 = x1
9 changes: 9 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/SEAIJRC_covid
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
dx1/dt = -b*x1*x7*x3*q - b*x1*x7*x4 - b*x1*x7*x5;
dx2/dt = b*x1*x7*x3*q + b*x1*x7*x4 + b*x1*x7*x5 - x2*k;
dx3/dt = -x2*k*r + x2*k - x3*g1;
dx4/dt = -alpha*x4 + x2*k*r - g1*x4;
dx5/dt = alpha*x4 - g2*x5;
dx6/dt = alpha*x4;
dx7/dt = 0;
y1 = x6;
y2 = x7
7 changes: 7 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/SIRS_forced
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
dx1/dt = -b1*b0*x1*x4*x2 - b0*x1*x2 - x1*mu + mu + g*x3;
dx2/dt = -nu*x2 + b1*b0*x1*x4*x2 + b0*x1*x2 - mu*x2;
dx3/dt = nu*x2 - mu*x3 - g*x3;
dx4/dt = -M*x5;
dx5/dt = M*x4;
y1 = x2;
y2 = x3
5 changes: 5 additions & 0 deletions benchmarking/IdentifiableFunctions/COMBOS/SLIQR
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dx1/dt = -b*x3*x1*Ninv - x1*Ninv*u1;
dx2/dt = b*x3*x1*Ninv - a*x2;
dx3/dt = -x3*g + s*x4 + a*x2;
dx4/dt = -e*x3*g + x3*g - s*x4;
y1 = x3*Ninv
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