From 9b7403a73a3c99e254f3ecdd1bdd7d4c4ad24dbf Mon Sep 17 00:00:00 2001 From: Center for Reproducible Biomodeling Modeling Bot Date: Thu, 2 Jan 2025 22:41:30 +0000 Subject: [PATCH] Automated update fixed versions of entries --- .../BIOMD0000000696/BIOMD0000000696-matlab.m | 301 ------------------ .../BIOMD0000000696/BIOMD0000000696-octave.m | 301 ------------------ final/BIOMD0000000696/BIOMD0000000696.ode | 8 +- final/BIOMD0000000696/BIOMD0000000696_url.xml | 40 ++- final/BIOMD0000000696/manifest.xml | 2 - 5 files changed, 34 insertions(+), 618 deletions(-) delete mode 100644 final/BIOMD0000000696/BIOMD0000000696-matlab.m delete mode 100644 final/BIOMD0000000696/BIOMD0000000696-octave.m diff --git a/final/BIOMD0000000696/BIOMD0000000696-matlab.m b/final/BIOMD0000000696/BIOMD0000000696-matlab.m deleted file mode 100644 index b519be597d..0000000000 --- a/final/BIOMD0000000696/BIOMD0000000696-matlab.m +++ /dev/null @@ -1,301 +0,0 @@ -% This file works with MATLAB and is automatically generated with -% the System Biology Format Converter (http://sbfc.sourceforge.net/) -% from an SBML file. -% To run this file with Octave you must edit the comments providing -% the definition of the ode solver and the signature for the -% xdot function. -% -% The conversion system has the following limitations: -% - You may have to re order some reactions and Assignment Rules definition -% - Delays are not taken into account -% - You should change the lsode parameters (start, end, steps) to get better results -% - -% -% Model name = Boada2016 - Incoherent type 1 feed-forward loop (I1-FFL) -% -% is http://identifiers.org/biomodels.db/MODEL1511290000 -% is http://identifiers.org/biomodels.db/BIOMD0000000696 -% isDescribedBy http://identifiers.org/pubmed/26968941 -% is http://identifiers.org/biomodels.db/MODEL1511290000 -% - - -function main() -%Initial conditions vector - x0=zeros(11,1); - x0(10) = 0.0; - x0(11) = 0.0; - x0(1) = 12.3973509933775; - x0(2) = 28336.8022705771; - x0(3) = 0.0; - x0(4) = 0.0; - x0(5) = 0.0; - x0(6) = 0.0; - x0(7) = 0.0; - x0(8) = 0.0; - x0(9) = 9000.0; - - -% Depending on whether you are using Octave or Matlab, -% you should comment / uncomment one of the following blocks. -% This should also be done for the definition of the function f below. -% Start Matlab code - tspan=[0:0.01:100]; - opts = odeset('AbsTol',1e-3); - [t,x]=ode23tb(@f,tspan,x0,opts); -% End Matlab code - -% Start Octave code -% t=linspace(0,100,100); -% x=lsode('f',x0,t); -% End Octave code - - - plot(t,x); -end - - - -% Depending on whether you are using Octave or Matlab, -% you should comment / uncomment one of the following blocks. -% This should also be done for the definition of the function f below. -% Start Matlab code -function xdot=f(t,x) -% End Matlab code - -% Start Octave code -%function xdot=f(x,t) -% End Octave code - -% Compartment: id = Cell, name = Cell, constant - compartment_Cell=1.0; -% Compartment: id = Extracellular, name = Extracellular, constant - compartment_Extracellular=1.0; -% Parameter: id = k_mA_C_gA, name = k_mA*C_gA - global_par_k_mA_C_gA=104.0; -% Parameter: id = k_mB_C_gB, name = k_mB*C_gB - global_par_k_mB_C_gB=1.0; -% Parameter: id = k_mC_C_gC, name = k_mC*C_gC - global_par_k_mC_C_gC=1.0; -% Parameter: id = d_mA, name = d_mA - global_par_d_mA=0.3624; -% Parameter: id = d_mB, name = d_mB - global_par_d_mB=0.3624; -% Parameter: id = d_mC, name = d_mC - global_par_d_mC=0.3624; -% Parameter: id = k_pA, name = k_pA - global_par_k_pA=80.0; -% Parameter: id = k_pB, name = k_pB - global_par_k_pB=1.0; -% Parameter: id = k_pC, name = k_pC - global_par_k_pC=11.42; -% Parameter: id = d_A, name = d_A - global_par_d_A=0.035; -% Parameter: id = d_B, name = d_B - global_par_d_B=0.016; -% Parameter: id = d_C, name = d_C - global_par_d_C=0.2784; -% Parameter: id = k_d, name = k_d - global_par_k_d=0.06; -% Parameter: id = k_2f, name = k_2f - global_par_k_2f=0.1; -% Parameter: id = k_3f, name = k_3f - global_par_k_3f=0.1; -% Parameter: id = k_2r, name = k_2r - global_par_k_2r=20.0; -% Parameter: id = k_3r, name = k_3r - global_par_k_3r=1.0; -% Parameter: id = gamma_1, name = gamma_1 - global_par_gamma_1=107.4; -% Parameter: id = gamma_2, name = gamma_2 - global_par_gamma_2=0.2; -% Parameter: id = gamma_3, name = gamma_3 - global_par_gamma_3=0.01; -% Parameter: id = gamma_4, name = gamma_4 - global_par_gamma_4=1.15; -% Parameter: id = gamma_5, name = gamma_5 - global_par_gamma_5=8.56; -% Parameter: id = Beta_1, name = Beta_1 - global_par_Beta_1=0.05; -% Parameter: id = Beta_2, name = Beta_2 - global_par_Beta_2=0.05; -% Parameter: id = d_I, name = d_I - global_par_d_I=0.0164; -% Parameter: id = d_Ie, name = d_Ie - global_par_d_Ie=0.0164; -% Parameter: id = d_AI, name = d_AI - global_par_d_AI=0.035; -% Parameter: id = d_AI2, name = d_AI2 - global_par_d_AI2=0.035; -% Parameter: id = M, name = M -% Parameter: id = K_cells, name = K_cells -% Parameter: id = V_cell, name = V_cell - global_par_V_cell=1.0E-15; -% Parameter: id = N_cells, name = N_cells - global_par_N_cells=2.4E8; -% Parameter: id = V_medium, name = V_medium - global_par_V_medium=180.0; -% Parameter: id = sum_abs_dx8, name = sum(abs_dx8) -% Parameter: id = J1, name = J1 -% Parameter: id = J2, name = J2 -% Parameter: id = Sensitivity, name = Sensitivity -% Parameter: id = Precision, name = Precision -% Parameter: id = P_theta, name = P_theta -% Parameter: id = Metabolite_16, name = Initial for x8 - global_par_Metabolite_16=0.0; -% Parameter: id = Metabolite_17, name = Initial for x9 - global_par_Metabolite_17=9000.0; -% assignmentRule: variable = J1 - global_par_J1=2*abs(x(9)-global_par_Metabolite_17)/global_par_sum_abs_dx8; -% assignmentRule: variable = Sensitivity - global_par_Sensitivity=1/global_par_J1; -% assignmentRule: variable = J2 - global_par_J2=(x(8)-global_par_Metabolite_16)/(x(9)-global_par_Metabolite_17); -% assignmentRule: variable = Precision - global_par_Precision=1/global_par_J2; -% assignmentRule: variable = M - global_par_M=-(global_par_d_AI+global_par_k_2r)/(4*global_par_k_3f)+1/(4*global_par_k_3f)*((global_par_d_AI+global_par_k_2r)^2+8*global_par_k_3f*(global_par_k_2f*x(2)*x(3)+2*global_par_k_3r*x(4)))^(0.5); -% assignmentRule: variable = K_cells - global_par_K_cells=global_par_V_cell*global_par_N_cells/global_par_V_medium; -% rateRule: variable = sum_abs_dx8 -global_par_sum_abs_dx8 = x(10); -% rateRule: variable = P_theta -global_par_P_theta = x(11); - -% Reaction: id = r002___A_translation, name = r002 - A_translation - reaction_r002___A_translation=compartment_Cell*global_par_k_pA*x(1); - -% Reaction: id = r003___mA_degradation, name = r003 - mA_degradation - reaction_r003___mA_degradation=compartment_Cell*global_par_d_mA*x(1); - -% Reaction: id = r004___A_degradation, name = r004 - A_degradation - reaction_r004___A_degradation=compartment_Cell*global_par_d_A*x(2); - -% Reaction: id = r005___AI2_dim_1, name = r005 - AI2_dim_1 - reaction_r005___AI2_dim_1=compartment_Cell*global_par_k_2f*x(2)*x(3); - -% Reaction: id = r006a___I_transport, name = r006a - I_transport - reaction_r006a___I_transport=compartment_Cell*global_par_k_d*x(3); - -% Reaction: id = r007___I_degradation, name = r007 - I_degradation - reaction_r007___I_degradation=compartment_Cell*global_par_d_I*x(3); - -% Reaction: id = r008___Ie_degradation, name = r008 - Ie_degradation - reaction_r008___Ie_degradation=compartment_Extracellular*global_par_d_Ie*x(9); - -% Reaction: id = r009___AI2_degradation, name = r009 - AI2_degradation - reaction_r009___AI2_degradation=compartment_Cell*global_par_d_AI2*x(4); - -% Reaction: id = r010___mB_transcription, name = r010 - mB_transcription - reaction_r010___mB_transcription=compartment_Cell*function_for_r010___x5_transcription(global_par_k_mB_C_gB, x(4), global_par_gamma_1); - -% Reaction: id = r011___B_translation, name = r011 - B_translation - reaction_r011___B_translation=compartment_Cell*global_par_k_pB*x(5); - -% Reaction: id = r012___B_degradation, name = r012 - B_degradation - reaction_r012___B_degradation=compartment_Cell*global_par_d_B*x(6); - -% Reaction: id = r013___mB_degradation, name = r013 - mB_degradation - reaction_r013___mB_degradation=compartment_Cell*global_par_d_mB*x(5); - -% Reaction: id = r014___mC_transcription, name = r014 - mC_transcription - reaction_r014___mC_transcription=compartment_Cell*function_for_r014___C_translation(global_par_k_mC_C_gC, x(4), global_par_Beta_1, global_par_gamma_4, x(6), global_par_Beta_2, global_par_gamma_5, global_par_gamma_2, global_par_gamma_3); - -% Reaction: id = r015___C_translation, name = r015 - C_translation - reaction_r015___C_translation=compartment_Cell*global_par_k_pC*x(7); - -% Reaction: id = r016___C_degradation, name = r016 - C_degradation - reaction_r016___C_degradation=compartment_Cell*global_par_d_C*x(8); - -% Reaction: id = r017___mC_degradation, name = r017 - mC_degradation - reaction_r017___mC_degradation=compartment_Cell*global_par_d_mC*x(7); - -% Reaction: id = r018___AI2_dim_2, name = r018 - AI2_dim_2 - reaction_r018___AI2_dim_2=compartment_Cell*global_par_k_3r*x(4); - -% Reaction: id = r019___AI2_dim_3, name = r019 - AI2_dim_3 - reaction_r019___AI2_dim_3=compartment_Cell*function_for_r019___AI2_dim_3(global_par_k_2r, global_par_M); - -% Reaction: id = r020___AI2_dim_4, name = r020 - AI2_dim_4 - reaction_r020___AI2_dim_4=compartment_Cell*function_for_r020___AI2_dim_4(global_par_k_3f, global_par_M); - -% Reaction: id = r006b___I_transport, name = r006b - I_transport - reaction_r006b___I_transport=global_par_k_d*x(9); - -% Reaction: id = r006c___I_transport, name = r006c - I_transport - reaction_r006c___I_transport=compartment_Extracellular*function_for_r006c(global_par_K_cells, global_par_k_d, x(9)); - -% Reaction: id = r006d___I_transport, name = r006d - I_transport - reaction_r006d___I_transport=function_for_r006d(global_par_K_cells, global_par_k_d, x(3)); - - xdot=zeros(11,1); - % rateRule: variable = sum_abs_dx8 - xdot(10) = abs(x(8)); - % rateRule: variable = P_theta - xdot(11) = abs(x(6)); - -% Species: id = x1, name = x1, affected by kineticLaw - xdot(1) = (1/(compartment_Cell))*(( 1.0 * reaction_r001___mA_transcription) + (-1.0 * reaction_r002___A_translation) + ( 1.0 * reaction_r002___A_translation) + (-1.0 * reaction_r003___mA_degradation)); - -% Species: id = x2, name = x2, affected by kineticLaw - xdot(2) = (1/(compartment_Cell))*(( 1.0 * reaction_r002___A_translation) + (-1.0 * reaction_r004___A_degradation) + (-1.0 * reaction_r005___AI2_dim_1) + ( 1.0 * reaction_r019___AI2_dim_3)); - -% Species: id = x3, name = x3, affected by kineticLaw - xdot(3) = (1/(compartment_Cell))*((-1.0 * reaction_r005___AI2_dim_1) + (-1.0 * reaction_r006a___I_transport) + (-1.0 * reaction_r007___I_degradation) + ( 1.0 * reaction_r019___AI2_dim_3) + ( 1.0 * reaction_r006b___I_transport)); - -% Species: id = x4, name = x4, affected by kineticLaw - xdot(4) = (1/(compartment_Cell))*((-1.0 * reaction_r009___AI2_degradation) + (-1.0 * reaction_r018___AI2_dim_2) + ( 1.0 * reaction_r020___AI2_dim_4)); - -% Species: id = x5, name = x5, affected by kineticLaw - xdot(5) = (1/(compartment_Cell))*(( 1.0 * reaction_r010___mB_transcription) + (-1.0 * reaction_r011___B_translation) + ( 1.0 * reaction_r011___B_translation) + (-1.0 * reaction_r013___mB_degradation)); - -% Species: id = x6, name = x6, affected by kineticLaw - xdot(6) = (1/(compartment_Cell))*(( 1.0 * reaction_r011___B_translation) + (-1.0 * reaction_r012___B_degradation)); - -% Species: id = x7, name = x7, affected by kineticLaw - xdot(7) = (1/(compartment_Cell))*(( 1.0 * reaction_r014___mC_transcription) + (-1.0 * reaction_r015___C_translation) + ( 1.0 * reaction_r015___C_translation) + (-1.0 * reaction_r017___mC_degradation)); - -% Species: id = x8, name = x8, affected by kineticLaw - xdot(8) = (1/(compartment_Cell))*(( 1.0 * reaction_r015___C_translation) + (-1.0 * reaction_r016___C_degradation)); - -% Species: id = x9, name = x9, affected by kineticLaw - xdot(9) = (1/(compartment_Extracellular))*((-1.0 * reaction_r008___Ie_degradation) + (-1.0 * reaction_r006b___I_transport) + ( 1.0 * reaction_r006b___I_transport) + (-1.0 * reaction_r006c___I_transport) + ( 1.0 * reaction_r006d___I_transport)); -end - -function z=Constant_flux__irreversible(v), z=(v);end - -function z=function_for_r014___C_translation(KmCCgC,x4,Beta1,gamma4,x6,Beta2,gamma5,gamma2,gamma3), z=(KmCCgC*(x4+Beta1*gamma4*x6+Beta2*gamma5*x4*x6)/(gamma2+gamma3*x4+gamma4*x6+gamma5*x4*x6));end - -function z=function_for_r020___AI2_dim_4(k3,M), z=(k3*M*M);end - -function z=function_for_r019___AI2_dim_3(k_2r,M), z=(k_2r*M);end - -function z=function_for_r006d(Kcells,kd,x3), z=(Kcells*kd*x3);end - -function z=function_for_r010___x5_transcription(K_mbC_gB,x4,gamma1), z=(K_mbC_gB*x4/(gamma1+x4));end - -function z=function_for_r006c(Kcells,kd,x9), z=(Kcells*kd*x9);end - -% adding few functions representing operators used in SBML but not present directly -% in either matlab or octave. -function z=pow(x,y),z=x^y;end -function z=root(x,y),z=y^(1/x);end -function z = piecewise(varargin) - numArgs = nargin; - result = 0; - foundResult = 0; - for k=1:2: numArgs-1 - if varargin{k+1} == 1 - result = varargin{k}; - foundResult = 1; - break; - end - end - if foundResult == 0 - result = varargin{numArgs}; - end - z = result; -end - - diff --git a/final/BIOMD0000000696/BIOMD0000000696-octave.m b/final/BIOMD0000000696/BIOMD0000000696-octave.m deleted file mode 100644 index 274b28c876..0000000000 --- a/final/BIOMD0000000696/BIOMD0000000696-octave.m +++ /dev/null @@ -1,301 +0,0 @@ -% This file works with OCTAVE and is automatically generated with -% the System Biology Format Converter (http://sbfc.sourceforge.net/) -% from an SBML file. -% To run this file with Matlab you must edit the comments providing -% the definition of the ode solver and the signature for the -% xdot function. -% -% The conversion system has the following limitations: -% - You may have to re order some reactions and Assignment Rules definition -% - Delays are not taken into account -% - You should change the lsode parameters (start, end, steps) to get better results -% - -% -% Model name = Boada2016 - Incoherent type 1 feed-forward loop (I1-FFL) -% -% is http://identifiers.org/biomodels.db/MODEL1511290000 -% is http://identifiers.org/biomodels.db/BIOMD0000000696 -% isDescribedBy http://identifiers.org/pubmed/26968941 -% is http://identifiers.org/biomodels.db/MODEL1511290000 -% - - -function main() -%Initial conditions vector - x0=zeros(11,1); - x0(10) = 0.0; - x0(11) = 0.0; - x0(1) = 12.3973509933775; - x0(2) = 28336.8022705771; - x0(3) = 0.0; - x0(4) = 0.0; - x0(5) = 0.0; - x0(6) = 0.0; - x0(7) = 0.0; - x0(8) = 0.0; - x0(9) = 9000.0; - - -% Depending on whether you are using Octave or Matlab, -% you should comment / uncomment one of the following blocks. -% This should also be done for the definition of the function f below. -% Start Matlab code -% tspan=[0:0.01:100]; -% opts = odeset('AbsTol',1e-3); -% [t,x]=ode23tb(@f,tspan,x0,opts); -% End Matlab code - -% Start Octave code - t=linspace(0,100,100); - x=lsode('f',x0,t); -% End Octave code - - - plot(t,x); -end - - - -% Depending on whether you are using Octave or Matlab, -% you should comment / uncomment one of the following blocks. -% This should also be done for the definition of the function f below. -% Start Matlab code -%function xdot=f(t,x) -% End Matlab code - -% Start Octave code -function xdot=f(x,t) -% End Octave code - -% Compartment: id = Cell, name = Cell, constant - compartment_Cell=1.0; -% Compartment: id = Extracellular, name = Extracellular, constant - compartment_Extracellular=1.0; -% Parameter: id = k_mA_C_gA, name = k_mA*C_gA - global_par_k_mA_C_gA=104.0; -% Parameter: id = k_mB_C_gB, name = k_mB*C_gB - global_par_k_mB_C_gB=1.0; -% Parameter: id = k_mC_C_gC, name = k_mC*C_gC - global_par_k_mC_C_gC=1.0; -% Parameter: id = d_mA, name = d_mA - global_par_d_mA=0.3624; -% Parameter: id = d_mB, name = d_mB - global_par_d_mB=0.3624; -% Parameter: id = d_mC, name = d_mC - global_par_d_mC=0.3624; -% Parameter: id = k_pA, name = k_pA - global_par_k_pA=80.0; -% Parameter: id = k_pB, name = k_pB - global_par_k_pB=1.0; -% Parameter: id = k_pC, name = k_pC - global_par_k_pC=11.42; -% Parameter: id = d_A, name = d_A - global_par_d_A=0.035; -% Parameter: id = d_B, name = d_B - global_par_d_B=0.016; -% Parameter: id = d_C, name = d_C - global_par_d_C=0.2784; -% Parameter: id = k_d, name = k_d - global_par_k_d=0.06; -% Parameter: id = k_2f, name = k_2f - global_par_k_2f=0.1; -% Parameter: id = k_3f, name = k_3f - global_par_k_3f=0.1; -% Parameter: id = k_2r, name = k_2r - global_par_k_2r=20.0; -% Parameter: id = k_3r, name = k_3r - global_par_k_3r=1.0; -% Parameter: id = gamma_1, name = gamma_1 - global_par_gamma_1=107.4; -% Parameter: id = gamma_2, name = gamma_2 - global_par_gamma_2=0.2; -% Parameter: id = gamma_3, name = gamma_3 - global_par_gamma_3=0.01; -% Parameter: id = gamma_4, name = gamma_4 - global_par_gamma_4=1.15; -% Parameter: id = gamma_5, name = gamma_5 - global_par_gamma_5=8.56; -% Parameter: id = Beta_1, name = Beta_1 - global_par_Beta_1=0.05; -% Parameter: id = Beta_2, name = Beta_2 - global_par_Beta_2=0.05; -% Parameter: id = d_I, name = d_I - global_par_d_I=0.0164; -% Parameter: id = d_Ie, name = d_Ie - global_par_d_Ie=0.0164; -% Parameter: id = d_AI, name = d_AI - global_par_d_AI=0.035; -% Parameter: id = d_AI2, name = d_AI2 - global_par_d_AI2=0.035; -% Parameter: id = M, name = M -% Parameter: id = K_cells, name = K_cells -% Parameter: id = V_cell, name = V_cell - global_par_V_cell=1.0E-15; -% Parameter: id = N_cells, name = N_cells - global_par_N_cells=2.4E8; -% Parameter: id = V_medium, name = V_medium - global_par_V_medium=180.0; -% Parameter: id = sum_abs_dx8, name = sum(abs_dx8) -% Parameter: id = J1, name = J1 -% Parameter: id = J2, name = J2 -% Parameter: id = Sensitivity, name = Sensitivity -% Parameter: id = Precision, name = Precision -% Parameter: id = P_theta, name = P_theta -% Parameter: id = Metabolite_16, name = Initial for x8 - global_par_Metabolite_16=0.0; -% Parameter: id = Metabolite_17, name = Initial for x9 - global_par_Metabolite_17=9000.0; -% assignmentRule: variable = J1 - global_par_J1=2*abs(x(9)-global_par_Metabolite_17)/global_par_sum_abs_dx8; -% assignmentRule: variable = Sensitivity - global_par_Sensitivity=1/global_par_J1; -% assignmentRule: variable = J2 - global_par_J2=(x(8)-global_par_Metabolite_16)/(x(9)-global_par_Metabolite_17); -% assignmentRule: variable = Precision - global_par_Precision=1/global_par_J2; -% assignmentRule: variable = M - global_par_M=-(global_par_d_AI+global_par_k_2r)/(4*global_par_k_3f)+1/(4*global_par_k_3f)*((global_par_d_AI+global_par_k_2r)^2+8*global_par_k_3f*(global_par_k_2f*x(2)*x(3)+2*global_par_k_3r*x(4)))^(0.5); -% assignmentRule: variable = K_cells - global_par_K_cells=global_par_V_cell*global_par_N_cells/global_par_V_medium; -% rateRule: variable = sum_abs_dx8 -global_par_sum_abs_dx8 = x(10); -% rateRule: variable = P_theta -global_par_P_theta = x(11); - -% Reaction: id = r002___A_translation, name = r002 - A_translation - reaction_r002___A_translation=compartment_Cell*global_par_k_pA*x(1); - -% Reaction: id = r003___mA_degradation, name = r003 - mA_degradation - reaction_r003___mA_degradation=compartment_Cell*global_par_d_mA*x(1); - -% Reaction: id = r004___A_degradation, name = r004 - A_degradation - reaction_r004___A_degradation=compartment_Cell*global_par_d_A*x(2); - -% Reaction: id = r005___AI2_dim_1, name = r005 - AI2_dim_1 - reaction_r005___AI2_dim_1=compartment_Cell*global_par_k_2f*x(2)*x(3); - -% Reaction: id = r006a___I_transport, name = r006a - I_transport - reaction_r006a___I_transport=compartment_Cell*global_par_k_d*x(3); - -% Reaction: id = r007___I_degradation, name = r007 - I_degradation - reaction_r007___I_degradation=compartment_Cell*global_par_d_I*x(3); - -% Reaction: id = r008___Ie_degradation, name = r008 - Ie_degradation - reaction_r008___Ie_degradation=compartment_Extracellular*global_par_d_Ie*x(9); - -% Reaction: id = r009___AI2_degradation, name = r009 - AI2_degradation - reaction_r009___AI2_degradation=compartment_Cell*global_par_d_AI2*x(4); - -% Reaction: id = r010___mB_transcription, name = r010 - mB_transcription - reaction_r010___mB_transcription=compartment_Cell*function_for_r010___x5_transcription(global_par_k_mB_C_gB, x(4), global_par_gamma_1); - -% Reaction: id = r011___B_translation, name = r011 - B_translation - reaction_r011___B_translation=compartment_Cell*global_par_k_pB*x(5); - -% Reaction: id = r012___B_degradation, name = r012 - B_degradation - reaction_r012___B_degradation=compartment_Cell*global_par_d_B*x(6); - -% Reaction: id = r013___mB_degradation, name = r013 - mB_degradation - reaction_r013___mB_degradation=compartment_Cell*global_par_d_mB*x(5); - -% Reaction: id = r014___mC_transcription, name = r014 - mC_transcription - reaction_r014___mC_transcription=compartment_Cell*function_for_r014___C_translation(global_par_k_mC_C_gC, x(4), global_par_Beta_1, global_par_gamma_4, x(6), global_par_Beta_2, global_par_gamma_5, global_par_gamma_2, global_par_gamma_3); - -% Reaction: id = r015___C_translation, name = r015 - C_translation - reaction_r015___C_translation=compartment_Cell*global_par_k_pC*x(7); - -% Reaction: id = r016___C_degradation, name = r016 - C_degradation - reaction_r016___C_degradation=compartment_Cell*global_par_d_C*x(8); - -% Reaction: id = r017___mC_degradation, name = r017 - mC_degradation - reaction_r017___mC_degradation=compartment_Cell*global_par_d_mC*x(7); - -% Reaction: id = r018___AI2_dim_2, name = r018 - AI2_dim_2 - reaction_r018___AI2_dim_2=compartment_Cell*global_par_k_3r*x(4); - -% Reaction: id = r019___AI2_dim_3, name = r019 - AI2_dim_3 - reaction_r019___AI2_dim_3=compartment_Cell*function_for_r019___AI2_dim_3(global_par_k_2r, global_par_M); - -% Reaction: id = r020___AI2_dim_4, name = r020 - AI2_dim_4 - reaction_r020___AI2_dim_4=compartment_Cell*function_for_r020___AI2_dim_4(global_par_k_3f, global_par_M); - -% Reaction: id = r006b___I_transport, name = r006b - I_transport - reaction_r006b___I_transport=global_par_k_d*x(9); - -% Reaction: id = r006c___I_transport, name = r006c - I_transport - reaction_r006c___I_transport=compartment_Extracellular*function_for_r006c(global_par_K_cells, global_par_k_d, x(9)); - -% Reaction: id = r006d___I_transport, name = r006d - I_transport - reaction_r006d___I_transport=function_for_r006d(global_par_K_cells, global_par_k_d, x(3)); - - xdot=zeros(11,1); - % rateRule: variable = sum_abs_dx8 - xdot(10) = abs(x(8)); - % rateRule: variable = P_theta - xdot(11) = abs(x(6)); - -% Species: id = x1, name = x1, affected by kineticLaw - xdot(1) = (1/(compartment_Cell))*(( 1.0 * reaction_r001___mA_transcription) + (-1.0 * reaction_r002___A_translation) + ( 1.0 * reaction_r002___A_translation) + (-1.0 * reaction_r003___mA_degradation)); - -% Species: id = x2, name = x2, affected by kineticLaw - xdot(2) = (1/(compartment_Cell))*(( 1.0 * reaction_r002___A_translation) + (-1.0 * reaction_r004___A_degradation) + (-1.0 * reaction_r005___AI2_dim_1) + ( 1.0 * reaction_r019___AI2_dim_3)); - -% Species: id = x3, name = x3, affected by kineticLaw - xdot(3) = (1/(compartment_Cell))*((-1.0 * reaction_r005___AI2_dim_1) + (-1.0 * reaction_r006a___I_transport) + (-1.0 * reaction_r007___I_degradation) + ( 1.0 * reaction_r019___AI2_dim_3) + ( 1.0 * reaction_r006b___I_transport)); - -% Species: id = x4, name = x4, affected by kineticLaw - xdot(4) = (1/(compartment_Cell))*((-1.0 * reaction_r009___AI2_degradation) + (-1.0 * reaction_r018___AI2_dim_2) + ( 1.0 * reaction_r020___AI2_dim_4)); - -% Species: id = x5, name = x5, affected by kineticLaw - xdot(5) = (1/(compartment_Cell))*(( 1.0 * reaction_r010___mB_transcription) + (-1.0 * reaction_r011___B_translation) + ( 1.0 * reaction_r011___B_translation) + (-1.0 * reaction_r013___mB_degradation)); - -% Species: id = x6, name = x6, affected by kineticLaw - xdot(6) = (1/(compartment_Cell))*(( 1.0 * reaction_r011___B_translation) + (-1.0 * reaction_r012___B_degradation)); - -% Species: id = x7, name = x7, affected by kineticLaw - xdot(7) = (1/(compartment_Cell))*(( 1.0 * reaction_r014___mC_transcription) + (-1.0 * reaction_r015___C_translation) + ( 1.0 * reaction_r015___C_translation) + (-1.0 * reaction_r017___mC_degradation)); - -% Species: id = x8, name = x8, affected by kineticLaw - xdot(8) = (1/(compartment_Cell))*(( 1.0 * reaction_r015___C_translation) + (-1.0 * reaction_r016___C_degradation)); - -% Species: id = x9, name = x9, affected by kineticLaw - xdot(9) = (1/(compartment_Extracellular))*((-1.0 * reaction_r008___Ie_degradation) + (-1.0 * reaction_r006b___I_transport) + ( 1.0 * reaction_r006b___I_transport) + (-1.0 * reaction_r006c___I_transport) + ( 1.0 * reaction_r006d___I_transport)); -end - -function z=Constant_flux__irreversible(v), z=(v);end - -function z=function_for_r014___C_translation(KmCCgC,x4,Beta1,gamma4,x6,Beta2,gamma5,gamma2,gamma3), z=(KmCCgC*(x4+Beta1*gamma4*x6+Beta2*gamma5*x4*x6)/(gamma2+gamma3*x4+gamma4*x6+gamma5*x4*x6));end - -function z=function_for_r020___AI2_dim_4(k3,M), z=(k3*M*M);end - -function z=function_for_r019___AI2_dim_3(k_2r,M), z=(k_2r*M);end - -function z=function_for_r006d(Kcells,kd,x3), z=(Kcells*kd*x3);end - -function z=function_for_r010___x5_transcription(K_mbC_gB,x4,gamma1), z=(K_mbC_gB*x4/(gamma1+x4));end - -function z=function_for_r006c(Kcells,kd,x9), z=(Kcells*kd*x9);end - -% adding few functions representing operators used in SBML but not present directly -% in either matlab or octave. -function z=pow(x,y),z=x^y;end -function z=root(x,y),z=y^(1/x);end -function z = piecewise(varargin) - numArgs = nargin; - result = 0; - foundResult = 0; - for k=1:2: numArgs-1 - if varargin{k+1} == 1 - result = varargin{k}; - foundResult = 1; - break; - end - end - if foundResult == 0 - result = varargin{numArgs}; - end - z = result; -end - - diff --git a/final/BIOMD0000000696/BIOMD0000000696.ode b/final/BIOMD0000000696/BIOMD0000000696.ode index 50c2707234..84d62c6ec4 100644 --- a/final/BIOMD0000000696/BIOMD0000000696.ode +++ b/final/BIOMD0000000696/BIOMD0000000696.ode @@ -20,6 +20,8 @@ ceil(x)=flr(1+x) @delay=50 +# FunctionDefinition id = rateOf +# Inconsistent mathML operators in Function Definition, function ignored # FunctionDefinition id = Constant_flux__irreversible, name = Constant flux (irreversible) Constant_(v)=(v) @@ -186,7 +188,7 @@ Precision=1/J2 aux Precision=Precision # assignmentRule: variable = M -M=-(d_AI+k_2r)/(4*k_3f)+1/(4*k_3f)*((d_AI+k_2r)^2+8*k_3f*(k_2f*x2*x3+2*k_3r*x4))^(0.5) +M=(-(d_AI+k_2r)/(4*k_3f))+1/(4*k_3f)*((d_AI+k_2r)^2+8*k_3f*(k_2f*x2*x3+2*k_3r*x4))^(0.5) aux M=M # assignmentRule: variable = K_cells @@ -195,11 +197,11 @@ aux K_cells=K_cells # rateRule: variable = sum_abs_dx8 init sum_abs_d=0.0 -dsum_abs_d/dt=abs(x8) +dsum_abs_d/dt=abs(rateOf(x8)) # rateRule: variable = P_theta init P_theta=0.0 -dP_theta/dt=abs(x6) +dP_theta/dt=abs(rateOf(x6)) # Reaction: id = r001___mA_transcription, name = r001 - mA_transcription diff --git a/final/BIOMD0000000696/BIOMD0000000696_url.xml b/final/BIOMD0000000696/BIOMD0000000696_url.xml index 558e921022..46fc2da058 100644 --- a/final/BIOMD0000000696/BIOMD0000000696_url.xml +++ b/final/BIOMD0000000696/BIOMD0000000696_url.xml @@ -1531,7 +1531,7 @@ a biological device demonstrating desired behaviour. - + @@ -1729,8 +1729,12 @@ a biological device demonstrating desired behaviour. - 1 - J1 + 1 + + + 1 -15 + J1 + @@ -1739,14 +1743,24 @@ a biological device demonstrating desired behaviour. - - x8 - Metabolite_16 + + + + x8 + Metabolite_16 + - - x9 - Metabolite_17 + + 1 -15 + + + + + x9 + Metabolite_17 + + @@ -1755,8 +1769,12 @@ a biological device demonstrating desired behaviour. - 1 - J2 + 1 + + + 1 -15 + J2 + diff --git a/final/BIOMD0000000696/manifest.xml b/final/BIOMD0000000696/manifest.xml index fe1da03d04..52def30752 100644 --- a/final/BIOMD0000000696/manifest.xml +++ b/final/BIOMD0000000696/manifest.xml @@ -2,8 +2,6 @@ - -