# IGEM:Melbourne/2008/BioClock/David Version/clock code

function xdot = Stephen_clock(time,x)

format long e; global pulse g_p;

% synopsis:
% xdot = (time, x)
% x0 =
%
% can be used with odeN functions as follows:
%
% x0 = ;
% [t,x] = ode23s(@, [0 100], );
% plot (t,x);
%
% where 100 is the end time
%
% When is used without any arguments it returns a vector of
% the initial concentrations of the 14 floating species.
% Otherwise should be called with two arguments:
% time and x. time is the current time. x is the vector of the
% concentrations of the 14 floating species.
% When these parameters are supplied returns a vector of
% the rates of change of the concentrations of the 14 floating species.
%
% the following table shows the mapping between the vector
% index of a floating species and the species name.
%
% NOTE for compartmental models
% matlab translator generates code that when simulated in matlab,
% produces results which have the units of species amounts. Users
% should divide the results for each species with the volume of the
% compartment it resides in, in order to obtain concentrations.
%
% Indx Name
% x(1) EnvZ_dephos
% x(2) OmpR_dephos
% x(3) X
% x(4) GFP
% x(5) RiboKey1
% x(6) Y
% x(7) RFP
% x(8) Off_X
% x(9) RiboKey2
% x(10) GFP_sink
% x(11) RFP_sink
% x(12) X_sink
% x(13) Y_sink
% x(14) EnvZ_dephos_sink
% x(15) OmpR_dephos_sink
% x(16) Intermediate1
% x(17) RiboKey1_sink
% x(18) Intermediate2
% x(19) Intermediate3
% x(20) X_sink_617291

xdot = zeros(20, 1); g_p = ones(30,1);

% List of Compartments vol__compartment = 1;

% Global Parameters g_p(1) = 0.1; % j1_k g_p(2) = 0.1; % j10_k g_p(3) = 0.1; % j14_k g_p(4) = 0.1; % j16_k g_p(5) = 5; % j2_vmax g_p(6) = 0.2; % j2_km1 g_p(7) = 0.3; % j2_ki g_p(8) = 0.5; % j5_vmax g_p(9) = 0.3; % j5_km1 g_p(10) = 0.1; % j5_ki g_p(11) = 0.5; % j12_vmax g_p(12) = 0.3; % j12_km1 g_p(13) = 1; % j12_ki g_p(14) = 0.5; % j19_k g_p(15) = 0.1; % j20_k g_p(16) = 2; % j21_k g_p(17) = 0.5; % j8_vmax g_p(18) = 0.3; % j8_km1 g_p(19) = 0.1; % j8_ki g_p(20) = 0.5; % j9_vmax g_p(21) = 0.3; % j9_km1 g_p(22) = 0.1; % j9_ki g_p(23) = 0.1; % j17_k g_p(24) = 0.1; % j22_k g_p(25) = 1; % j18_k g_p(26) = 0.1; % j23_vmax g_p(27) = 1e-005; % j23_km1 g_p(28) = 0.1; % j24_k g_p(29) = 0.1; % j25_k g_p(30) = 5000; % j26_k

% Boundary Conditions
g_p31 = 1; % envz_phos [Concentration]
%g_p32 = 0; % red_light [Concentration]
g_p33 = 1; % ompr_phos [Concentration]
g_p34 = 0; % off_y [Concentration]

if pulse == 1 g_p32 = getSG0(time); %red_light similar pulse to Sg0 in the other model dlmwrite('time_v2.dat',time,'-append'); dlmwrite('sg0_v2.dat',g_p32,'-append'); else g_p32 = 0; % red_light [Concentration] end

% Other Parameters

if (nargin == 0) % set initial conditions xdot(1) = 0*vol__compartment; % EnvZ_dephos [Concentration] xdot(2) = 0*vol__compartment; % OmpR_dephos [Concentration] xdot(3) = 0*vol__compartment; % X [Concentration] xdot(4) = 0*vol__compartment; % GFP [Concentration] xdot(5) = 0*vol__compartment; % RiboKey1 [Concentration] xdot(6) = 0*vol__compartment; % Y [Concentration] xdot(7) = 0*vol__compartment; % RFP [Concentration] xdot(8) = 0*vol__compartment; % Off_X [Concentration] xdot(9) = 0*vol__compartment; % RiboKey2 [Concentration] xdot(10) = 0*vol__compartment; % GFP_sink [Concentration] xdot(11) = 0*vol__compartment; % RFP_sink [Concentration] xdot(12) = 0*vol__compartment; % X_sink [Concentration] xdot(13) = 0*vol__compartment; % Y_sink [Concentration] xdot(14) = 0*vol__compartment; % EnvZ_dephos_sink [Concentration] xdot(15) = 0*vol__compartment; % OmpR_dephos_sink [Concentration] xdot(16) = 0*vol__compartment; % Intermediate1 [Concentration] xdot(17) = 0*vol__compartment; % RiboKey1_sink [Concentration] xdot(18) = 0*vol__compartment; % Intermediate2 [Concentration] xdot(19) = 0*vol__compartment; % Intermediate3 [Concentration] xdot(20) = 0*vol__compartment; % X_sink_617291 [Concentration]

else

% calculate rates of change R0 = g_p(1)*(x(1)/vol__compartment)*(g_p33/vol__compartment); R1 = g_p(5)*(x(2)/vol__compartment)/(g_p(6)*(1+(g_p33/vol__compartment)/g_p(7))+(x(2)/vol__compartment)); R2 = g_p(8)*(x(3)/vol__compartment)/(g_p(9)*(1+(x(8)/vol__compartment)/g_p(10))+(x(3)/vol__compartment)); R3 = g_p(17)*(x(6)/vol__compartment)/(g_p(18)*(1+(g_p34/vol__compartment)/g_p(19))+(x(6)/vol__compartment)); R4 = g_p(20)*(x(6)/vol__compartment)/(g_p(21)*(1+(g_p34/vol__compartment)/g_p(22))+(x(6)/vol__compartment)); R5 = g_p(2)*(x(6)/vol__compartment); R6 = g_p(11)*(x(3)/vol__compartment)/(g_p(12)*(1+(x(8)/vol__compartment)/g_p(13))+(x(3)/vol__compartment)); R7 = g_p(3)*(g_p31/vol__compartment)*(g_p32/vol__compartment); R8 = g_p(4)*(x(8)/vol__compartment); R9 = g_p(25)*(x(4)/vol__compartment); R10 = g_p(14)*(x(7)/vol__compartment); R11 = g_p(15)*(x(3)/vol__compartment); R12 = g_p(16)*(x(6)/vol__compartment); R13 = g_p(23)*(x(1)/vol__compartment); R14 = g_p(24)*(x(2)/vol__compartment); R15 = g_p(26)*(x(3)/vol__compartment)/(g_p(27)+(x(3)/vol__compartment)); R16 = g_p(28)*(x(5)/vol__compartment); R17 = g_p(29)*(x(16)/vol__compartment)*(x(2)/vol__compartment); R18 = g_p(30)*(x(16)/vol__compartment)*(x(3)/vol__compartment);

xdot = [ - R0 + R7 - R13 + R0 - R1 - R14 - R17 + R1 + R2 - R2 - R6 - R11 - R15 - R18 + R6 - R9 + 50*R15 - R16 + R3 - R3 - R4 - R5 - R12 + 20*R17 + R4 - R10 + R8 - R8 + R5 + R9 + R10 + R11 + R12 + R13 + R14 + R16 - R17 - R18 0 0 0 + R18 ]; end;