Implementing a code from Berkley Madonna into Matlab

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KayLynn 2014-3-1

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评论： Star Strider 2014-3-4

I am trying to implement a code from Berkley Madonna into Matlab. I want to carry out a simulation and produce the results graphically by using ode solvers directly. Here is this Berkley Madonna code I am trying to incorporate:

Listing of program in Berkeley Madonna notation:

DT=1e-4

STOPTIME=100

d/dt (C) = Synthesis - Degradation

INIT C = 0.01

Synthesis = 0.025

Degradation = vd*X*(C/(Kd+C)) - kdd*C

d/dt (M) = Phosphatase1 - Kinase1

INIT M = 0.01

Phosphatase1 = VM1*(C/(Kc+C))*((1-M)/(K1+(1-M)))

Kinase1 = V2*(M/(K2+M))

d/dt (X) = Phosphatase2 - Kinase2

INIT X = 0.01

Phosphatase2 = M*VM3*((1-X)/(K3+(1-X)))

Kinase2 = V4*(X/(K4+X))

K1 = 0.005

K2 = 0.005

K3 = 0.005

K4 = 0.005

Kc = 0.5

Kd = 0.02

kdd = 0.01

V2 = 1.5

V4 = 0.5

vd = 0.25

VM1 = 3

VM3 = 1.

I have first two questions about this: First is the equation set up given by Berkley Madonna in correct use for matlab. Second question....I am unable to use the ode solvers correctly. It seems I somehow have re written over the ode solvers that are built into Matlab. Is there a way to correct this without uninstalling MATLAB and re installing it.

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Ingrid Tigges 2014-3-3

Are you aware of this Import Berkley Madonna models into SimBiology entry from the file exchange? It gives you an easy way to implement the models into SimBiology.

Star Strider 2014-3-3

编辑：Star Strider 2014-3-3

That’s good to know. Thank you.

KayLynn doesn’t have SimBiology, though. (That was in a subsequent post.) Neither do I.

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Answer 1

Star Strider 2014-3-1

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/119720-implementing-a-code-from-berkley-madonna-into-matlab#answer_126708

编辑：Star Strider 2014-3-1

在 MATLAB Online 中打开

Just for fun (and because I’m interested in biochemistry), I decided to code this as best I could. It gives interesting results, but certainly not out of character for some biochemical systems. (I copied the equations directly from your code, pasted them into the function, and did a ‘Search - Replace’ with the Editor.)

K1 = 0.005;
K2 = 0.005;
K3 = 0.005;
K4 = 0.005;
Kc = 0.5;
Kd = 0.02;
kdd = 0.01;
V2 = 1.5;
V4 = 0.5;
vd = 0.25;
VM1 = 3;
VM3 = 1.;
Synth = 0.025;
% Original Equations: 
% PhsKnsKnt = [Synth-vd*X*(C/(Kd+C)) - kdd*C;    M*VM3*((1-X)/(K3+(1-X))) - V4*(X/(K4+X));    VM1*(C/(Kc+C))*((1-M)/(K1+(1-M))) - V2*(M/(K2+M))];
% Anonymous Function with substitutions: 
PhsKnsKnt = @(T, P)  [Synth - vd*P(2)*(P(1)/(Kd+P(1))) - kdd*P(1);    P(3)*VM3*((1-P(2))/(K3+(1-P(2)))) - V4*(P(2)/(K4+P(2)));    VM1*(P(1)/(Kc+P(1)))*((1-P(3))/(K1+(1-P(3)))) - V2*(P(3)/(K2+P(3)))];
[T P] = ode45(PhsKnsKnt, [0  100],  [0.01;  0.01;  0.01]);
C = P(:,1);
X = P(:,2);
M = P(:,3);
figure(1)
plot(T, P)
legend('[C] (µ\itM\rm)',  '[X] (µ\itM\rm)',  '[M] (µ\itM\rm)', 'Location','NorthWest')
xlabel('Time (s)')
ylabel('Concentration')
grid

Just out of curiosity, what biochemical system is this?

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Star Strider 2014-3-4

编辑：Star Strider 2014-3-4

I missed your earlier post about perturbations and SFO rankings. I’m not familiar with them, but they look like numerical derivatives. I’ll do a search later to see what I can find. (I found it interesting that when I plotted the ratio of the two for Kd, the effect was most pronounced at lower concentrations. If Kd is the dissociation constant, that entirely makes sense.)

I looked at both threads and didn’t find an uploaded paper or a mention of it. (The only reference I saw was my link to the SimBiology documentation on the mitotic oscillator. It linked to two PNAS papers by Goldbeter, and I believe are freely available online. Did you mean one of them?) If you upload the PDF of the paper you referred to as an attachment to your initial post here, I’ll be glad to take a look at it.

You probably want to ‘poison’ the system somehow, but I’m not having read the paper yet, I’m not certain how you want to do that.

I’ll look for the uploaded paper (or a link to the free paper PDF) and reply when I’ve read it.

Star Strider 2014-3-4

I need to be offline for a bit, but I’ll download it as soon as I see you’ve uploaded it. Not having read it, I can’t comment further just now.

Star Strider 2014-3-4

I couldn’t find anything on ‘SFO ranking’ in an Internet search (DuckDuckGo and PubMed). The problem with ‘perturbation’ is that it means different things in different contexts. I couldn’t find anything dealing specifically with enzyme kinetics.

As far as ‘poisoning’ the system, that probably only requires changing one or more binding constants. Shouldn’t screw up the code for the DEs.

This paper ‘Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation’ may be what you want to do, but it’s not available online.

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