[Ecell-users] implementing new processes

[giuseppe a. <apr...@gm...>]

Dear all,

I am giuseppe and I am using IE-Cell SE Version 3.1.106 on kubuntu 8.04.
I am experiencing some problems in implementig new processes.
I am trying to use ecell as an ode solver: the differential equations are:

pow1a=(ks3/x(3))^n3;
pow1b=(ks4/x(4))^n4;
pow2a=(x(3)/sm3)^a3;
pow2b=(x(4)/sm4)^a4;
mu=mu1*(1/(1+pow1a))*(1/(1+pow1b))*(1-pow2a)*(1-pow2b)

dx(1)dt = mu*x(1)
dx(2)dt = ((k1*mu)+k2)*x(1)
dx(3)dt = -((alp*mu)+gam)*x(1)
dx(4)dt = -((mu/yRS2)+mS2)*x(1)

where ks3,ks4,n3,n4,sm3,sm4,a3,a4,mu1,k1,k2,alp,gam,yRS2,mS2
are numerical parameters; they keep the same value throughout the
computation. I wrote 4 new processes (which are attached); one for
each equation. As far as I understand ona can use ecell to as an ode
solver once given a process for each equation. the system should
assign to each "1" entry in the VariableReferenceList the proper
velocity in the following way. Given this entry in .em file:

...........
Process       ODE2Process( ODE2 )
       {
				mu1  0.303;
				n1  3.5938;
				n2  2.213;
				ks1  22.836;
				ks2  0.234;
				sm1  90.11;
				sm2  10.11;
				a1  3.19;
				a2  0.97;
				k1  0.008;
				k2  0.034;
				VariableReferenceList[X1 Variable:.:BIOMASS -1]
									 [X2 Variable:.:PHA 1]
									 [X3 Variable:.:NUTRIENT -1]
									 [X4 Variable:.:INHIBITOR -1];
       }
...........

I guess ecell will associate ODE2Process' velocity to X2 Variable (PHA).
Is that right?

Now I have 2 problems:

- during compilation I get los of warnings of the kind:
"/usr/include/ecell-3.1/libecs/Entity.hpp:73: warning: comparison with
string literal results in unspecified behaviour"
I don't really understand if I am doing some fatal error in the code,
anyway I successfully get my .so objacts. Can I ignore this warning?

- if I compare the results with matlab ones they are quite different
both quantitatively (~20%) and qualitatively after "only" 60 sec.

By the way, does anybody know if there is some documentation about
Stepper settings (timestep, tolerance) or about how to make your own Stepper?

Many Thanks in advance,

Giuseppe