Hello Casper,

There are following possibilities of using of SBML and MATLAB in
current version of BioUML:

SBML plug-in allows customer to use existing SBML models (they can be
imported as SBML module), edit them or create new ones. In SBML
module SBML format is used for model storage. Diagram layout is
stored using SBML <annotations> mechanism.
See http://www.biouml.org/plugin_sbml.shtml?overview for further
details.

MATLAB plug-in allows user to generate MATLAB files for SBML models
and BioUML standard simulation diagram type. For this purpose user
should open corresponding diagram, select MATLAB tab in right bottom
pane, specify MATLAB working directory, where generated files will be
stored and press 'Start MATLAB engine' button. The plug-in will
generate two files:

modelName_script.m
script file for model simulation and graphic results presentation

modelName_dy.m
function to calculate dy/dt for the model.

Then the plug-in will try to start the MATLAB and invoke the
generated script file for model simulation and results visualization.

Alternatively you can invoke SBW MatlabTranslator service to generate
corresponding MATLAB files for SBML models using JavaScript console.

In further we plan to provide conversion utility that will be able
convert content of standard BioUML pathway simulation diagram to SBML
format.

With best regards,
Fedor.

----------------------------------------------------------------------
These are examples of generated MATLAB files by MATLAB plug-in:

CellCycle_1991Gol_script.m
---------------------------
%script for 'CellCycle_1991Gol' model simulation

%constants declaration
global Reaction1_vi Reaction2_kd Reaction3_kd Reaction3_vd
Reaction4_K1 Reaction4_Kc Reaction4_VM1 Reaction5_K3 Reaction5_VM3
Reaction6_K2 Reaction6_V2 Reaction7_K4 Reaction7_V4 cytoplasm_EmptySet
Reaction1_vi = 0.023
Reaction2_kd = 0.00333
Reaction3_kd = 0.00333
Reaction3_vd = 0.1
Reaction4_K1 = 0.1
Reaction4_Kc = 0.3
Reaction4_VM1 = 0.5
Reaction5_K3 = 0.1
Reaction5_VM3 = 0.2
Reaction6_K2 = 0.1
Reaction6_V2 = 0.167
Reaction7_K4 = 0.1
Reaction7_V4 = 0.1

%Model boundary variables, they are declared as constants
cytoplasm_EmptySet = 0.0 % boundary variable
$cytoplasm.EmptySet

%Model rate variables and their initial values
y = []
y(1) = 0.0 % y(1) - $cytoplasm.C
y(2) = 0.0 % y(2) - $cytoplasm.M
y(3) = 0.0 % y(3) - $cytoplasm.X

%numeric equation solving
[t,y] = ode23('CellCycle_1991Gol_dy',[0 100],y)

%plot the solver output
plot(t,y(:,1),'-',t,y(:,2),'-',t,y(:,3),'-')
title ('Solving Goldbeter problem')
ylabel ('y(t)')
xlabel ('x(t)')
legend('$cytoplasm.C','$cytoplasm.M','$cytoplasm.X');


CellCycle_1991Gol_dy.m
----------------------
function dy = CellCycle_1991Gol_dy(t, y)
% Calculates dy/dt for 'CellCycle_1991Gol' model.

%constants declaration
global Reaction1_vi Reaction2_kd Reaction3_kd Reaction3_vd
Reaction4_K1 Reaction4_Kc Reaction4_VM1 Reaction5_K3 Reaction5_VM3
Reaction6_K2 Reaction6_V2 Reaction7_K4 Reaction7_V4 cytoplasm_EmptySet

% write rules to calculate some eqution parameters
rateOfReaction1 = Reaction1_vi;
rateOfReaction2 = y(1)*Reaction2_kd;
rateOfReaction3 = (y(1)*Reaction3_vd*y(3))/(y(1) + Reaction3_kd);
rateOfReaction4 = ((1 - y(2))*Reaction4_VM1*y(1))/((1 + Reaction4_K1 -
y(2))*(Reaction4_Kc + y(1)));
rateOfReaction5 = (Reaction5_VM3*(1 - y(3))*y(2))/(1 + Reaction5_K3 -
y(3));
rateOfReaction6 = (y(2)*Reaction6_V2)/(Reaction6_K2 + y(2));
rateOfReaction7 = (Reaction7_V4*y(3))/(Reaction7_K4 + y(3));


% calculates dy/dt for 'CellCycle-1991Gol.xml' model
dy = [ + rateOfReaction1 - rateOfReaction2 - rateOfReaction3
+ rateOfReaction4 - rateOfReaction6
+ rateOfReaction5 - rateOfReaction7]


--- In biouml@yahoogroups.com, "Casper Frederiksen" <in_silico@h...>
wrote:
> Hi Fedor,
>
>
> >I am not confident that I understood the question.
>
> Thanks. You understood the question correctly. Actually I thought
that you
> could save in SMBL or matlab, but as far as I can see that will be
included
> in a later version. It would also be nice with the possibility to
import
> SBML
>
>
> Regards,
>
> Casper
>
> _________________________________________________________________
> FÅ gode tilbud direkte i din mailbox http://jatak.msn.dk