In [5]:

    

%matplotlib inline
from __future__ import print_function
import tellurium as te

# to get the tellurium version use
print('te.__version__')
print(te.__version__)
# or
print('te.getTelluriumVersion()')
print(te.getTelluriumVersion())

# to print the full version info use
print('-' * 80)
te.printVersionInfo()
print('-' * 80)


    

    




te.__version__
2.0.0
te.getTelluriumVersion()
2.0.0
--------------------------------------------------------------------------------
tellurium : 2.0.0
roadrunner : 1.4.21; Compiler: gcc 4.8.2, C++ version: 199711; JIT Compiler: LLVM-3.3; Date: Jul  5 2017, 18:38:02; LibSBML Version: 5.14.0
antimony : 2.9.3
libsbml : 5.15.0
libsedml : 402
phrasedml : 1.0.7
--------------------------------------------------------------------------------

In [8]:

    

from builtins import range
# Load SBML file
r = te.loada("""
model test
    J0: X0 -> X1; k1*X0;
    X0 = 10; X1=0;
    k1 = 0.2
end
""")

import matplotlib.pyplot as plt

# Turn of notices so they don't clutter the output
te.noticesOff()
for i in range(0, 20):
    result = r.simulate (0, 10)
    r.reset()
    r.plot(result, loc=None, show=False, 
           linewidth=2.0, linestyle='-', color='black', alpha=0.8)
    r.k1 = r.k1 + 0.2
# Turn the notices back on
te.noticesOn()


    

In [6]:

    

# create tmp file
import tempfile
ftmp = tempfile.NamedTemporaryFile(suffix=".xml")
# load model
r = te.loada('S1 -> S2; k1*S1; k1 = 0.1; S1 = 10')
# save to file
te.saveToFile(ftmp.name, r.getMatlab())

# or easier via
r.exportToMatlab(ftmp.name)

# load file
sbmlstr = te.readFromFile(ftmp.name)
print('%' + '*'*80)
print('Converted MATLAB code')
print('%' + '*'*80)
print(sbmlstr)


    

    




%********************************************************************************
Converted MATLAB code
%********************************************************************************
%  How to use:
%
%  __main takes 3 inputs and returns 3 outputs.
%
%  [t x rInfo] = __main(tspan,solver,options)
%  INPUTS: 
%  tspan - the time vector for the simulation. It can contain every time point, 
%  or just the start and end (e.g. [0 1 2 3] or [0 100]).
%  solver - the function handle for the odeN solver you wish to use (e.g. @ode23s).
%  options - this is the options structure returned from the MATLAB odeset
%  function used for setting tolerances and other parameters for the solver.
%  
%  OUTPUTS: 
%  t - the time vector that corresponds with the solution. If tspan only contains
%  the start and end times, t will contain points spaced out by the solver.
%  x - the simulation results.
%  rInfo - a structure containing information about the model. The fields
%  within rInfo are: 
%     stoich - the stoichiometry matrix of the model 
%     floatingSpecies - a cell array containing floating species name, initial
%     value, and indicator of the units being inconcentration or amount
%     compartments - a cell array containing compartment names and volumes
%     params - a cell array containing parameter names and values
%     boundarySpecies - a cell array containing boundary species name, initial
%     value, and indicator of the units being inconcentration or amount
%     rateRules - a cell array containing the names of variables used in a rate rule
%
%  Sample function call:
%     options = odeset('RelTol',1e-12,'AbsTol',1e-9);
%     [t x rInfo] = __main(linspace(0,100,100),@ode23s,options);
%
function [t x rInfo] = __main(tspan,solver,options)
    % initial conditions
    [x rInfo] = model();

    % initial assignments

    % assignment rules

    % run simulation
    [t x] = feval(solver,@model,tspan,x,options);

    % assignment rules

function [xdot rInfo] = model(time,x)
%  x(1)        S1
%  x(2)        S2

% List of Compartments 
vol__default_compartment = 1;		%default_compartment

% Global Parameters 
rInfo.g_p1 = 0.1;		% k1

if (nargin == 0)

    % set initial conditions
   xdot(1) = 10*vol__default_compartment;		% S1 = S1 [Concentration]
   xdot(2) = 0*vol__default_compartment;		% S2 = S2 [Concentration]

   % reaction info structure
   rInfo.stoich = [
      -1
      1
   ];

   rInfo.floatingSpecies = {		% Each row: [Species Name, Initial Value, isAmount (1 for amount, 0 for concentration)]
      'S1' , 10, 0
      'S2' , 0, 0
   };

   rInfo.compartments = {		% Each row: [Compartment Name, Value]
      'default_compartment' , 1
   };

   rInfo.params = {		% Each row: [Parameter Name, Value]
      'k1' , 0.1
   };

   rInfo.boundarySpecies = {		% Each row: [Species Name, Initial Value, isAmount (1 for amount, 0 for concentration)]
   };

   rInfo.rateRules = { 		 % List of variables involved in a rate rule 
   };

else

    % calculate rates of change
   R0 = rInfo.g_p1*(x(1));

   xdot = [
      - R0
      + R0
   ];
end;


%listOfSupportedFunctions
function z = pow (x,y) 
    z = x^y; 


function z = sqr (x) 
    z = x*x; 


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; 


function z = gt(a,b) 
   if a > b 
   	  z = 1; 
   else 
      z = 0; 
   end 


function z = lt(a,b) 
   if a < b 
   	  z = 1; 
   else 
      z = 0; 
   end 


function z = geq(a,b) 
   if a >= b 
   	  z = 1; 
   else 
      z = 0; 
   end 


function z = leq(a,b) 
   if a <= b 
   	  z = 1; 
   else 
      z = 0; 
   end 


function z = neq(a,b) 
   if a ~= b 
   	  z = 1; 
   else 
      z = 0; 
   end 


function z = and(varargin) 
		result = 1;		 
		for k=1:nargin 
		   if varargin{k} ~= 1 
		      result = 0; 
		      break; 
		   end 
		end 
		z = result; 


function z = or(varargin) 
		result = 0;		 
		for k=1:nargin 
		   if varargin{k} ~= 0 
		      result = 1; 
		      break; 
		   end 
		end 
		z = result; 


function z = xor(varargin) 
		foundZero = 0; 
		foundOne = 0; 
		for k = 1:nargin 
			if varargin{k} == 0 
			   foundZero = 1; 
			else 
			   foundOne = 1; 
			end 
		end 
		if foundZero && foundOne 
			z = 1; 
		else 
		  z = 0; 
		end 
		 


function z = not(a) 
   if a == 1 
   	  z = 0; 
   else 
      z = 1; 
   end 


function z = root(a,b) 
	z = a^(1/b);