Antimony Tutorial

A human-readable, human-writable, model definition language



In [7]:

    
%matplotlib inline
from __future__ import print_function, division
import os.path
import antimony

def _checkAntimonyReturnCode(code):
    """ Helper for checking the antimony response code.
    Raises Exception if error in antimony.

    :param code: antimony response
    :type code: int
    """
    if code < 0:
        raise Exception('Antimony: {}'.format(antimony.getLastError()))

def a2sbml(ant):
    """ Convert Antimony to SBML string.

    :param ant: Antimony string or file
    :type ant: str | file
    :return: SBML
    :rtype: str
    """
    if os.path.isfile(ant):
        code = antimony.loadAntimonyFile(ant)
    else:
        code = antimony.loadAntimonyString(ant)
    _checkAntimonyReturnCode(code)
    mid = antimony.getMainModuleName()
    return antimony.getSBMLString(mid)

Species and Reactions



In [28]:

    
# reversible reaction '->'
a2sbml("""
model reaction_rev
    J0: S1 + E -> ES; k1*k2*S1*E - k2*ES;
    k1 = 3; k2 = 1.4;
    S1 = 30.4; E = 1.2; ES = 2.1;
end
""");

# irreversible reaction '=>'
a2sbml("""
model reaction_rev
    J0: S1 + E => ES; k1*k2*S1*E;
    k1 = 3; k2 = 1.4;
    S1 = 30.4; E = 1.2; ES = 2.1;
end
""");

Modules



In [30]:

    
s = a2sbml("""
model example
S + E -> ES;
end
""");

# reuse model
a2sbml("""
model example
    S + E -> ES;
end

model example2
    example();
end
""");



In [31]:

    
# set values in the included model
a2sbml("""
model example
    S + E -> ES;
end

model example2
    A: example();
    A.S = 3;
end
""");



In [32]:

    
# more complex model composition
a2sbml("""
model example
    S + E -> ES;
end

model example2
    A: example();
    A.S = 3;
end

model example3
    A: example();
    B: example();
    C: example2();
end
""");



In [33]:

    
# use species defined in submodules in new reactions
s = a2sbml("""
model example
    S + E -> ES;
end

model example4
    A: example();
    A.S -> ; kdeg*A.S;
end
""");

When combining multiple submodules, you can also 'attach' them to each other by declaring that a species in one submodule is the same species as is found in a different submodule by using the is keyword.



In [34]:

    
s = a2sbml("""
model side_reaction
    J0: S + E -> SE; k1*k2*S*E - k2*ES;
    S = 5; E = 3;
    SE = E+S;
    k1 = 1.2; k2 = 0.4;
end

model full_reaction
    A: side_reaction();
    B: side_reaction();
    A.S is B.S;
end
""");

If you wanted, you could give the identical species a new name to more easily use it in the full_reaction module:



In [35]:

    
a2sbml("""
model side_reaction
    J0: S + E -> SE; k1*k2*S*E - k2*ES;
    S = 5; E = 3;
    SE = E+S;
    k1 = 1.2; k2 = 0.4;
end

model full_reaction
    var species S;
    A: side_reaction();
    B: side_reaction()
    A.S is S;
    B.S is S;
end
""");

In this system, S is involved in two reversible reactions with exactly the same reaction kinetics and initial concentrations. Let's now say the reaction rate of the second side-reaction takes the same form, but that the kinetics are twice as fast, and the starting conditions are different:



In [36]:

    
a2sbml("""
model side_reaction
    J0: S + E -> SE; k1*k2*S*E - k2*ES;
    S = 5; E = 3;
    SE = E+S;
    k1 = 1.2; k2 = 0.4;
end

model full_reaction
    var species S;
    
    A: side_reaction();
    A.S is S;
    
    B: side_reaction();
    B.S is S;
    B.k1 = 2.4;
    B.k2 = 0.8;
    B.E = 10;
end
""");

Finally, we add a third side reaction, one in which S binds irreversibly, and where the complex it forms degrades. We'll need a new reaction rate, and a whole new reaction as well:



In [37]:

    
a2sbml("""
model side_reaction
    J0: S + E -> SE; k1*k2*S*E - k2*ES;
    S = 5; E = 3;
    SE = E+S;
    k1 = 1.2; k2 = 0.4;
end

model full_reaction
    var species S;
    
    A: side_reaction();
    A.S is S;
    
    B: side_reaction();
    B.S is S;
    B.k1 = 2.4;
    B.k2 = 0.8;
    B.E = 10;
    
    C: side_reaction();
    C.S is S;
    C.J0 = C.k1*C.k2*S*C.E
    J3: C.SE -> ; C.SE*k3;
    k3 = 0.02;
end
""");

For convenience and style, modules may define an interface where some symbols in the module are more easily renamed. To do this, first enclose a list of the symbols to export in parentheses after the name of the model when defining it:



In [38]:

    
a2sbml("""
model side_reaction(S, k1)
    J0: S + E -> SE; k1*k2*S*E - k2*ES;
    S = 5;
    E = 3;
    SE = E+S;
    k1 = 1.2;
    k2 = 0.4;
end
""");

Then when you use that module as a submodule, you can provide a list of new symbols in parentheses:

A: side_reaction(spec2, k2);



In [ ]: