Low Deficiency Approach

Now that we have constructed the SBML file using the guidelines of CellDesigner Walkthrough, we will proceed by testing the Deficiency Zero and One Theorems of [Fei79]. We will complete this test for Fig1Ci.xml. The first step we must take is importing crnt4sbml. To do this open up a python script and add the following line:

import crnt4sbml

Next, we will take the SBML file created using CellDesigner and import it into the code. This is done by instantiating CRNT with a string representation of the path to the SBML file. An example of this instantiation is as follows:

network = crnt4sbml.CRNT("/path/to/Fig1Ci.xml")

Once this line is ran the class CRNT takes the SBML file and parses it into a Python NetworkX object which is then used to identify the basic Chemical Reaction Network Theory properties of the network. To obtain a full list of what is provided by this instantiation, please see the getter methods of crnt4sbml.CRNT(). To obtain a print out of the number of species, complexes, reactions and deficiency of the network complete the following command:


For the closed portion of the C-graph the output should be as follows:

Number of species: 7
Number of complexes: 9
Number of reactions: 9
Network deficiency: 2

It is important for the user to verify that the number of species, complexes, reactions, and if possible deficiency values are correct at this stage. To provide another check to make sure the parsing and CellDesigner model were constructed correctly, one is encouraged to print the network constructed. To do this, add the following command to the script:


After running this command for the constructed SBML file, the following output is obtained.

Reaction graph of the form
reaction -- reaction label:
s1+s2 -> s3  --  re1
s3 -> s1+s2  --  re1r
s3 -> s6+s2  --  re2
s6+s7 -> s16  --  re3
s16 -> s6+s7  --  re3r
s16 -> s7+s1  --  re4
s1+s6 -> s15  --  re5
s15 -> s1+s6  --  re5r
s15 -> 2*s6  --  re6

Notice that this output describes the reactions in terms of the species’ id and not the species’ name. Along with the reactions, the reaction labels constructed during parsing are also returned. For this example the first reaction s1+s2 -> s3 has a reaction label of ‘re1’ and the reaction s15 -> s1+s6 has a reaction label of ‘re5r’. Please note that the species id and reaction labels may be different if the user has constructed the SBML file themselves. Further information of the network can be found by analyzing the getter methods of crnt4sbml.Cgraph().

Once one has verified that the network and CellDesigner model were created correctly, we can begin to check the properties of the network. If one is only interested in whether or not the network precludes bistability, it is best to first check the Deficiency Zero and One Theorems of Chemical Reaction Network Theory. To do this add the following lines to the script:

ldt = network.get_low_deficiency_approach()

This provides the following output for the closed portion of the C-graph:

The network does not satisfy the Deficiency Zero Theorem, multistability cannot be excluded.
The network does not satisfy the Deficiency One Theorem, multistability cannot be excluded.

For information on the possible output for this run, please see crnt4sbml.LowDeficiencyApproach.report_deficiency_one_theorem() and crnt4sbml.LowDeficiencyApproach.report_deficiency_zero_theorem().