Topology analysis

Definitions and examples

From the perspective of topology, we first compared the distribution of reaction degree of species, defined as the number of reactions one species belonged to. We also observed the distribution of reaction distance between a random pair of species, defined as the minimum number of reactions between the two species. As an extreme case, if two species belonged to one reaction, the reaction distance was zero. The figure below shows the two topological distributions of our generated synthetic random signaling networks compared with the signaling networks from the BioModels Database.

Code availability

The Python scripts for the topology analysis of reaction degree distributions and reaction distance distributions were also available on GitHub. The code made use of libSBML with a zip file of SBML files as input and distributions as output.

Using

1. To use the Python script rxn_degree_dist.py to generate reaction degree distributions.

For example, to analyze a set of SBML files of signaling networks downloaded from the BioModels Database.

• First of all, create a folder Biomodels as on GitHub (https://github.com/sys-bio/artificial_random_signaling_network/tree/master/topology_analysis/degree_dist/Biomodels).

• Then, put the zip file of the SBML files into the folder.

• Finally, run the Python script rxn_degree_dist.py.

• The generated results include the degree distribution data saved as degree_dist.txt, the plot of the degree distribution saved as Degree_Distribution.pdf, and the zip file would also get unzipped as a folder BioModels.

Users can use a similar procedure to generate reaction degree distributions for synthetic signaling networks referring to the example on GitHub (https://github.com/sys-bio/artificial_random_signaling_network/tree/master/topology_analysis/degree_dist/synthetic_networks).

2. To use the Python script rxn_distance_dist.py to generate reaction distance distributions.

For example, to analyze a set of SBML files of signaling networks downloaded from BioModels Database.

• First of all, create a folder Biomodels as on GitHub (https://github.com/sys-bio/artificial_random_signaling_network/tree/master/topology_analysis/distance_dist/Biomodels).

• Then, put the zip file of the SBML files into the folder.

• Finally, run the Python script rxn_distance_dist.py.

• The generated results include the distance distribution data saved as distance_dist.txt, the plot of the distance distribution saved as Distance_Distribution.pdf, and the zip file would also get unzipped as a folder BioModels.

Users can use a similar procedure to generate reaction distance distributions for synthetic signaling networks referring to the example on GitHub (https://github.com/sys-bio/artificial_random_signaling_network/tree/master/topology_analysis/distance_dist/synthetic_networks).