The Azimuth Project
Blog - connections: Petri nets and beyond (part 2)

This is an initial outline for part 2 of a blog series.

TODO reiterate key ideas from part 1

Part 1 in this series glossed over a crucial intermediate step when transforming the stochastic Petri net to a system of GNU Octave compatible differential equations. The transformation had two steps, one from Xholon to SBML, and a second from SBML to GNU Octave. This article discusses SBML, and its important role as a transformation hub.

TODO introduce systems biology, SBML, and the large SBxx community

TODO discuss MathML as the SBML syntax for specifying kinetics. Mention the numerous types of kinetics already defined for SBML, and available with many SBML tools.

TODO describe COPASI as an example of a modeling and simulation tool that can process SBML

TODO SBGN as a graphics standard for displaying SBML and similar models

TODO mention SBFC and its uses

SBML has many similarities with reaction networks, and could be used as an interchange format for Petri nets and reaction networks. SBML includes many features that go beyond what’s available with Petri nets and reaction networks.