Tools, Formats, & Solutions

Survey of literature found 3 interesting ways Petri Nets are usedBioPNML – Petri Nets for BioGJobDL – Petri Nets for Grid ComputingPNML – Petri Net abstraction for everyone!

Tries to create a standard interchange format for bioinformatics

Abstracts biological processes as Petri Nets

Built to resemble PNML, with the same Place, Transition, Arc definitions

Adds Bionet section that defines biochemical processes modeled by the network

Applies the PetriNet model to Grid Computing

Grid resources are mapped to Places, and transitions represent control transfer between resources.

E.g. a process that may run only after two separate processes finish could be modeled with the Petri Net below:

The Petri Net Markup Language project (pnml.org) aims to standardize a Petri Net format.

The previous works reference PNML, but both independently decide to create a new format.While the projects probably could have

integrated with PNML, they likely saw a lack of benefit since no “general” PNML editor could handle their complex extensions to the PN model.

Specification at http://www.pnml.org/papers/cd_1.1.4.pdf

Allows definition of both graphical and logical petri net structures.

High-level element <net> contains multiple <place>, <transition>, and <arc> elements

<place> and <transition> have an id attribute, referenced in <arc source=“id” target=“id”>

Pages allow separation of logical net sections

RefPlace is used to reference a Place defined in a different Page

Page notation just a graphical convenience (pages can easily be merged into one Petri Net), but can be very powerful in designing useful abstractions

PNML can be extended in arbitrary ways.New child tags, attributes, etc.

Unfortunately, a general PNML tool (such as TINA in next slide) will not be able to handle arbitrary extensions in the most useful ways.A particularly robust tool may allow editing

the String values of attributes or tags, but still cannot understand their underlying logic

Many components for PN analysis, but specifically, it includes:nd (NetDraw): An editor for graphically or

textually described Petri nets, Time Petri net and Automata.

Create Place/Transition netsExports to PNML format!

Launch demo

Adds custom behaviors to PNML files Requires purpose-built Petri Net

simulator, acting on the PNML structures and integrated into our SIS SystemCan completely discard visual data, as this

is only useful for design

Program extending the simulator can invoke actions such as PutToken(PlaceNode) directly through a Java API

By building the simulator as an SIS component, other comp.s can signal the PNML Simulator as well

Custom message types can be defined for Petri NetsE.g. PutTokenMsg, TransitionFiredMsg

Using multiple tools to design Petri Nets probably too cumbersome

Merging of design and logic editors would make design more accessible.

Ability to use advanced features of PNM language such as sub-nets, multiple pages, and other Petri Net types.