1. Tools, Formats, & Solutions

2.  Survey of literature found 3 interesting ways Petri Nets are used  BioPNML – Petri Nets for Bio  GJobDL – Petri Nets for Grid Computing  PNML – Petri Net abstraction for everyone!

3.  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

4.  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:

5.  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.

6.  Specification at http://www.pnml.org/papers/cd_1.1.4.pdf http://www.pnml.org/papers/cd_1.1.4.pdf  Allows definition of both graphical and logical petri net structures.  High-level element contains multiple,, and elements  and have an id attribute, referenced in

7.  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

8.  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

9.  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 nets  Exports to PNML format!

10.  Launch demo Launch demo

11.  Adds custom behaviors to PNML files  Requires purpose-built Petri Net simulator, acting on the PNML structures and integrated into our SIS System  Can completely discard visual data, as this is only useful for design

12.  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 Nets  E.g. PutTokenMsg, TransitionFiredMsg

14.  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.