Web-based Petri net animation, Sampler
latest change: 05/14/2013
Hints:
- Pick a Petri net,
- zoom in/out using the vertical slider,
- increase token number by left mouse klick,
- decrease token number by shift+left mouse klick,
- select firing strategy (single/intermediate/maximal step),
- animate by klick on enabled transition or panel button,
. . . and enjoy.
Known bugs:
- does not work with Internet Explorer (xsl technology not supported yet);
- problems occasionally reported with Safari, Chrome;
- Opera has problems with hierarchical nets, initial marking not given;
- seems to work fine with Firefox;
- firing of logical transitions buggy;
- comments appear not always at the right position;
- splines are not supported;
Some Basic Structures
to introduce the firing rule: 2 H2 + O2 -> 2 H2O
some basic scenarios
metabolic versus signal transduction networks
four types of special arcs
some software patterns
Some Teaching Examples
a simple one-way tramway system
a simple tramway system -
branching and joining tracks
a simple tramway system -
one-way vs two-way
a simple tramway system -
sequence of one-way steps
a simple tramway system -
safety by single distance
a simple tramway system -
safety by double distance
a simple lift controller
Some Case Studies
combined glycolysis/pentose phosphate pathway in erythrocytes [Reddy 1994], [Heiner 1998], ...
apoptosis [GON 2003], [Heiner 2004]
RKIP/ERK signalling pathway, basic version [Cho 2003], ... , [Gilbert 2006]
hierarchical version
RKIP/ERK signalling pathway, extended version [Calder 2007]
signalling cascade [Levchenko 2000], [Gilbert 2007]
repressilator, inspired by [Phillips 2008], animation of logical transitions buggy
self-powering biosensor, template [Gilbert 2008]
pain switch, two first basic models [Hucho 2008]
circadian clock [Barkai 2000], [PRISM Tutorial]
. . . t h e e n d . . .
Any comments or questions are welcome. Please direct them to:
snoopy(at)informatik(dot)tu-cottbus(dot)de