data structures and software dependability

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Web-based Petri net animation, Sampler

latest change: April 19, 2021, at 10:49 AM

Hints:

• pick a Petri net,
• zoom in/out using the vertical slider,
• increase token number by left mouse click,
• decrease token number by shift+left mouse click,
• select firing strategy (single/intermediate/maximal step),
• animate by clicking 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 is buggy;
• comments do not always appear at the right position;
• splines are not supported

Some basic structures

• to introduce the firing rule: 2H₂ + O₂ → 2H₂O
• some basic scenarios
• metabolic vs. signal transduction networks
• four types of special arcs - available in xpn
• some software patterns - making use of xpn

Some teaching examples

• a simple one-way tramway system
  • branching and joining tracks
  • one-way vs. two-way
  • sequence of one-way steps
  • safety by single distance
  • safety by double distance
• a simple lift controller
• a simple travel planer

Dependability Engineering

• google file system, components
• google file system, subsystem
• google file system

Software fault tolerance

• memorising execution traces
• N-version programming
• recovery block scheme

Some case studies

• combined glycolysis/pentose phosphate pathway in erythrocytes [Reddy 1996], [H98.sld], ...
• apoptosis [GON 2003], [HKW04]
• RKIP/ERK signalling pathway [Cho 2003], ..., [GH06]
  • basic version
  • hierarchical version
• RKIP/ERK signalling pathway, extended version [Calder 2007]
• signalling cascade [Levchenko 2000], [Gilbert 2007]
• repressilator, inspired by [Phillips 2008], animation of logical transition buggy
• self-powered biosensor, template [Gilbert 2008]
• pain switch, two first basic models [Hucho 2008]
• circadian clock [Barkai 2000], [PRISM Tutorial]

. . . more case studies

• Petri nets for multiscale Systems Biology