PETRI N ET B ASED DEPENDABILITY E NGINEERING OF · PDF filedependability engineering & Petri nets October 2014 [email protected] 1 - 13 / 27 ANOTHER APPLICATION: BIOCHEMICAL SYSTEMS,

dependability engineering & Petri nets October 2014

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Brandenburg Universityof Technology,

Computer Science Institute

PETRI NET BASED

DEPENDABILITY ENGINEERING

OF REACTIVE SYSTEMS

MONIKA HEINER

[email protected]://www.informatik.tu-cottbus.de


[email protected] 1 - 2 / 27

BASIC STRUCTURE

OF REACTIVE SYSTEMS

controller

environment model

plant / devices

actuatorssensors

preprocess

postprocess



feed

bel

t (be

lt 1

)

depo

sit b

elt (

belt

2)

elev

atin

g ro

tary

tabl

e

robo

t

arm

1

arm

2

pres

s

trav

elli

ng c

rane

EX

AM

PL

E, P

RO

DU

CT

ION

CE

LL:

14 s

enso

rs34

com

man

ds



EXAMPLE,CONCURRENT PUSHERS

Pos. 3 Pos. 2

Pus

her

1

R 2

R 1

Pusher 2

M

M

Piece, Pos. 1

Controller 2

R 2

R 1

Controller 1



EXAMPLE,CRUISE CONTROL

❑ pressing on, while car ignition is switched on -> current speed is recorded and

system is enabled

❑ pressing brake, accelerator or off -> system is disabled

❑ pressing resume-> re-enables the system



MOTIVATION

CONCURRENCY IS WIDESPREAD, BUT ERROR PRONE

❑ Therac-25 computerized radiation therapy machine

-> concurrent programming errors contributed toaccidents causing deaths and serious injuries

❑ Mars Rover

-> problems with interaction between concurrenttasks caused periodic software resets reducing availability for exploration

❑ . . .

OBVIOUS QUESTIONS

❑ is a system safe ?

❑ is a system reliable ?

❑ would testing be sufficient to discover all errors ?



PRELIMINARIES

❑ DEPENDABILITY

ability of a systemto fulfill its predefined task(in spite of any hardware and/or software faults)

❑ dependability modelling

❑ engineer’s basic principle:

KEEP EVERYTHING AS SIMPLE AS POSSIBLE!

Which kind of models?

Where do the models come from?

dedicated models for different kinds of properties;



METHODS

MANUAL

COMPUTER-AIDED

FAULT AVOIDANCE

FAULT REMOVAL

FAULT TOLERANCE

FAULT MASKING

FAULT RECOVERY

FAULT PREVENTION

development

operation

DEFENSIVE

DIVERSITY

SOFTWARE DEPENDABILITY

phase

phase

animation / simulation / testing

context checking (static analysis)

consistency checking (verification)

VALIDATION



MODEL BASED

SYSTEM VALIDATION,GENERAL PRINCIPLE

PetrinetzmodelProblemsystem

systemproperties

modelproperties

What was in the beginning ?



MODEL-BASED

SYSTEM VALIDATION,TWO APPROACHES

Petrinetz

Problemproblem

model

implementation

validation

modelling

validation

Petrinetzmodel Petrinetzsystem

Petrinetzsystem



A POSTERIORI MODEL BASED

SYSTEM VALIDATION,PROCESS AND TOOLS

requirements

controller environmentsafety

requirements

compiler modelling

temporal

library

control model

environmentmodel

set oftemporal

composition

systemmodel

verification methods errors /

formulae

logic

functional

inconsistencies



OBJECTTIVE -REUSE OF

CERTIFIED COMPONENTS

REALPROGRAM

DREAMPROGRAM

SAFETY REQUIREMENTS

FUNCTIONALREQUIREMENTS



ANOTHER APPLICATION:BIOCHEMICAL SYSTEMS,

EXAMPLES

❑ metabolic pathways / networks

->stoichiometric relations known

->concentrations of metabolites often known

❑ signal transduction pathways / networks

->stoichiometric relations unknown

->read arcs / test arcs

->inhibitor arcs

❑ gene regulatory networks

-> stoichiometric relations unknown

->mRNA concentrations often known

->protein concentrations are hard to be measured

->often a mixture of metabolic and signal transduction pathways

=>> networks of elementary actions



MODEL- BASED

SYSTEM ENGINEERING

Petrinetzmodel

Problemsystem systemproperties

modelproperties

biochemicalsystem

known

unknown properties

properties

behaviour predictionU

ND

ER

STA

ND

ING validation

GENERALIZATION TO BIOCHEMICAL SYSTEMS



BIONETWORK, EX 1G-PP PATHWAYS

Ru5P4

5

Xu5P

R5P

6S7P

GAP

7E4P

F6P

8

GAP

15

NAD+

+Pi

NADH

G6P F6P10

ATP ADP

FBP11 12

DHAP

13

14ATP ADP

9Gluc

1,3-BPG

ATP ADP

16

ATP ADP

19

NAD+ NADH

203PG

172PGPEP

18PyrLac

NADP+ 2

NADPH 2

2 GSH 2

2 31

2 GSSG

GLYCOLYSIS / PENTOSE PHOSPHATE PATHWAYS IN ERYTHROCYTES

[Reddy 1996]



BIONETWORK, EX 1AS PETRI NET,

VERSION 1

2

22 2

F6PGAP

ATP ADP ADPATP

NADHNAD+ ATP ADP

Lac Pyr PEP 2PG 3PG 1,3-BPG

DHAP

FBP

G6P

Gluc F6P

E4P

GAP

S7P

R5P

Xu5PRu5P

GSH

GSSG NADPH

NADP+

NAD+

ADPATP

Pi

glucose1.spped

NADH

1 2 3

4

5

6 7 8

9 10 11 1213

14

15

1617181920



BIONETWORK, EX2,APOPTOSIS

http://www.genomicObject.net

APOPTOSIS IN MAMMALIAN CELLS



BIONETWORK, EX2,AS PETRI NET,

VERSION 1

s6

s4

s3

s13

s12

s2

s11

s10

s5

s8

s9

s7

s1

Mitochondrion

DNA-Fragment

DNA

DFF40-Oligomer

CleavedDFF45

DFF

Caspase-3

Procaspase-3

Caspase-9

Procaspase-9

(m22)

(m20)

Apaf-1

dATP/ATP

CytochromeC

Bcl-2_Bcl-xL

Apoptotic_Stimuli

Bax_Bad_Bim

BidC-TerminalBid

Caspase-8

Procaspase-8FADD

Fas-Ligand

fas1.spped



BIONETWORK, EX3,POTATO TUBER

R1. SuSy: sucrose synthase Suc + UDP <--> UDPglc + Frc

R2. UGPase: UDPglucose pyrophosphorylaseUDPglc + PP <--> G1P + UTP

R3. PGM: phosphoglucomutase G6P <--> G1P

R4. FK: fructokinase Frc + ATP --> F6P + ADP

R5. PGI: phosphoglucose isomerase G6P <--> F6P

R6. HK: hexokinase Glc + ATP --> G6P +ADP

R7. Inv: invertase Suc --> Glc + Frc

R8. Glyc(b): glycolysis F6P + 29 ADP + 28 Pi --> 29 ATP

R9. SPS: sucrose phospahate synthase F6P + UDPglc <--> S6P + UDP

R10. SPP: sucrose phosphate phosphataseS6P --> Suc + Pi

R11. NDPkin: NDP kinaseUDP + ATP <--> UTP +ADP

R12. SucTrans: sucrose transportereSuc --> Suc

R13. ATPcons(b): ATP consumptionATP --> ADP + Pi

R14. StaSy(b): starch synthesis G6P + ATP --> starch + ADP + PP

R15. AdK: adenylate kinase ATP + AMP <--> 2 ADP

R16: PPase: pyrophosphatase PP --> 2 Pi



BIONETWORK, EX3,AS PETRI NET

22

2

28 29

29

PPase

rStarch

ATPcons(b)

Glyc(b)

geSuc

StaSy(b)

SPP

FKHK

Inv

SucTrans

29 ADPAMP

ATP

28 Pi

28Pi

starch

28Pi

ATP

29 ADP

PP

UDP

29 ADP

ATP

PP

29ADP

ATP

28 Pi

S6P

29 ADP

ATP

29 ADP

ATP

UTP

UDP

G1P

F6P

G6P

UDPglcFrcGlc

eSuc

Suc

7. AdK

6. UGPase

5. NDPkin 4. PGM

3. PGI

2. SPS

1. SuSy

potato.spped



WHY PETRI NETS?

❑ a suitable intermediate representation for

different (specification/programming) languages,

different phases of software development cycle,

different validation methods;

❑ modelling power

partial order (true concurrency) semantics

applicable on any abstraction level

specification of limited resources possible

❑ analyzing power

not restricted to reachability graph

❑ BUT: modelling power <-> analyzing power

❑ integration of qualitative and quantitative analyses



INTEGRATION OF

QUALITATIVE &QUANTITATIVE ANALYSES

net-basedtesting andmonitoring

net-basedqualitativeanalysis

net-basedquantitative

analysis



MODEL

CLASSES

context checking byPetri net theory

verification bytemporal logics

performanceprediction

reliabilityprediction

PETRI NETS

PLACE/TRANSITION

(COLOURED PN)

TIME-DEPENDENT PN

NON-STOCHASTIC

STOCHASTIC

PETRI NET

PETRI NET

PETRI NET

worst-caseevaluation



TOOL

OVERVIEW

❑ Snoopy

design / animation / simulation of Petri nets, e.g.

QPN - XPN - SPN - XSPN - CPN - HPN,

and the coloured counterparts,

... and many more ...

special features

logical places / transitions

macro transition / places

❑ Charlie

standard Petri net analysis techniques, e.g.

structural properties

P/T-invariants

Siphon/Trap Property, rank theorem

reachability/coverability graph

(explicit) CTL model checking

❑ Marcie

QPN - symbolic CTL model checking

SPN - symbolic CSL model checking,

XSPN - simulative PLTLc model checking



CASE STUDIES

ACADEMIC:

❑ botanical garden

❑ low-level mutex algorithm

❑ Dijkstra’s philosophers

❑ Milner’s scheduler

❑ solitaire

❑ . . .

MORE REALISTIC

❑ production cell

❑ concurrent pushers

❑ cruise control

❑ . . .



REFERENCES I

Snoopy

G Czichy (1993)Design and Implementation of a graphical editor for hierarchical Petri net models (inGerman);TU Dresden, Dep. of CS, Master Thesis 1993.

R TIEDEMANN (1997)PED - Hierarchical Petri Net Editor, Manual (in German);BTU Cottbus, Dep. of CS, Internal Techn. Report, May 1997.

T MENZEL (1996)Design and Implementation of a Petri Net Tool Kit Framework Integrating Animation andSimulation (in German); BTU Cottbus, Dep. of CS, Major Individual Project, 1996.

M Fieber (2004)Design and Implementation of a Generic and Adaptive Graph Tool (in German), BTU Cottbus, Dep. of CS, Master Thesis, July 2004

M Heiner, R Richter, M Schwarick (2008)Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms;Proc. PNTAP 2008, associated to SIMUTools 2008, ACM digital library, 2008.

C Rohr, W Marwan, M Heiner (2010)Snoopy - a unifying Petri net framework to investigate biomolecular networks;Bioinformatics 26(7):974-975, 2010.

M Heiner, M Herajy, F Liu, C Rohr, M Schwarick (2012)Snoopy – a unifying Petri net tool;Proc. PETRI NETS 2012, Hamburg, Springer, LNCS 7347, 398-407, June 2012.

Fei Liu (2012)Colored Petri Nets for Systems Biology;PhD thesis, BTU Cottbus, Dep. of CS, January 2012.

M Herajy (2013)Computational Steering of Multi-Scale Biochemical Networks;PhD thesis, BTU Cottbus, Dep. of CS, January 2013.

S Laarz (2013)Scalable Petri nets in Snoopy (in German), BTU Cottbus, Dep. of CS, Master Thesis, Februar 2013



REFERENCES II

Charlie

PH Starke, S Roch (1997) INA - Integrated Net Analyser version 1.7; Technical report, Humbold-Universität zu Berlin, 1997.

M Schwarick (2006):A Tool to analyse Petri net models (in German);BTU Cottbus, Dep. of CS, Master Thesis, September 2006.

A Fischer (2009)Reachability graph analysis of time-dependent Petri nets (in German);BTU Cottbus, Dep. of CS, Master Thesis, Oktober 2009.

A Franzke (2009)Charlie 2.0 - a multi-threaded Petri net analyzer, BTU Cottbus, Dep. of CS, Master Thesis, December 2009

J Wegener, M Schwarick, M Heiner (2011)A Plugin System for Charlie;Proc. CSP 2011, Biaystok University of Technology, 531-554, September 2011.

Marcie

A Noack (1999)A ZBBD Package for Efficient Model Checking of Petri Nets (in German); BTU Cottbus, Dep. of CS, Major Individual Project, 1999.

A Tovchigrechko (2008)Efficient symbolic analysis of bounded Petri nets using Interval Decision Diagrams;PhD thesis, BTU Cottbus, Dep. of CS, October 2008.

M Heiner, M Schwarick, A Tovchigrechko (2009)DSSZ-MC – A Tool for Symbolic Analysis of Extended Petri Nets;Proc. PETRI NETS 2009, Paris, Springer, LNCS, volume 5606, pages 323–332, June 2009

M Schwarick, A Tovchigrechko (2010)IDD-based model validation of biochemical networks;Theoretical Computer Science, July 2010.

M Schwarick, C Rohr, M Heiner (2011)MARCIE - Model checking And Reachability analysis done effiCIEntly;Proc. QEST 2011, Aachen, Germany, IEEE CS Press, pages 91–100, September 2011.

M Heiner, C Rohr, M Schwarick (2013)MARCIE - Model checking And Reachability analysis done effiCIEntly;Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 389–399, June 2013.

M Schwarick (2014)Symbolic on-the-fly analysis of stochastic Petri nets;PhD thesis, BTU Cottbus, Dep. of CS, June 2014.