Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP

Saadat Anwar, Chitta Baral, Katsumi Inoue

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

It presents how Petri nets and answer set programming (ASP) can be used to answer simulation-based reasoning questions about biological systems. It shows how Petri nets can be encoded in ASP in an intuitive manner. The chapter discusses how additional Petri net extensions, such as firing semantics, reset arcs, inhibit arcs, read arcs, timed arcs, priority transitions and higher level extensions, such as colored tokens, can be easily encoded by making localized changes to the initial encoding and put these extensions in a biological perspective. The chapters approach is different from others in that it model questions to be answered as interventions and observations on the evolution trajectories of the pathway being modeled. ASP encoding enables easy filtering of Petri Net trajectories through observations. ASP syntax allows more general observations to be easily encoded as compared to encoding such observations directly in Petri Nets.

Original languageEnglish (US)
Title of host publicationLogical Modeling of Biological Systems
Publisherwiley
Pages207-243
Number of pages37
ISBN (Print)9781119005223, 9781848216808
DOIs
StatePublished - Sep 9 2014

Fingerprint

Petri nets
Semantics
Trajectories
Biological systems

Keywords

  • Answer set programming (ASP)
  • Biological pathways
  • Colored tokens
  • Firing semantics
  • Petri nets
  • Priority transitions
  • Simulation-based reasoning
  • Timed arcs

ASJC Scopus subject areas

  • Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Anwar, S., Baral, C., & Inoue, K. (2014). Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP. In Logical Modeling of Biological Systems (pp. 207-243). wiley. https://doi.org/10.1002/9781119005223.ch6

Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP. / Anwar, Saadat; Baral, Chitta; Inoue, Katsumi.

Logical Modeling of Biological Systems. wiley, 2014. p. 207-243.

Research output: Chapter in Book/Report/Conference proceedingChapter

Anwar, S, Baral, C & Inoue, K 2014, Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP. in Logical Modeling of Biological Systems. wiley, pp. 207-243. https://doi.org/10.1002/9781119005223.ch6
Anwar S, Baral C, Inoue K. Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP. In Logical Modeling of Biological Systems. wiley. 2014. p. 207-243 https://doi.org/10.1002/9781119005223.ch6
Anwar, Saadat ; Baral, Chitta ; Inoue, Katsumi. / Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP. Logical Modeling of Biological Systems. wiley, 2014. pp. 207-243
@inbook{614d2062744e45809c8171818ef8e214,
title = "Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP",
abstract = "It presents how Petri nets and answer set programming (ASP) can be used to answer simulation-based reasoning questions about biological systems. It shows how Petri nets can be encoded in ASP in an intuitive manner. The chapter discusses how additional Petri net extensions, such as firing semantics, reset arcs, inhibit arcs, read arcs, timed arcs, priority transitions and higher level extensions, such as colored tokens, can be easily encoded by making localized changes to the initial encoding and put these extensions in a biological perspective. The chapters approach is different from others in that it model questions to be answered as interventions and observations on the evolution trajectories of the pathway being modeled. ASP encoding enables easy filtering of Petri Net trajectories through observations. ASP syntax allows more general observations to be easily encoded as compared to encoding such observations directly in Petri Nets.",
keywords = "Answer set programming (ASP), Biological pathways, Colored tokens, Firing semantics, Petri nets, Priority transitions, Simulation-based reasoning, Timed arcs",
author = "Saadat Anwar and Chitta Baral and Katsumi Inoue",
year = "2014",
month = "9",
day = "9",
doi = "10.1002/9781119005223.ch6",
language = "English (US)",
isbn = "9781119005223",
pages = "207--243",
booktitle = "Logical Modeling of Biological Systems",
publisher = "wiley",

}

TY - CHAP

T1 - Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP

AU - Anwar, Saadat

AU - Baral, Chitta

AU - Inoue, Katsumi

PY - 2014/9/9

Y1 - 2014/9/9

N2 - It presents how Petri nets and answer set programming (ASP) can be used to answer simulation-based reasoning questions about biological systems. It shows how Petri nets can be encoded in ASP in an intuitive manner. The chapter discusses how additional Petri net extensions, such as firing semantics, reset arcs, inhibit arcs, read arcs, timed arcs, priority transitions and higher level extensions, such as colored tokens, can be easily encoded by making localized changes to the initial encoding and put these extensions in a biological perspective. The chapters approach is different from others in that it model questions to be answered as interventions and observations on the evolution trajectories of the pathway being modeled. ASP encoding enables easy filtering of Petri Net trajectories through observations. ASP syntax allows more general observations to be easily encoded as compared to encoding such observations directly in Petri Nets.

AB - It presents how Petri nets and answer set programming (ASP) can be used to answer simulation-based reasoning questions about biological systems. It shows how Petri nets can be encoded in ASP in an intuitive manner. The chapter discusses how additional Petri net extensions, such as firing semantics, reset arcs, inhibit arcs, read arcs, timed arcs, priority transitions and higher level extensions, such as colored tokens, can be easily encoded by making localized changes to the initial encoding and put these extensions in a biological perspective. The chapters approach is different from others in that it model questions to be answered as interventions and observations on the evolution trajectories of the pathway being modeled. ASP encoding enables easy filtering of Petri Net trajectories through observations. ASP syntax allows more general observations to be easily encoded as compared to encoding such observations directly in Petri Nets.

KW - Answer set programming (ASP)

KW - Biological pathways

KW - Colored tokens

KW - Firing semantics

KW - Petri nets

KW - Priority transitions

KW - Simulation-based reasoning

KW - Timed arcs

UR - http://www.scopus.com/inward/record.url?scp=84948978574&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84948978574&partnerID=8YFLogxK

U2 - 10.1002/9781119005223.ch6

DO - 10.1002/9781119005223.ch6

M3 - Chapter

AN - SCOPUS:84948978574

SN - 9781119005223

SN - 9781848216808

SP - 207

EP - 243

BT - Logical Modeling of Biological Systems

PB - wiley

ER -