Petri nets are a biologist's best friend

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Abstract

Understanding how genes regulate each other and how gene expression is controlled in living cells is crucial to cure genetic diseases such as cancer and represents a fundamental step towards personalised medicine. The complexity and the high concurrency of gene regulatory networks require the use of formal techniques to analyse the dynamical properties that control cell proliferation and differentiation. However, for these techniques to be used and be useful, they must be accessible to biologists, who are currently not trained to operate with abstract formal models of concurrency. Petri nets, owing to their appealing graphical representation, have proved to be able to bridge this interdisciplinary gap and provide an accessible framework for the construction and execution of biological networks. In this paper, we propose a novel Petri net representation, tightly designed around the classic basic definition of the formalism by introducing only a small number of extensions while making the framework intuitively accessible to a biology-trained audience with no expertise in concurrency theory. Finally, we show how this Petri net framework has been successfully applied in practice to capture haematopoietic stem cell differentiation, and the value of this approach in understanding the heterogeneity of a stem cell population.

Original languageEnglish
Title of host publicationFormal Methods in Macro-Biology
Subtitle of host publicationFirst International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings
PublisherSpringer/Verlag
Pages102-116
Number of pages15
ISBN (Electronic)9783319103976
ISBN (Print)9783319103976
DOIs
Publication statusPublished - 2014
Event1st International Conference on Formal Methods in Macro-Biology, FMMB 2014 - Noumea, New Caledonia
Duration: 22 Sep 201424 Sep 2014

Publication series

NameLecture Notes in Computer Science
PublisherSpringer Verlag
Volume8738
ISSN (Print)0302-9743
Name Lecture Notes in Bioinformatics book sub series (LNBI)
Volume8738

Conference

Conference1st International Conference on Formal Methods in Macro-Biology, FMMB 2014
CountryNew Caledonia
CityNoumea
Period22/09/1424/09/14

Fingerprint

Concurrency
Petri nets
Petri Nets
Cell Differentiation
Stem Cells
Stem cells
Genes
Cell Proliferation
Gene Regulatory Network
Cell Population
Biological Networks
Graphical Representation
Cell proliferation
Formal Model
Expertise
Gene expression
Medicine
Gene Expression
Biology
Cancer

Keywords

  • biology
  • gene regulatory networks
  • Petri nets

Cite this

Bonzanni, N., Feenstra, K. A., Fokkink, W. J., & Heringa, J. (2014). Petri nets are a biologist's best friend. In Formal Methods in Macro-Biology: First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings (pp. 102-116). (Lecture Notes in Computer Science; Vol. 8738), ( Lecture Notes in Bioinformatics book sub series (LNBI); Vol. 8738). Springer/Verlag. https://doi.org/10.1007/978-3-319-10398-3_8
Bonzanni, N. ; Feenstra, K.A. ; Fokkink, W.J. ; Heringa, J. / Petri nets are a biologist's best friend. Formal Methods in Macro-Biology: First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings. Springer/Verlag, 2014. pp. 102-116 (Lecture Notes in Computer Science). ( Lecture Notes in Bioinformatics book sub series (LNBI)).
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Bonzanni, N, Feenstra, KA, Fokkink, WJ & Heringa, J 2014, Petri nets are a biologist's best friend. in Formal Methods in Macro-Biology: First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings. Lecture Notes in Computer Science, vol. 8738, Lecture Notes in Bioinformatics book sub series (LNBI), vol. 8738, Springer/Verlag, pp. 102-116, 1st International Conference on Formal Methods in Macro-Biology, FMMB 2014, Noumea, New Caledonia, 22/09/14. https://doi.org/10.1007/978-3-319-10398-3_8

Petri nets are a biologist's best friend. / Bonzanni, N.; Feenstra, K.A.; Fokkink, W.J.; Heringa, J.

Formal Methods in Macro-Biology: First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings. Springer/Verlag, 2014. p. 102-116 (Lecture Notes in Computer Science; Vol. 8738), ( Lecture Notes in Bioinformatics book sub series (LNBI); Vol. 8738).

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

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Bonzanni N, Feenstra KA, Fokkink WJ, Heringa J. Petri nets are a biologist's best friend. In Formal Methods in Macro-Biology: First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings. Springer/Verlag. 2014. p. 102-116. (Lecture Notes in Computer Science). ( Lecture Notes in Bioinformatics book sub series (LNBI)). https://doi.org/10.1007/978-3-319-10398-3_8