A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets

Gao, Qian; Liu, Fei; Gilbert, David; Heiner, Monika; Tree, David

doi:10.1145/2037509.2037538

Cited by 10 publications

(6 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Coloured Petri nets [ 130 ] provide a means to deal with multiple possible values associated with each place and produce a more compact system representation [ 131 ]. Petri nets can also be defined in discrete and continuous semantics.…”

Section: Modelling Approaches For Biological and Biochemical Systemsmentioning

confidence: 99%

Verifiable biology

Konur

Gheorghe

Krasnogor

2023

J. R. Soc. Interface.

View full text Add to dashboard Cite

The formalization of biological systems using computational modelling approaches as an alternative to mathematical-based methods has recently received much interest because computational models provide a deeper mechanistic understanding of biological systems. In particular, formal verification, complementary approach to standard computational techniques such as simulation, is used to validate the system correctness and obtain critical information about system behaviour. In this study, we survey the most frequently used computational modelling approaches and formal verification techniques for computational biology. We compare a number of verification tools and software suites used to analyse biological systems and biochemical networks, and to verify a wide range of biological properties. For users who have no expertise in formal verification, we present a novel methodology that allows them to easily apply formal verification techniques to analyse their biological or biochemical system of interest.

show abstract

Section: Modelling Approaches For Biological and Biochemical Systemsmentioning

confidence: 99%

Verifiable biology

Konur

Gheorghe

Krasnogor

2023

J. R. Soc. Interface.

View full text Add to dashboard Cite

show abstract

“…Gao et al [18, 19, 52, 53] created a more complex multilevel model of the planar cell polarity in Drosophila wing with hierarchical ColSPNs and ColCPNs. The model considers an array of hexagonal epithelial cells in the wing tissue, and each cell is further divided into seven virtual compartments.…”

Section: Applicationsmentioning

confidence: 99%

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems

Liu

Heiner

Gilbert

2017

Briefings in Bioinformatics

Self Cite

View full text Add to dashboard Cite

Owing to the availability of data of one biological phenomenon at different levels/scales, modelling of biological systems is moving from single level/scale to multiple levels/scales, which introduces a number of challenges. Coloured Petri nets (ColPNs) have been successfully applied to multilevel, multiscale and multidimensional modelling of some biological systems, addressing many of these challenges. In this article, we first review the basics of ColPNs and some popular extensions, and then their applications for multilevel, multiscale and multidimensional modelling of biological systems. This understanding of how to use ColPNs for modelling biological systems will assist readers in selecting appropriate ColPN classes for specific modelling circumstances.

show abstract

“…Processes in process algebra can be attributed with spatial coor-dinates, e.g. (John et al 2010), as can be tokens in colored Petri nets (Gao et al 2011). Rule-based approaches support to combine spatial dynamics of entities relative to each other in form of dynamic nestings and dynamics referring to spatial coordinates, e.g.…”

Section: Modeling Languages -Syntax and Semantics Matter!mentioning

confidence: 99%

Panel on grand challenges for modeling and simulation

Taylor¹,

Fujimoto²,

Page³

et al. 2012

Proceedings Title: Proceedings of the 2012 Winter Simulation Conference (WSC)

View full text Add to dashboard Cite

It has been a decade since the Workshop on Grand Challenge for Modeling & Simulation (M&S) was held at Dagstuhl in Germany (www.dagstuhl.de/02351). Grand challenges provide a critical focal point for research and development and can potentially create the critical mass needed to bring substantial transformation and benefit to a community. The Workshop addressed a wide variety of M&S theoretical, methodological and technological issues across many application areas. This Panel reflects on progress made since the Workshop, new Grand Challenges that have emerged over the past ten years and key M&S milestones for the next decade.

show abstract

A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets

Cited by 10 publications

References 32 publications

Verifiable biology

Verifiable biology

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems

Panel on grand challenges for modeling and simulation

Contact Info

Product

Resources

About