Charlie – An Extensible Petri Net Analysis Tool

Heiner, Monika; Schwarick, Martin; Wegener, Jan-Thierry

doi:10.1007/978-3-319-19488-2_10

Cited by 42 publications

(39 citation statements)

References 27 publications

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“…The Charlie analysis tool (Charlie, version v2.0.194.229) [48] was used to perform structural net analysis. We refined our SPN model until it was fully covered by 1 minimal T-invariant (CTI), such that it represented a full pathway.…”

Section: Methodsmentioning

confidence: 99%

A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease

Somekh

Peleg

Eran

et al. 2016

Journal of Biomedical Informatics

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We propose a model-driven methodology aimed to shed light on complex disorders. Our approach enables exploring shared etiologies of comorbid diseases at the molecular pathway level. The method, Comparative Comorbidities Simulation (CCS), uses stochastic Petri net simulation for examining the phenotypic effects of perturbation of a network known to be involved in comorbidities to predict new roles for mutations in comorbid conditions. To demonstrate the utility of our novel methodology, we investigated the molecular convergence of autism spectrum disorder (ASD) and inflammatory bowel disease (IBD) on the autophagy pathway. In addition to validation by domain experts, we used formal analyses to demonstrate the model’s self-consistency. We then used CCS to compare the effects of loss of function (LoF) mutations previously implicated in either ASD or IBD on the autophagy pathway. CCS identified similar dynamic consequences of these mutations in the autophagy pathway. Our method suggests that two LoF mutations previously implicated in IBD may contribute to ASD, and one ASD-implicated LoF mutation may play a role in IBD. Future targeted genomic or functional studies could be designed to directly test these predictions.

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Section: Methodsmentioning

confidence: 99%

A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease

Somekh

Peleg

Eran

et al. 2016

Journal of Biomedical Informatics

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“…We illustrate how to build corresponding Petri net models and discuss what we can obtain by applying some Petri net analysis techniques. We use the tools Snoopy [14], Charlie [15] and 4ti2 [1] for editing and analysing the Petri net models.…”

Section: Petri Nets For Analysing Trophic Networkmentioning

confidence: 99%

Petri Nets for Modelling and Analysing Trophic Networks

Baldan

Bocci

Brigolin

et al. 2018

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Abstract. We consider trophic networks, a kind of networks used in ecology to represent feeding interactions (what-eats-what) in an ecosystem. We observe that trophic networks can be naturally modelled as Petri nets and this suggests the possibility of exploiting Petri nets for the analysis and simulation of trophic networks. Some preliminary steps in this directions and some ideas for future development are presented.

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“… export to external model checkers for temporal analysis, for example Uppaal [17],  export of a model to Petri net form for the analysis under Charlie Petri net analyzer [18] -to obtain a structural analysis,  alternative formulation of a system as Distributed Automata, for facilitation of a system specification and simulation in terms of distributed components -automata representing server processes or agent processes.…”

Section: Communication Papers Of the Fedcsis Prague 2017mentioning

confidence: 99%

“…The notation is intuitional: server types are defined (lines 2, 9, 16, (formal parameters specify agents and other servers used)). Every server includes states (l.3, 10, 17), services (l. 4,11,18) and actions (l.6-7, 13-14, 20-21) (an action ((a,s,r),(s,v))((a,s',r'),(s,v')) has the form {a.s.r, s.v}→{a.s'.r', s.v'}). Then, server and agent variables are declared (l. [23][24].…”

Section: Simple Example -Buffermentioning

confidence: 99%