Snoopy—a unifying Petri net framework to investigate biomolecular networks

Röhr, Christian; Marwan, Wolfgang; Heiner, Monika

doi:10.1093/bioinformatics/btq050

Cited by 119 publications

(86 citation statements)

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“…B/S architecture is a program structure based on browser and server running on IIS service information manager. It is a popular program structure [13]. B/S architecture has solved the problem that program cannot access to the Internet.…”

Section: Technologies For Multimedia Teaching Developmentmentioning

confidence: 99%

“…In .Net environment, a unified Internet standard (such as XML) is applied to link different systems together, "alliancetype" supervisory program is implemented to manage active service programs, and a powerful security protection backend is provided for the programs. .NET Framework [13] is a software development platform launched by Microsoft, which mainly supports C# language.…”

Section: Technologies For Multimedia Teaching Developmentmentioning

confidence: 99%

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Design of Multimedia Teaching Platform for Chinese Folk Art Performance Based on Virtual Reality Technology

2017

Int. J. Emerg. Technol. Learn.

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Abstract-Virtual reality (VR) technology can bring us immersive, so it can be widely applied in all professions and trades. The application of multimedia in Chinese folk art performance teaching has many problems and defects, and VR technology can help overcome such problems and defects. This paper aims to develop and design multimedia teaching with VR technology from the aspects of system structure, system function, system multimedia, and system implementation based on the defects in the course of Chinese Folk Art Performance, to combine virtual situations created with VR technology with the teaching of Chinese folk art performance, and decompose classic teaching cases. Contrast experiment shows that the VR-based multiple teaching systems is helpful for students to improve their theoretical knowledge reserve and enhance students' self-regulation of learning, arouse students' learning interest, and improve classroom atmosphere. These findings indicate this teaching design can help students comprehend the teaching contents of Chinese folk art performance, and improve students' learning ability and efficiency.

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Section: Technologies For Multimedia Teaching Developmentmentioning

confidence: 99%

Section: Technologies For Multimedia Teaching Developmentmentioning

confidence: 99%

Design of Multimedia Teaching Platform for Chinese Folk Art Performance Based on Virtual Reality Technology

2017

Int. J. Emerg. Technol. Learn.

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“…All Petri nets were modelled with Snoopy [16] and analysed with MARCIE [13]. The experiments were carried out on a machine with 4x AMD Opteron™ 6276 with 2.3 GHz and 256GB RAM running CentOS 6.…”

Section: Case Studiesmentioning

confidence: 99%

Simulative Model Checking of Steady State and Time-Unbounded Temporal Operators

Röhr

2013

Transactions on Petri Nets and Other Models of Concurrency VIII

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Abstract. When working with large stochastic models simulation remains the only possible analysis technique. Therefore, simulative model checking is the way to go. While finite time horizon algorithms are well known for probabilistic linear-time temporal logic, we provide an infinite time horizon procedure as well as steady state computation, based on exact stochastic simulation algorithms. We demonstrate the approach on models of the RKIP inhibited ERK pathway and angiogenetic process.

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“…This approach has rapidly developed in Systems Biology for reasoning on large interaction networks, with for instance, the analysis of qualitative attractors in a logical dynamics of gene networks à la Thomas [3,4,5], reachability and temporal logic properties in reaction networks [6,7,8,9,10], structural invariants in the Petri net representation of the reactions [11,12,13,14,15,16], or model reductions using graph theory concepts [17,18]. These qualitative analysis tools do not rely on kinetic information, but on the structure of the reaction network which has thus to be correctly written as a set of formal reactions, with well-identified reactants, products and modifiers (and in certain cases their stoichiometry) for each reaction.…”

Section: Introductionmentioning

confidence: 99%

Inferring reaction systems from ordinary differential equations

Fages

Gay

Soliman

2015

Theoretical Computer Science

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In Mathematical Biology, many dynamical models of biochemical reaction systems are presented with Ordinary Differential Equations (ODE). Once kinetic parameter values are fixed, this simple mathematical formalism completely defines the dynamical behavior of a system of biochemical reactions and provides powerful tools for deterministic simulations, parameter sensitivity analysis, bifurcation analysis, etc. However, without requiring any information on the reaction kinetics and parameter values, various qualitative analyses can be performed using the structure of the reactions, provided the reactants, products and modifiers of each reaction are precisely defined. In order to apply these structural methods to parametric ODE models, we study a mathematical condition for expressing the consistency between the structure and the kinetics of a reaction, without restricting to Mass Action law kinetics. This condition, satisfied in particular by standard kinetic laws, entails a remarkable property of independence of the influence graph from the kinetics of the reactions. We derive from this study a heuristic algorithm which, given a system of ODEs as input, computes a system of reactions with the same ODE semantics, by inferring well-formed reactions whenever possible. We show how this strategy is capable of automatically curating the writing of ODE models in SBML, and present some statistics obtained on the model repository biomodels.net. 1 .

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Snoopy—a unifying Petri net framework to investigate biomolecular networks

Abstract: Our tool with Petri net samples is available free of charge for non-commercial use at http://www-dssz.informatik.tu-cottbus.de/snoopy.html; supported operating systems: Mac OS X, Windows and Linux (selected distributions).

Cited by 119 publications

References 1 publication

Design of Multimedia Teaching Platform for Chinese Folk Art Performance Based on Virtual Reality Technology

Design of Multimedia Teaching Platform for Chinese Folk Art Performance Based on Virtual Reality Technology

Simulative Model Checking of Steady State and Time-Unbounded Temporal Operators

Inferring reaction systems from ordinary differential equations

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