Activity Networks with Delays An application to toxicity analysis

@article{Delaplace2018ActivityNW,
  title={Activity Networks with Delays An application to toxicity analysis},
  author={Franck Delaplace and Cinzia Di Giusto and Jean-Louis Giavitto and Hanna Klaudel},
  journal={Fundam. Informaticae},
  year={2018},
  volume={160},
  pages={119-142}
}
ANDy , Activity Networks with Delays, is a discrete time framework aimed at the qualitative modelling of time-dependent activities. The modular and concise syntax makes ANDy suitable for an easy and natural modelling of time-dependent biological systems (i.e., regulatory pathways). Activities involve entities playing the role of activators, inhibitors or products of biochemical network operation. Activities may have given duration, i.e., the time required to obtain results. An entity may… 

Figures from this paper

Analysis of Discrete Models for Ecosystem Ecology

The proposed method allows detecting patterns (i.e., ecological processes or sets of processes) in ecosystems and is used to simplify models removing redundant information.

Pattern Matching in Discrete Models for Ecosystem Ecology

A rule-based method allowing to compare ecosystems and to detect patterns in ecosystems, which relies on a measure of similarity and on an optimization algorithm.

ABCD: A User-Friendly Language for Formal Modelling and Analysis

This paper presents an algebra of coloured Petri nets called the Asynchronous Box Calculus with Data, or abcd, which is the first complete and formal presentation of the language and its semantics.

Biomedical Engineering Systems and Technologies: 12th International Joint Conference, BIOSTEC 2019, Prague, Czech Republic, February 22–24, 2019, Revised Selected Papers

Details of a platform for the rehabilitation of people with severe balance impairment, based upon a commercially available static parapodium modified to fit force sensors, designed to give a new, safe tool to physiotherapists are discussed.

References

SHOWING 1-10 OF 43 REFERENCES

Petri net representation of multi-valued logical regulatory graphs

A generic method to qualitatively model regulatory interactions in the standard elementary and coloured Petri net frameworks is proposed, which allows to determine the functionality contexts of regulatory circuits, i.e. constraints on external regulator states enabling the corresponding dynamical properties.

BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge

BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model, and it then becomes possible to analyze, query, verify and maintain the model with respect to those properties.

Integrated regulatory networks (IRNs): Spatially organized biochemical modules

Formal molecular biology

Petri nets for modelling metabolic pathways: a survey

A comprehensive review of recent research on the representation and analysis of metabolic pathways by using Petri nets is presented in order to assess the maturity of the field and the availability of a methodology for modelling a metabolic pathway by a corresponding Petri net.

Membrane Systems with Qualitative Evolution Rules

This paper introduces so-called set membrane systems, a variant of membrane systems with qualitative evolution rules inspired by reaction systems, and relates them to Petri nets which leads to a new class of Petrinets: set-nets with localities.

Reaction Systems with Duration

It is demonstrated that duration/decay is a result of an interaction with a "structured environment", and fundamental properties of state sequences of reaction systems with duration are investigated.

How Might Petri Nets Enhance Your Systems Biology Toolkit

The extent to which the Petri net approach can be used as an umbrella formalism to support the process of BioModel Engineering includes the facilitation of an active and productive interaction between biomodellers and bioscientists during the construction and analysis of dynamic models of biological systems.

Charlie - An Extensible Petri Net Analysis Tool

The tool is in use for model verification of technical systems, especially software-based systems, as well as for model validation of natural systems, i.e. biochemical networks, such as metabolic, signal transduction, and gene regulatory networks.

A synthetic oscillatory network of transcriptional regulators

This work used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli, which periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells.