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Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks [article]

Juraj Kolčák, David Šafránek, Stefan Haar, Loïc Paulevé
2018 arXiv   pre-print
Then, an unfolding semantics for Parametric Regulatory Networks is defined, taking advantage of concurrency between transitions to provide a compact representation of reachable transitions.  ...  The modelling of discrete regulatory networks combines a graph specifying the pairwise influences between the variables of the system, and a parametrisation from which can be derived a discrete transition  ...  Main ideas of this paper have been set during JK's and DS's research visits partially supported by Inria and by Université Paris-Sud, France.  ... 
arXiv:1803.06157v1 fatcat:3e6ygno4s5e7hel5jnkasvo6wu

Parameter space abstraction and unfolding semantics of discrete regulatory networks

Juraj Kolčák, David Šafránek, Stefan Haar, Loïc Paulevé
2018 Theoretical Computer Science  
Then, an unfolding semantics for Parametric Regulatory Networks is defined, taking advantage of concurrency between transitions to provide a compact representation of reachable transitions.  ...  The modelling of discrete regulatory networks combines a graph specifying the pairwise influences between the variables of the system, and a parametrisation from which can be derived a discrete transition  ...  Main ideas of this paper have been set during JK's and DS's research visits partially supported by Inria and by Université Paris-Sud, France.  ... 
doi:10.1016/j.tcs.2018.03.009 fatcat:zti7ej3yjzexpbmiuvmsx53g4u

Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics [article]

Stefan Haar, Juraj Kolčák, Loïc Paulevé
2018 arXiv   pre-print
This paper addresses the restriction of the abstract execution of parametric regulatory (discrete) networks by the means of static analysis of reachability properties (goal states).  ...  Parametric models abstract part of the specification of dynamical models by integral parameters.  ...  Parametric Regulatory Networks (PRNs) allow to decouple this specification by having on the one hand a fixed architecture of the network, so-called influence graph, and on the other hand discrete parameters  ... 
arXiv:1811.12377v1 fatcat:76d7yxe3afd2beakgji6k2ihiy

BioModel engineering for multiscale Systems Biology

Monika Heiner, David Gilbert
2013 Progress in Biophysics and Molecular Biology  
We illustrate our approach with case studies demonstrating hierarchical flattening, treatment of space, and hierarchical organisation of space. Ó 2012 Elsevier Ltd. Motivation BioModel Engineering.  ...  We can vary the degree of abstraction and the specific information abstracted away from along each of the following dimensions. 1.  ...  The phase variation in bacterial colony growth case study has been provided by Nigel Saunders [NS] of Brunel University.  ... 
doi:10.1016/j.pbiomolbio.2012.10.001 pmid:23067820 fatcat:mf4cq3jawbbfrgqb6kut5b4equ

Unfolding of Parametric Boolean Networks

Juraj Kolčák, David Šafránek, Stefan Haar, Loïc Paulevé
2018 Electronical Notes in Theoretical Computer Science  
First, we introduce a new compact representation of admissible parameters using Boolean lattices. Then, we define the unfolding of parametric Boolean networks.  ...  In this paper, we focus on partially specified models where the missing information is abstracted in the form of parameters.  ...  The formalization of an extension of our parameter space encoding and unfolding to parametric multivalued regulatory networks is currently under investigation.  ... 
doi:10.1016/j.entcs.2018.03.009 fatcat:5vwiz6lgcbdyvmej3lvn2drf7q

On the Use of Temporal Formal Logic to Model Gene Regulatory Networks [chapter]

Gilles Bernot, Jean-Paul Comet
2010 Lecture Notes in Computer Science  
It is illustrated in the discrete modelling framework of genetic regulatory networks due to René Thomas.  ...  the parameter identication problem.  ...  It is illustrated in the discrete modelling framework of genetic regulatory networks due to René Thomas. 1 Introduction: modelling gene regulatory networks Since the advent of molecular biology, biologists  ... 
doi:10.1007/978-3-642-14571-1_9 fatcat:i5pda6rtf5cdbaxver5nlsi6ca

Integrated regulatory networks (IRNs): Spatially organized biochemical modules

Jean-Louis Giavitto, Hanna Klaudel, Franck Pommereau
2012 Theoretical Computer Science  
The resulting formalisms, called integrated regulatory networks (IRNs) is equipped with a transition systems semantics that preserves the possibility of an enumerative and exhaustive state space exploration  ...  In particular, it can be seen as an extension of logical regulatory networks (à la Thomas) with information about cells' physical state and environment, e.g., their spatial relationships.  ...  Delaplace of the University of Évry and the organizers and participants of MeCBIC'2010 for fruitful discussions and their valuable comments.  ... 
doi:10.1016/j.tcs.2011.12.054 fatcat:uukd3cnavjewjmcx4korzswzaa

Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case

Guy Karlebach, Ron Shamir
2010 BMC Systems Biology  
Mathematical modeling of biological networks is an essential part of Systems Biology. Developing and using such models in order to understand gene regulatory networks is a major challenge.  ...  Conclusion: Our method allows perturbation analysis of regulatory networks and can overcome incomplete information.  ...  Acknowledgements We thank Yoel Kloog and Marcelo Ehrlich for helpful discussions and comments. This study was supported in part by the European Community's  ... 
doi:10.1186/1752-0509-4-15 pmid:20184733 pmcid:PMC2851584 fatcat:mfpakf2wr5cw5cbsb646oihfpm

Action-based analysis of discrete regulatory networks with short-term stimuli

Christian Krause, Carola Krause, Erik P. de Vink
2010 Proceedings of the 8th International Conference on Computational Methods in Systems Biology - CMSB '10  
To incorporate instant effects and different timescales within a single biological system, an extension of discrete regulatory networks with short-term stimuli is proposed.  ...  The approach is implemented by means of a front-end to the mCRL2 tool set and illustrated for the switching of bacteriophage lambda and a bio-medical case study related to TGFβ driven fibrotic conditions  ...  DISCRETE REGULATORY NETWORKS Discrete regulatory networks or generalized logical networks as advocated by Thomas c.s. [35] , constitute a discrete multi-valued abstraction of regulatory networks.  ... 
doi:10.1145/1839764.1839773 dblp:conf/cmsb/KrauseKV10 fatcat:2jog6paaxnefrhoes74h4sne4i

Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks [chapter]

Wolfgang Marwan, Christian Rohr, Monika Heiner
2011 Msphere  
Using the example of phosphate regulation in enteric bacteria, we demonstrate the particular suitability of stochastic Petri nets to model biochemical phenomena and their simulative exploration by various  ...  features of the software tool Snoopy.  ...  Tokens can be interpreted as the available amount of a given species in number of molecules or any abstract, i.e. discrete concentration level.  ... 
doi:10.1007/978-1-61779-361-5_21 pmid:22144165 fatcat:ltlv3x6iijhsfo3xrevqof75mu

Linear cuts in Boolean networks [article]

Aurélien Naldi and Adrien Richard and Elisa Tonello
2022 arXiv   pre-print
We introduce and study the class of networks with linear cuts, where linear components -- intermediates with a single regulator and a single target -- eliminate the aforementioned regulatory conflicts.  ...  Linear cuts provide the base for a new interpretation of the Boolean semantics that captures all behaviours of multi-valued refinements with regulatory thresholds that are uniquely defined for each interaction  ...  Funding AN was supported by the Deutsche Forschungsgemeinschaft (GRK 1772) and French National Research Agency (ANR-MOST project ANR-16-CE18-0029 "BIOPSY").  ... 
arXiv:2203.01620v1 fatcat:smjioe52ezcv3cucmiajkmtjsq

The Mythic Multiverse Through the Scope of Language: The "Procedural Anatomy" of Verbal Modelling

Oleksandr Kolesnyk
2021 Cognitive Studies | Études cognitives  
The Mythic Multiverse Through the Scope of Language: The "Procedural Anatomy" of Verbal ModellingThis article discusses the logical and cognitive premises of verbal world modelling and focuses on the phenomena  ...  of irrationally triggered categorization and myth-oriented semiosis as the fundamental mechanisms of construing alternative realities.  ...  Space occupied by humans [during their life-time]" or, in a more abstract sense, "space occupied by a sustainable system containing energy and capable of multiplication": O.E. woruld, worold "man's age  ... 
doi:10.11649/cs.2447 fatcat:usjumnbllvclhkwpklfmdfsfoq

Algebras of coloured Petri nets

Pommereau Franck
2019 Zenodo  
An implementation of the framework is also presented, as well as applications to the modelling and verification of security protocols, and to the modelling and analysis of biological regulatory networks  ...  Extensions are made in such a way that the underlying model of coloured Petri net is preserved and the usual analysis tools and techniques can still be used.  ...  We rely on a qualitative discrete framework for the modelling of regulatory networks, namely the generalised logical formalism, initially proposed by R. Thomas [105, 106] .  ... 
doi:10.5281/zenodo.3478451 fatcat:okuk6z4gavaklbn4nvprilulxy

Computational analysis of the roles of ER-Golgi network in the cell cycle

Haijun Gong, Lu Feng
2014 BMC Systems Biology  
It is of importance to investigate the roles of ER-Golgi network in the cell cycle progression and some diseases.  ...  ER-Golgi network plays an important role in the processing, sorting and transport of proteins, and it's also a site for many signaling pathways that regulate the cell cycle.  ...  Acknowledgements This work was partially supported by HG's new faculty start-up grant and President's Research Fund award (230152) from the Saint Louis University.  ... 
doi:10.1186/1752-0509-8-s4-s3 pmid:25522186 pmcid:PMC4290691 fatcat:l4x67m7ujzho3kx4v22rujwzd4

Qualitative dynamics semantics for SBGN process description

Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc Paulevé
2016 BMC Systems Biology  
Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters.  ...  Conclusion: The proposed semantics provide a direct formalization of SBGN-PD networks in dynamical qualitative models that can be further analyzed using standard tools for discrete models.  ...  Authors' contributions AR, CF, LC and LP contributed to the intellectual design of the described techniques and to the writing of the paper. AR implemented the automatic identification of stories.  ... 
doi:10.1186/s12918-016-0285-0 pmid:27306057 pmcid:PMC4910245 fatcat:pvlk5iqh5reethauyqff6w5vea
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