A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Filters
Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks
[article]
2018
arXiv
pre-print
Preserved Fulltext
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
2018
Theoretical Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2018
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2013
Progress in Biophysics and Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2018
Electronical Notes in Theoretical Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2010
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2012
Theoretical Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2010
BMC Systems Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2010
Proceedings of the 8th International Conference on Computational Methods in Systems Biology - CMSB '10
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2012; you can also visit the original URL.
The file type is application/pdf.
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]
2011
Msphere
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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]
2022
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2021
Cognitive Studies | Études cognitives
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2019
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2014
BMC Systems Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2016
BMC Systems Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 1,472 results