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Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis

Loic Pauleve
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In this paper, we describe a method to reduce a qualitative model for enhancing the tractability of analysis of transient reachability properties.  ...  Qualitative models of dynamics of signalling pathways and gene regulatory networks allow to capture temporal properties of biological networks while requiring few parameters.  ...  Results on model reduction We conducted experiments on Automata Networks (ANs) that model dynamics of biological networks.  ... 
doi:10.1109/tcbb.2017.2749225 pmid:28885158 fatcat:hrkd4jhc7be6xbw5w6gc2mlrqu

Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface [chapter]

Loïc Paulevé
2017 Lecture Notes in Computer Science  
Pint implements formal approximations of transient reachabilityrelated properties, including mutation prediction and model reduction.  ...  The software Pint is devoted to the scalable analysis of the traces of automata networks, which encompass Boolean and discrete networks.  ...  Introduction The computational analysis of the qualitative dynamics of biological networks faces the state space explosion problem, limiting the tractability of detailed models.  ... 
doi:10.1007/978-3-319-67471-1_20 fatcat:cykgyteznzerxgnwsibhe3ossq

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves (+12 others)
2013 BMC Systems Biology  
of biological networks.  ...  We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools.  ...  Acknowledgements Authors thank the members of the SBML qual mailing list for their contributions and/or feedback during the development of the qual package specification.  ... 
doi:10.1186/1752-0509-7-135 pmid:24321545 pmcid:PMC3892043 fatcat:t5bqbcvifze4do5djgi4srvcxm

Boolean modeling in systems biology: an overview of methodology and applications

Rui-Sheng Wang, Assieh Saadatpour, Réka Albert
2012 Physical Biology  
In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean  ...  We finally demonstrate how Boolean models can be applied to perform the structural analysis of cellular networks.  ...  Boolean rule-based structural analysis of cellular networks Boolean dynamic modeling is a powerful tool for analyzing the dynamic characteristics of biological systems.  ... 
doi:10.1088/1478-3975/9/5/055001 pmid:23011283 fatcat:74rmwbgjgnhapj2u7tter4ez6e

Model-Checking an Ecosystem Model for Decision-Aid

Marie-Odile Cordier, Christine Largouet, Yulong Zhao
2014 2014 IEEE 26th International Conference on Tools with Artificial Intelligence  
This work stems on the idea that timed automata models and model-checking techniques may bring much in a decision-aid context when dealing with large and interacting qualitative models.  ...  of the fish species SP0 and SP1.  ...  population dynamics of biological systems [11] .  ... 
doi:10.1109/ictai.2014.87 dblp:conf/ictai/CordierLZ14 fatcat:6psizuhdd5gihocum4vq2ubjfm

Editorial: Foundations of Theoretical Approaches in Systems Biology

Alberto Marin-Sanguino, Julio Vera, Rui Alves
2018 Frontiers in Genetics  
They describe a method in which all possible qualitatively different types of dynamical behavior, or phenotypes, of the system can be mapped from the conceptual representation and identify the parameter  ...  We need general techniques that automatically derive and analyze mathematical models of such reconstructed networks.  ...  Dolatshahi and Voit explore and discuss strategies for model parameters estimation that extend the use of dynamic flux estimation method for the analysis of metabolic time series data to general, slightly  ... 
doi:10.3389/fgene.2018.00290 pmid:30158950 fatcat:mkjqfkf6fvedtdeyr6qxjbvex4

Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit

O. Eriksson, B. Brinne, J. Björkegren, Y. Zhou, J. Tegnér
2009 IET Systems Biology  
The approach which includes utilising biological simplifying conditions, identification of dynamical modules and mathematical reduction of the model complexity may be applicable to other well-characterised  ...  computational model of a protein -protein network.  ...  In addition to topologically largescale networks, there is now an increasing number of publications on the analysis of small-scale mathematical dynamical models of important biological regulatory circuits  ... 
doi:10.1049/iet-syb.2007.0028 pmid:19292565 fatcat:7zacfcrxxndfdlqits4ecn2i6m

Reconciling Qualitative, Abstract, and Scalable Modeling of Biological Networks [article]

Loïc Paulevé, Juraj Kolčák, Thomas Chatain, Stefan Haar
2020 bioRxiv   pre-print
Logical modeling, notably with Boolean Networks (BNs), is a well-established approach which enables reasoning on the qualitative dynamics of networks accounting for many species.  ...  Moreover, MPBNs significantly reduce the complexity of dynamical analysis, enabling to model genome-scale networks.  ...  This research was funded by the French Agence Nationale pour la Recherche (ANR) in the context of ANR-FNR project "AlgoReCell" (ANR-16-CE12-0034)  ... 
doi:10.1101/2020.03.22.998377 fatcat:dxrcgw3hxfe27pt2tioccyxeta

Reconciling qualitative, abstract, and scalable modeling of biological networks

Loïc Paulevé, Juraj Kolčák, Thomas Chatain, Stefan Haar
2020 Nature Communications  
Moreover, MPBNs significantly reduce the complexity of dynamical analysis, enabling to model genome-scale networks.  ...  Logical modeling, notably with Boolean Networks (BNs), is a well-established approach that enables reasoning on the qualitative dynamics of networks.  ...  The authors thank aSciStance Ltd. for their scientific advices and editing services.  ... 
doi:10.1038/s41467-020-18112-5 pmid:32848126 fatcat:a3yrbhjb2fdrpaxtvzkl47vguy

Model Checking of Biological Systems [chapter]

Luboš Brim, Milan Češka, David Šafránek
2013 Lecture Notes in Computer Science  
We present a selection of approaches used for modeling biological systems and formalizing their interesting properties in temporal logics.  ...  Model checking together with other formal methods and techniques is being adapted for applications to biological systems.  ...  BioDiVinE (Barnat et al.[18, 20] ) BioDiVinE 1 is a tool-box for automated analysis of biological systems by means of applying model checking to qualitative and quantitative biological models.  ... 
doi:10.1007/978-3-642-38874-3_3 fatcat:gko33i5f6fe33jl4zi2cdte6ha

ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative-quantitative modeling

S. Streif, A. Savchenko, P. Rumschinski, S. Borchers, R. Findeisen
2012 Bioinformatics  
Often competing hypotheses for biochemical networks exist in the form of different mathematical models with unknown parameters.  ...  The toolbox allows the integration of quantitative measurement data, a priori knowledge of parameters and states, and qualitative information on the dynamic or steady-state behavior.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts137 pmid:22451270 pmcid:PMC3338024 fatcat:jqip5g2aanb57nnufevy7jhzm4

Boolean modeling of biological regulatory networks: A methodology tutorial

Assieh Saadatpour, Réka Albert
2013 Methods  
The combination of network analysis and dynamic modeling enables one to investigate the behavior of the underlying system as a whole and to make experimentally testable predictions for less-understood  ...  In this paper, we present a tutorial on the fundamental steps for Boolean modeling of biological regulatory networks.  ...  The network representation provides a backbone for structural analysis and dynamic modeling of the underlying biological system.  ... 
doi:10.1016/j.ymeth.2012.10.012 pmid:23142247 fatcat:re5ymveeyzenvnhfyelqskdota

Application of Systems Engineering Principles and Techniques in Biological Big Data Analytics: A Review

Q. Peter He, Jin Wang
2020 Processes  
of parsimony in addressing overfitting, the dynamic analysis of biological data, and the role of domain knowledge in biological data analytics.  ...  Different from all existing reviews, this work focuses on the application of systems, engineering principles and techniques in addressing some of the common challenges in big data analytics for biological  ...  dynamic analysis of these networks.  ... 
doi:10.3390/pr8080951 fatcat:7mylwzrcxjdyba7iw6a52pjzde

Noise, transient dynamics, and the generation of realistic interspike interval variation in square-wave burster neurons

Bóris Marin, Reynaldo Daniel Pinto, Robert C. Elson, Eduardo Colli
2014 Physical Review E  
We show that incorporation of dynamical noise into minimal neuron models of square-wave bursting (either conductance-based or abstract) produces signatures akin to those observed in biological examples  ...  We show that noise causes the dynamics to populate a complex transient scaffolding or skeleton in state space, even for models that (without added noise) generate only periodic activity (whether in bursting  ...  Note also that the qualitative resemblance between model and biological isi maps was obtained without special tuning of model parameters.  ... 
doi:10.1103/physreve.90.042718 pmid:25375534 fatcat:bdqpxsyhbvf57oj6pbgwo5rpyy

Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

Réka Albert, Juilee Thakar
2014 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
A fruitful way of modeling interacting biomolecular systems is by network-based dynamic models that characterize each component by a state variable, and describe the change in the state variables due to  ...  Boolean models integrate the body of knowledge regarding the components and interactions of biomolecular systems, and capture the system's dynamic repertoire, for example the existence of multiple cell  ...  This network representation is the basis for structural analysis and dynamic modeling of the biological system.  ... 
doi:10.1002/wsbm.1273 pmid:25269159 fatcat:ahm4jh3upvfyzlc6odniktrsza
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