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A Formal and Integrated Framework to Simulate Evolution of Biological Pathways [chapter]

Lorenzo Dematté, Corrado Priami, Alessandro Romanel, Orkun Soyer
Lecture Notes in Computer Science  
We present a formal approach to the study of evolution of biological pathways.  ...  The basic idea is to use the Beta Workbench to model and simulate pathway in connection with evolutionary algorithms to implement mutations.  ...  Description of pathway dynamics To study biological evolution of pathways, we need to describe pathway dynamics and an algorithm to simulate pathway evolution from a generation to the next one.  ... 
doi:10.1007/978-3-540-75140-3_8 fatcat:hc7k5jpianhbbpb3stvx3xkyxu

Analysing Biochemical Oscillation through Probabilistic Model Checking

Paolo Ballarini, Radu Mardare, Ivan Mura
2009 Electronical Notes in Theoretical Computer Science  
There are two popular approaches to modelling and verification of biological systems.  ...  Relaying on temporal logic formalisms we investigate the possibility for a query language for stating biological properties of a system's model.  ...  ) model and simulation of a discrete stochastic model.  ... 
doi:10.1016/j.entcs.2009.02.002 fatcat:xvikdggc35etvclo4jld4t3nnu

A Novel Hybrid Logic-ODE Modeling Approach to Overcome Knowledge Gaps

Gianluca Selvaggio, Serena Cristellon, Luca Marchetti
2021 Frontiers in Molecular Biosciences  
We propose a hybrid modeling approach that integrates ordinary differential equations and logical formalism to describe distinct biological layers and their communication.  ...  Mathematical modeling allows using different formalisms to describe, investigate, and understand biological processes.  ...  The presence of Delta ligand ( where Model Integration and Simulations To simulate the pattern development, we integrated the two models.  ... 
doi:10.3389/fmolb.2021.760077 pmid:34988115 pmcid:PMC8721169 fatcat:nakb7mpe7bfjbfdpt72xjxeqca

Modeling formalisms in Systems Biology

Daniel Machado, Rafael S Costa, Miguel Rocha, Eugénio C Ferreira, Bruce Tidor, Isabel Rocha
2011 AMB Express  
We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including  ...  Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes.  ...  Systems and Synthetic Biology for the development of improved microbial cell factories" (MIT-Pt/ BS-BB/0082/2008).  ... 
doi:10.1186/2191-0855-1-45 pmid:22141422 pmcid:PMC3285092 fatcat:ksd26gsezvd3besmbybb5caf34

Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes

S. Sedwards, T. Mazza
2007 Bioinformatics  
The paradigm is flexible and extensible, permitting adaptation to other types of simulation and analysis and integration within standard platforms.  ...  We present Cyto-Sim, a stochastic simulator of membrane-enclosed hierarchies of biochemical processes, where the membranes comprise an inner, outer and integral layer.  ...  We have extended the basic Membrane Systems model to include peripheral and integral membrane proteins [1] and incorporate a Markov chain Monte Carlo algorithm to simulate the time evolution of the system  ... 
doi:10.1093/bioinformatics/btm416 pmid:17855418 fatcat:o2cxrvkw2be5hoz4dacjlm6via

Regenerative Systems - Challenges and Opportunities for Modeling, Simulation, and Visualizationfl

Adelinde M. Uhrmacher, Hans-Jörg Schulz, Heidrun Schumann, Lars Schwabe, Dirk Timmermann
2009 Proceedings of the 4th International ICST Conference on Performance Evaluation Methodologies and Tools  
Among them, variants of the π-calculus formalism, a portfolio of Gillespie related spatial simulation algorithms, means for automatically configuring simulators, and the integrated visualization methods  ...  More and more this ability of biological systems plays a role in designing technical systems, e.g., in sensor networks, as well.  ...  Figure 8 : 8 An integrated view on modeling and simulation applied to a part of the Wnt pathway [56]  ... 
doi:10.4108/icst.valuetools2009.7907 dblp:conf/valuetools/UhrmacherSSST09 fatcat:hiomha7jwzcybgzgcy3ly5eoee

An integrative modeling framework reveals plasticity of TGF-β signaling

Geoffroy Andrieux, Michel Le Borgne, Nathalie Théret
2014 BMC Systems Biology  
Results: Using a new formalism, CADBIOM, which is based on guarded transitions and includes temporal parameters, we have built the first discrete model of TGF-β signaling networks by automatically integrating  ...  Conclusions: As applied here to TGF-β signaling, CADBIOM allows, for the first time, a full integration of highly complex signaling pathways into dynamic models that permit to explore cell responses to  ...  The authors would like to thank Dr. Emmanuel Käs (CNRS UMR 5099, Toulouse, France) for help in writing this manuscript and the GenOuest Bioinformatics Platform for hosting the CADBIOM website.  ... 
doi:10.1186/1752-0509-8-30 pmid:24618419 pmcid:PMC4007780 fatcat:q55ydcqoendevkhdfrnzle5mpq

Hybrid Systems Modeling for (Cancer) Systems Biology [article]

Roel I.J. Dobbe, Claire J. Tomlin
2015 bioRxiv   pre-print
The advent of biological data of increasingly higher resolution in space and time has triggered the use of dynamic models to explain and predict the evolution of biological systems over space and time.  ...  Hybrid systems modeling provides a framework in which both continuous and discrete dynamics can be simulated and analyzed.  ...  This framework is easier to validate than a complete ODE model for large and complex signal pathways, for example to find unknown pathways to match the response to experimental data.  ... 
doi:10.1101/035022 fatcat:dmudhrni2zeirmoydr6qjm2zha

A Sense of Life: Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes

Bud Mishra, Raoul-Sam Daruwala, Yi Zhou, Nadia Ugel, Alberto Policriti, Marco Antoniotti, Salvatore Paxia, Marc Rejali, Archisman Rudra, Vera Cherepinsky, Naomi Silver, William Casey (+24 others)
2003 Omics  
We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure, and computational environment for understanding, experimenting with, manipulating, and modifying  ...  From a biological viewpoint, the basic issues are many: (i) understanding common and shared structural motifs among biological processes; (ii) modeling biological noise due to interactions among a small  ...  We need to develop a framework to integrate them into the larger system effortlessly.  ... 
doi:10.1089/153623103322452387 pmid:14583115 fatcat:dwlspzwk2ng6lk57y2mvlcgaoi

Systems immunology: a survey of modeling formalisms, applications and simulation tools

Vipin Narang, James Decraene, Shek-Yoon Wong, Bindu S. Aiswarya, Andrew R. Wasem, Shiang Rong Leong, Alexandre Gouaillard
2012 Immunologic research  
Particularly, we identify integrative frameworks to facilitate the coupling of different modeling formalisms and modeling the adaptation properties through evolution of immune systems as the next key research  ...  ., signaling pathways) of immune systems in a reductionist manner. In contrast, systems immunology aims to give a synthetic understanding of how these components function together as a whole.  ...  Modeling something as complex as the immune system will require integration of different formalisms in a common multiscale transcale framework.  ... 
doi:10.1007/s12026-012-8305-7 pmid:22528121 fatcat:et6tel52m5bftmia7nnxlgo7jy

Modelling the dynamics of biosystems

C. Priami
2004 Briefings in Bioinformatics  
The need for a more formal handling of biological information processing with stochastic and mobile process algebras is addressed.  ...  Biology can benefit this approach, yielding a better understanding of behavioural properties of cells, and computer science can benefit this approach, obtaining new computational models inspired by nature  ...  In conclusion, each of these approaches captures some of the information regarding pathways and their Exchange languages Integrated frameworks with GUI Approaches based on formal methods components  ... 
doi:10.1093/bib/5.3.259 pmid:15383212 fatcat:kooxjwbrnbgghjketwvsywz2pi

Mathematical Systems Biology: Genomic Cybernetics [chapter]

O. Wolkenhauer, W. Kolch, K.-H. Cho
2004 Natural Computing Series  
The purpose of mathematical systems biology is to investigate genome expression and regulation through mathematical modeling and systems theory in particular.  ...  The principal idea is to treat gene expression and regulatory mechanisms of the cell cycle, morphological development, cell differentiation and environmental responses as controlled dynamic systems.  ...  There is therefore a great need for an integration of mathematical models and to formalize the modeling process itself.  ... 
doi:10.1007/978-3-662-06369-9_17 fatcat:bmfheel4urfjjgzd4yuq6otvmu

A Discrete Event Based Stochastic Simulation Platform for 'In silico' Study of Molecular-level Cellular Dynamics

Simon Daefler
2012 Journal of Biotechnology & Biomaterials  
We present the core components of the simulation framework, called iSimBioSys, which interactively simulates the dynamics of a biological process.  ...  We analyze the effect of extracellular magnesium on the behavioral dynamics of this pathway using our framework and validate the results with a wet-lab experimental system.  ...  The challenge [3] is to develop a modeling technique that can easily integrate the molecular and genetic data together with available pathway and system knowledge, for a quantitative understanding of  ... 
doi:10.4172/2155-952x.s6-001 fatcat:frwma7psk5bcffhmns7mtnpqgq

Toward Integration of Systems Biology Formalism: The Gene Regulatory Networks Case

Raffaella Gentilini
2005 Genome Informatics Series  
We consider the problem of integrating different systems biology formalisms , namely, the process calculi based formalism, the modeling approach based on systems of differential equations , and the one  ...  Tools for extracting and reasoning on (approximate) solutions of S-systems have been recently developed in the literature , and can be exploited to establish a link with automata-based systems biology  ...  In [13, 17] a variant of stochastic 7r-calculus [14] (see Table 1 , below3) is implemented and applied to the simulation of a number of chemical and biological processes , showing evidence of high  ... 
doi:10.11234/gi1990.16.2_215 fatcat:frirnia6crarxmk7nyexxljtsa

Modeling the topological organization of cellular processes

Jean-Louis Giavitto, Olivier Michel
2003 Biosystems (Amsterdam. Print)  
This kind of dynamical systems is very challenging to model and simulate. New programming concepts must be developed to ease their modeling and simulation.  ...  That is, the exact phase space of the system cannot be fixed before the evolution and integrative cell models must state the evolution of the structure jointly with the evolution of the cell state.  ...  Cohen and the members of the "Simulation and Epigenesis" group at GENOPOLE-Evry for fruitful discussions, biological motivations and challenging questions. C. Boin and N.  ... 
doi:10.1016/s0303-2647(03)00037-6 pmid:12915272 fatcat:gy57osup4vec3oyxijp5h3ubl4
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