title: On the impact of discreteness and abstractions on modelling noise in gene regulatory networks.
abstract: In this paper, we explore the impact of different forms of model abstraction and the role of discreteness on the dynamical behaviour of a simple model of gene regulation where a transcriptional repressor negatively regulates its own expression. We first investigate the relation between a minimal set of parameters and the system dynamics in a purely discrete stochastic framework, with the twofold purpose of providing an intuitive explanation of the different behavioural patterns exhibited and of identifying the main sources of noise. Then, we explore the effect of combining hybrid approaches and quasi-steady state approximations on model behaviour (and simulation time), to understand to what extent dynamics and quantitative features such as noise intensity can be preserved.
authors.affiliation: Dip. di Informatica, Università di Pisa, Italy. Electronic address: chiara@di.unipi.it.
authors.forename: Chiara
authors.initials: C
authors.lastname: Bodei
authors.affiliation: Dip. di Matematica e Geoscienze, Università di Trieste, Italy; CNR-ISTI, Pisa, Italy; Modelling and Simulation Group, University of Saarland, Campus E 1 3, Saarbruecken, Germany. Electronic address: luca@dmi.units.it.
authors.forename: Luca
authors.initials: L
authors.lastname: Bortolussi
authors.affiliation: CNR-ISTI, Pisa, Italy; Max Planck Institut of Colloids and Interfaces, Potsdam, Germany. Electronic address: davide.chiarugi@mpikg.mpg.de.
authors.forename: Davide
authors.initials: D
authors.lastname: Chiarugi
authors.affiliation: Systems Biology Ireland, University College Dublin, Ireland. Electronic address: maria.guerriero@astrazeneca.com.
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Guerriero
authors.affiliation: Dip. di Matematica e Informatica, Università di Udine, Udine, Italy. Electronic address: policriti@dimi.uniud.it.
authors.forename: Alberto
authors.initials: A
authors.lastname: Policriti
authors.affiliation: Centre for Integrative Biology (CIBIO), University of Trento, Italy. Electronic address: romanel@science.unitn.it.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Romanel
mesh_terms: D000818:Animals; D003198:Computer Simulation; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D008957:Models, Genetic; D012097:Repressor Proteins / Q000235:genetics; D013269:Stochastic Processes; D015533:Transcriptional Activation
chemical_list: D012097:Repressor Proteins
keywords: Discrete modelling; Gene regulatory networks; Hybrid system; Quasi-steady state approximation; Stochastic noise