Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Modelling protein-trafficking with Bio-PEPA Vashti Galpin Laboratory for Foundations of Computer Science School of Informatics University of Edinburgh 29 April 2013 Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Outline Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Process algebras ◮ history ◮ developed to model concurrent computing (mid 1980’s) ◮ focus on dynamic behaviour ◮ originally no notion of time or space, some extensions ◮ Hillston developed PEPA, stochastic process algebra (1996) ◮ Hillston developed ODE interpretation of PEPA (2005) Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Process algebras ◮ history ◮ developed to model concurrent computing (mid 1980’s) ◮ focus on dynamic behaviour ◮ originally no notion of time or space, some extensions ◮ Hillston developed PEPA, stochastic process algebra (1996) ◮ Hillston developed ODE interpretation of PEPA (2005) ◮ Bio-PEPA, a biological process algebra (2009) ◮ close match between modelling artificial and natural systems ◮ developed by Ciocchetta and Hillston ◮ extension of PEPA, functional rates and stoichiometry Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Process algebras (cont) ◮ what is a process algebra? ◮ compact and elegant formal language ◮ behaviour given by semantics defined mathematically ◮ classical process algebras: labelled transition systems ◮ stochastic process algebras: continuous time Markov chains Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Process algebras (cont) ◮ what is a process algebra? ◮ compact and elegant formal language ◮ behaviour given by semantics defined mathematically ◮ classical process algebras: labelled transition systems ◮ stochastic process algebras: continuous time Markov chains ◮ why use Bio-PEPA? ◮ formalism to describe species and their interactions ◮ unambiguous and precise description ◮ different analyses available from a single description stochastic simulation (individual view), continuous time Markov chain with levels (abstract view) deterministic simulation (population view), Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Bio-PEPA (in brief) ◮ species: reactions, stoichiometry, locations def S @ L = ( α 1 , κ 1 ) op 1 S @ L + . . . + ( α n , κ n ) op n S @ L where op i ∈ {↓ , ↑ , ⊕ , ⊖ , ⊙} Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Bio-PEPA (in brief) ◮ species: reactions, stoichiometry, locations def S @ L = ( α 1 , κ 1 ) op 1 S @ L + . . . + ( α n , κ n ) op n S @ L where op i ∈ {↓ , ↑ , ⊕ , ⊖ , ⊙} ◮ model: quantities of species, interaction between species def P = S 1 @ L 1 ( x 1 ) ⊲ ∗ . . . ⊲ ∗ S p @ L p ( x p ) ⊳ ⊳ Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Bio-PEPA (in brief) ◮ species: reactions, stoichiometry, locations def S @ L = ( α 1 , κ 1 ) op 1 S @ L + . . . + ( α n , κ n ) op n S @ L where op i ∈ {↓ , ↑ , ⊕ , ⊖ , ⊙} ◮ model: quantities of species, interaction between species def P = S 1 @ L 1 ( x 1 ) ⊲ ∗ . . . ⊲ ∗ S p @ L p ( x p ) ⊳ ⊳ ◮ other information required for modelling L compartments and locations, dimensionality, sizes N species quantities, minimums, maximums, step size K parameter definitions F functional rates for reactions, definition of f α Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Bio-PEPA (in brief) ◮ species: reactions, stoichiometry, locations def S @ L = ( α 1 , κ 1 ) op 1 S @ L + . . . + ( α n , κ n ) op n S @ L where op i ∈ {↓ , ↑ , ⊕ , ⊖ , ⊙} ◮ model: quantities of species, interaction between species def P = S 1 @ L 1 ( x 1 ) ⊲ ∗ . . . ⊲ ∗ S p @ L p ( x p ) ⊳ ⊳ ◮ other information required for modelling L compartments and locations, dimensionality, sizes N species quantities, minimums, maximums, step size K parameter definitions F functional rates for reactions, definition of f α ◮ definition of behavioural semantics Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Bio-PEPA Eclipse Plug-in ◮ software tool for Bio-PEPA modelling Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Bio-PEPA Eclipse Plug-in ◮ software tool for Bio-PEPA modelling ◮ Eclipse front-end and separate back-end library editor for the Bio-PEPA language parser for the Bio-PEPA language problems view static analysis User Core Interface outline view for the reaction-centric view ISBJava time series analysis (ODE, SSA) graphing support via common plugin export facility (SBML; PRISM) Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Bio-PEPA Eclipse Plug-in ◮ software tool for Bio-PEPA modelling ◮ Eclipse front-end and separate back-end library editor for the Bio-PEPA language parser for the Bio-PEPA language problems view static analysis User Core Interface outline view for the reaction-centric view ISBJava time series analysis (ODE, SSA) graphing support via common plugin export facility (SBML; PRISM) ◮ available for download at www.biopepa.org ◮ case studies, publications, manuals Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Bio-PEPA Eclipse Plug-in (cont) Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Protein trafficking in the cell ◮ research from the Frame laboratory at Cancer Research UK Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Protein trafficking in the cell ◮ research from the Frame laboratory at Cancer Research UK ◮ focus on active form of oncoprotein Src, member of Src family Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Protein trafficking in the cell ◮ research from the Frame laboratory at Cancer Research UK ◮ focus on active form of oncoprotein Src, member of Src family ◮ Src inactive at perinuclear region, active at membrane Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Protein trafficking in the cell ◮ research from the Frame laboratory at Cancer Research UK ◮ focus on active form of oncoprotein Src, member of Src family ◮ Src inactive at perinuclear region, active at membrane ◮ Src is trafficked in endosomes Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
Process algebras Bio-PEPA Protein trafficking Model Results Other examples Conclusion Protein trafficking in the cell ◮ research from the Frame laboratory at Cancer Research UK ◮ focus on active form of oncoprotein Src, member of Src family ◮ Src inactive at perinuclear region, active at membrane ◮ Src is trafficked in endosomes ◮ results of experimental research Vashti Galpin Modelling protein-trafficking with Bio-PEPA 1st Quarterly Edinburgh Bioinformatics Meeting
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