Modeling Static Biological Compartments with Beta-binders

Modeling Static Biological Compartments with Beta-binders Maria Luisa Guerriero1 Corrado Priami1,2 Alessandro Romanel1,2 1 ICT Dept., University of Trento, Italy 2 The Microsoft Research-University of Trento Centre for Computational and Systems Biology, Italy M.L. Guerriero - AB 2007, Hagenberg, Austria

Outline of the talk • Introduction to process algebra and Beta-binders • Beta-binders extensions • Compartments • Localities and locality analysis • An example • Conclusions and future work M.L. Guerriero - AB 2007, Hagenberg, Austria

Process algebras • Languages for modeling concurrent systems • System components are concurrent interacting processes • Pairs of components synchronize by means of complementary input/output actions • Examples: biochemical stochastic п-calculus, BioAmbients, Brane calculus, Beta-binders • Tools and successful applications to biology M.L. Guerriero - AB 2007, Hagenberg, Austria

Beta-binders: an overview • Language of concurrent interacting processes with typed interaction sites • The Abstraction: M.L. Guerriero - AB 2007, Hagenberg, Austria

Interface: interactions Body: internal behavior Beta-binders processes Bio-process Two levels of concurrency: bio-processes and pi-processes P M.L. Guerriero - AB 2007, Hagenberg, Austria

Beta-binders operations • Input/output communications • Operations on interfaces • Merging/splitting of processes intra P’|Q’ P|Q inter P Q P’ Q’ M.L. Guerriero - AB 2007, Hagenberg, Austria

Operations on interfaces expose P P’ hide unhide P’’ P P’ M.L. Guerriero - AB 2007, Hagenberg, Austria

Merging/splitting of processes split P Q R join Q P R M.L. Guerriero - AB 2007, Hagenberg, Austria

B’ B B’’ Compartments: motivations • Beta-binders forbids nesting of bio-processes • Typing of sites virtual nesting • Problem: • Analysis of spatial distribution of objects M.L. Guerriero - AB 2007, Hagenberg, Austria

Compartments hierarchy • i-components (internal to compartments) • b-components (on membranes) 0 0,0 0,1 0,2 0,1,0 M.L. Guerriero - AB 2007, Hagenberg, Austria

Communications and movements • A bio-process can interact with others residing in the same compartment or on its borders • Movement of i-components among compartments: mediated by b-components M.L. Guerriero - AB 2007, Hagenberg, Austria

Movement operations P move 0,0 0,0 Q Q’ 0 in P’ 0,0 P’ move 0,0 0,0 Q Q’ 0 out P 0,0 M.L. Guerriero - AB 2007, Hagenberg, Austria

Localities • Labels on bio-processes: uniquely identify them • Labels on transitions: • Which action is executed? • Which bio-process executes it? • In which compartment it occurs? B1 ||0 B2 B3 ||1 ||0 ||1 ||1 M.L. Guerriero - AB 2007, Hagenberg, Austria

Locality analysis • Compartments locality relations on transitions φi and φj • Analysis of labels κ(φi ) and κ(φj ) • same-compartment κ(φi ) = κ(φj ) • son-father κ(φj ), m = κ(φi ) • father-son κ(φi ), m = κ(φj ) • sub-compartment • super-compartment • Inter-box locality relation on transitions φi and φj • Analysis of labels θ(φi ) and θ(φj ) • same-box M.L. Guerriero - AB 2007, Hagenberg, Austria

cAMP-signalling pathway in OSNs M.L. Guerriero - AB 2007, Hagenberg, Austria

Conclusions • Beta-binders: modeling, analysis and simulation of biological systems • Compartments: representation of static biological compartments, membrane proteins, and movement of molecules across membranes • Locality analysis: spatial relations between entities and between events M.L. Guerriero - AB 2007, Hagenberg, Austria

Future work • Dynamic compartments (creation, destruction, merging, movement of compartments, etc.) • Distinction of transmembrane proteins, internal/external side of membranes • Position of proteins within membranes • Implementation within the Beta Workbench M.L. Guerriero - AB 2007, Hagenberg, Austria

Thank you! M.L. Guerriero - AB 2007, Hagenberg, Austria

Modeling Static Biological Compartments with Beta-binders