Motivation Process algebra PEPA Current research The future Process algebra and systems biology Vashti Galpin Laboratory for Foundations of Computer Science School of Informatics University of Edinburgh 7 December 2007 (Thanks to Jane Hillston and Federica Ciocchetta) Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Motivation ◮ process algebra ◮ different model of computation, reactive system ◮ more explicit model than differential equations ◮ leads to multiple types of analysis Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Motivation ◮ process algebra ◮ different model of computation, reactive system ◮ more explicit model than differential equations ◮ leads to multiple types of analysis ◮ usefulness ◮ for systems biology ◮ for computer science ◮ for this seminar Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Motivation ◮ process algebra ◮ different model of computation, reactive system ◮ more explicit model than differential equations ◮ leads to multiple types of analysis ◮ usefulness ◮ for systems biology ◮ for computer science ◮ for this seminar ◮ survey of existing research ◮ what is a process algebra? ◮ what has been done? ◮ what can be done? Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Process algebra ◮ reactive system ◮ nonterminating, inherently parallel ◮ communicates with environment or other systems ◮ computes by reacting to stimuli Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Process algebra ◮ reactive system ◮ nonterminating, inherently parallel ◮ communicates with environment or other systems ◮ computes by reacting to stimuli ◮ process algebra or process calculus ◮ small number of operators to describe processes, compositional ◮ communication between processes by message passing ◮ mathematical definition of semantics ◮ equivalences equate similar processes ◮ established techniques and tools Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Process algebra ◮ reactive system ◮ nonterminating, inherently parallel ◮ communicates with environment or other systems ◮ computes by reacting to stimuli ◮ process algebra or process calculus ◮ small number of operators to describe processes, compositional ◮ communication between processes by message passing ◮ mathematical definition of semantics ◮ equivalences equate similar processes ◮ established techniques and tools ◮ three main approaches ◮ Communicating Sequential Processes (Hoare, Brooke, Roscoe) ◮ Algebra of Communicating Processes (Baeten, Klop) ◮ Calculus of Communicating Systems (Milner) Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Process algebra (continued) ◮ CSP, denotational semantics ◮ processes mapped to mathematical objects, � P � ◮ traces, failures, ready sets ◮ equivalence of processes from equality over these objects P ≡ Q if � P � = � Q � Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Process algebra (continued) ◮ CSP, denotational semantics ◮ processes mapped to mathematical objects, � P � ◮ traces, failures, ready sets ◮ equivalence of processes from equality over these objects P ≡ Q if � P � = � Q � ◮ ACP, algebraic/axiomatic semantics ◮ equations that describe processes with same behaviour P | Q ≡ Q | P ◮ infer other equivalent processes from equations Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Process algebra (continued) ◮ CCS, operational semantics ◮ rules to describe behaviour of operators ◮ process can perform actions, transitions to other processes ◮ behavioural equivalences defined on labelled transition system ◮ bisimulation Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Process algebra (continued) ◮ CCS, operational semantics ◮ rules to describe behaviour of operators ◮ process can perform actions, transitions to other processes ◮ behavioural equivalences defined on labelled transition system ◮ bisimulation ◮ π -calculus ◮ names, channels and data are not distinguished ◮ can express mobility Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Process algebra (continued) ◮ CCS, operational semantics ◮ rules to describe behaviour of operators ◮ process can perform actions, transitions to other processes ◮ behavioural equivalences defined on labelled transition system ◮ bisimulation ◮ π -calculus ◮ names, channels and data are not distinguished ◮ can express mobility ◮ stochastic process algebra ◮ passing of time associated with transitions, random variable ◮ describes dynamic behaviour and properties ◮ PEPA, Performance Evaluation Process Algebra (Hillston) Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future PEPA ◮ CCS-based but uses CSP-type multi-way synchronisation Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future PEPA ◮ CCS-based but uses CSP-type multi-way synchronisation ◮ syntax, PEPA model ◮ P ::= ( α, r ) . P | P + P | P ⊲ ⊳ L P | P / L | C Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future PEPA ◮ CCS-based but uses CSP-type multi-way synchronisation ◮ syntax, PEPA model ◮ P ::= ( α, r ) . P | P + P | P ⊲ ⊳ L P | P / L | C ◮ structured operational semantics, two example rules ( α, r ) ( α, r ) E − − − → E ′ F − − − → F ′ ( α ∈ L ) ( α, r ) ( α, r ) → E ′ ⊲ ( α, r ) . E − − − → E E ⊲ ⊳ L F − − − ⊳ L F ′ Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future PEPA ◮ CCS-based but uses CSP-type multi-way synchronisation ◮ syntax, PEPA model ◮ P ::= ( α, r ) . P | P + P | P ⊲ ⊳ L P | P / L | C ◮ structured operational semantics, two example rules ( α, r ) ( α, r ) E − − − → E ′ F − − − → F ′ ( α ∈ L ) ( α, r ) ( α, r ) → E ′ ⊲ ( α, r ) . E − − − → E E ⊲ ⊳ L F − − − ⊳ L F ′ ◮ can infer transitions using rules, labelled transition system � ⊲ ( α, r ) ◮ � ( α, r ) . P 1 + ( β, s ) . P 2 { α } ( α, r ) . Q ⊳ − − − → P 1 ⊲ ⊳ { α } Q � ⊲ ( β, s ) ◮ � ( α, r ) . P 1 + ( β, s ) . P 2 { α } ( α, r ) . Q ⊳ − − − → P 2 ⊲ { α } ( α, r ) . Q ⊳ Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Systems biology modelling ◮ general approach (Regev, Silverman, Shapiro) Concurrency Molecular Metabolism Signal biology transduction Concurrent molecules enzymes and interacting computational processes metabolites proteins Synchronous molecular binding and binding and communication interaction catalysis catalysis Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Systems biology modelling ◮ general approach (Regev, Silverman, Shapiro) Concurrency Molecular Metabolism Signal biology transduction Concurrent molecules enzymes and interacting computational processes metabolites proteins Synchronous molecular binding and binding and communication interaction catalysis catalysis ◮ molecules as processes or populations as processes? Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Motivation Process algebra PEPA Current research The future Systems biology modelling ◮ general approach (Regev, Silverman, Shapiro) Concurrency Molecular Metabolism Signal biology transduction Concurrent molecules enzymes and interacting computational processes metabolites proteins Synchronous molecular binding and binding and communication interaction catalysis catalysis ◮ molecules as processes or populations as processes? ◮ stochastic model or deterministic model? Vashti Galpin, LFCS, University of Edinburgh Process algebra and systems biology
Recommend
More recommend
