Cosimo Laneve

Formal molecular biology

A language of formal proteins, the K-calculus, is introduced. Interactions are modeled at the domain level, bonds are represented by means of shared names, and reactions are required to satisfy a causality requirement of monotonicity.An example of a simplified signalling pathway is introduced to illustrate how standard biological events can be expressed in our protein language. A more comprehensive example, the lactose operon, is also developed, bringing some confidence in the formalism considered as a modeling language.Then a finer-grained concurrent model, the mK-calculus, is considered, where interactions have to be at most binary. We show how to embed the coarser-grained language in the latter, a properly which we call self-assembly.Finally we show how the finer-grained language can itself be encoded in π-calculus, a standard foundational language for concurrency theory.

A Calculus for Long-Running Transactions

We study long-running transactions in open component-based distributed applications, such as Web Services platforms. Long-running transactions describe time-extensive activities that involve several distributed components. Henceforth, in case of failure, it is usually not possible to restore the initial state, and firing a compensation process is preferable. Despite the interest of such transactional mechanisms, a formal modeling of them is still lacking. In this paper we address this issue by designing an extension of the asynchronous π-calculus with long-running transactions (and sequences) – the πt -calculus. We study the practice of πt-calculus, by discussing few paradigmatic examples, and its theory, by defining a semantics and providing a correct encoding of πt-calculus into asynchronous π-calculus.

Foundations of web transactions

A timed extension of π-calculus with a transaction construct – the calculus Webπ – is studied. The underlying model of Webπ relies on networks of processes; time proceeds asynchronously at the network level, while it is constrained by the local urgency at the process level. Namely process reductions cannot be delayed to favour idle steps. The extensional model – the timed bisimilarity – copes with time and asynchrony in a different way with respect to previous proposals. In particular, the discriminating power of timed bisimilarity is weaker when local urgency is dropped. A labelled characterization of timed bisimilarity is also discussed.

A formal account of contracts for web services

We define a formal contract language along with subcontract and compliance relations. We then extrapolate contracts out of processes, that are a recursion-free fragment of ccs. We finally demonstrate that a client completes its interactions with a service provided the corresponding contracts comply. Our contract language may be used as a foundation of Web services technologies, such as wsdl and wscl.

The Must Preorder Revisited

We define a language for Web services contracts as a parallel-free fragment of ccs and we study a natural notion of compliance between clients and services in terms of their corresponding contracts. The induced contract preorder turns out to be valuable in searching and querying registries of Web services, it shows interesting connections with the must preorder, and it exhibits good precongruence properties when choreographies of Web services are considered. Our contract language may be used as a foundation of Web services technologies, such as wsdl and wscl.

Implicit Typing à la ML for the Join-Calculus

We adapt the Damas-Milner typing discipline to the join-calculus. The main result is a new generalization criterion that extends the polymorphism of ML to join-definitions. We prove the correctness of our typing rules with regard to a chemical semantics. We also relate typed extensions of the core join-calculus to functional languages.

Orchestrating Transactions in Join Calculus

We discuss the principles of distributed transactions, then we define an operational model which meets the basic requirements and we give a prototyping implementation for it in join-calculus. Our model: (1) extends BizTalk with multiway transactions; (2) exploits an original algorithm, for distributed commit; (3) can deal with dynamically changing communication topology; (4) is almost language-independent. In fact, the model is based on a two-level classification of resources, which should be easily conveyed to distributed calculi and languages, providing them with a uniform transactional mechanism.

Core formal molecular biology

A core modeling language for Molecular Biology is introduced, where two simple forms of interaction are considered, complexation and activation. This core language is equipped with two sensible bisimulation-based equivalences, and it is shown that interactions involving complex reactants are superfluous up to these notions. Strong compilations in π-calculus are given, following Regevs principle of translating physical connection as private name sharing.

Solos in concert

We present a calculus of mobile processes without prefix or summation, called the solos calculus. Using two different encodings, we show that the solos calculus can express both action prefix and guarded summation. One encoding gives a strong correspondence, but uses a match operator; the other yields a slightly weaker correspondence, but uses no additional operators. We also show that the expressive power of the solos calculus is still retained by the sub-calculus where actions carry at most two names. On the other hand, expressiveness is lost in the solos calculus without match and with actions carrying at most one name.

Graphs for Core Molecular Biology

A graphic language--the graphic ? calculus--modeling protein interactions at the domain level is introduced. Complexation, activation and mixed forms of interaction are expressed as graph rewriting rules. A compilation in a low-level graph rewriting calculus, called mobile ?, is given and shown to be correct up to some suitable notion of observational equivalence. This intermediate language is of independent interest and can be easily implemented in ?-like calculi.