Abstract State Machines 1988-1998: Commented ASM Bibliography

An annotated bibliography of papers which deal with or use Abstract State Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm

Engineering Resilient Collective Adaptive Systems by Self-Stabilisation

Collective adaptive systems are an emerging class of networked computational systems, particularly suited in application domains such as smart cities, complex sensor networks, and the Internet of Things. These systems tend to feature large scale, heterogeneity of communication model (including opportunistic peer-to-peer wireless interaction), and require inherent self-adaptiveness properties to address unforeseen changes in operating conditions. In this context, it is extremely difficult (if not seemingly intractable) to engineer reusable pieces of distributed behaviour so as to make them provably correct and smoothly composable. Building on the field calculus, a computational model (and associated toolchain) capturing the notion of aggregate network-level computation, we address this problem with an engineering methodology coupling formal theory and computer simulation. On the one hand, functional properties are addressed by identifying the largest-to-date field calculus fragment generating self-stabilising behaviour, guaranteed to eventually attain a correct and stable final state despite any transient perturbation in state or topology, and including highly reusable building blocks for information spreading, aggregation, and time evolution. On the other hand, dynamical properties are addressed by simulation, empirically evaluating the different performances that can be obtained by switching between implementations of building blocks with provably equivalent functional properties. Overall, our methodology sheds light on how to identify core building blocks of collective behaviour, and how to select implementations that improve system performance while leaving overall system function and resiliency properties unchanged.Comment: To appear on ACM Transactions on Modeling and Computer Simulatio

A Fixpoint Semantics of Event Systems with and without Fairness Assumptions

We present a fixpoint semantics of event systems. The semantics is presented in a general framework without concerns of fairness. Soundness and completeness of rules for deriving "leads-to" properties are proved in this general framework. The general framework is instantiated to minimal progress and weak fairness assumptions and similar results are obtained. We show the power of these results by deriving sufficient conditions for "leads-to" under minimal progress proving soundness of proof obligations without reasoning over state-traces

PLACES'10: The 3rd Workshop on Programmng Language Approaches to concurrency and Communication-Centric Software

Paphos, Cyprus. March 201

Flexible RNA design under structure and sequence constraints using formal languages

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013