Maude: specification and programming in rewriting logic

Maude is a high-level language and a high-performance system supporting executable specification and declarative programming in rewriting logic. Since rewriting logic contains equational logic, Maude also supports equational specification and programming in its sublanguage of functional modules and theories. The underlying equational logic chosen for Maude is membership equational logic, that has sorts, subsorts, operator overloading, and partiality definable by membership and equality conditions. Rewriting logic is reflective, in the sense of being able to express its own metalevel at the object level. Reflection is systematically exploited in Maude endowing the language with powerful metaprogramming capabilities, including both user-definable module operations and declarative strategies to guide the deduction process. This paper explains and illustrates with examples the main concepts of Maude's language design, including its underlying logic, functional, system and object-oriented modules, as well as parameterized modules, theories, and views. We also explain how Maude supports reflection, metaprogramming and internal strategies. The paper outlines the principles underlying the Maude system implementation, including its semicompilation techniques. We conclude with some remarks about applications, work on a formal environment for Maude, and a mobile language extension of Maude

High-level signatures and initial semantics

We present a device for specifying and reasoning about syntax for datatypes, programming languages, and logic calculi. More precisely, we study a notion of signature for specifying syntactic constructions. In the spirit of Initial Semantics, we define the syntax generated by a signature to be the initial object---if it exists---in a suitable category of models. In our framework, the existence of an associated syntax to a signature is not automatically guaranteed. We identify, via the notion of presentation of a signature, a large class of signatures that do generate a syntax. Our (presentable) signatures subsume classical algebraic signatures (i.e., signatures for languages with variable binding, such as the pure lambda calculus) and extend them to include several other significant examples of syntactic constructions. One key feature of our notions of signature, syntax, and presentation is that they are highly compositional, in the sense that complex examples can be obtained by assembling simpler ones. Moreover, through the Initial Semantics approach, our framework provides, beyond the desired algebra of terms, a well-behaved substitution and the induction and recursion principles associated to the syntax. This paper builds upon ideas from a previous attempt by Hirschowitz-Maggesi, which, in turn, was directly inspired by some earlier work of Ghani-Uustalu-Hamana and Matthes-Uustalu. The main results presented in the paper are computer-checked within the UniMath system.Comment: v2: extended version of the article as published in CSL 2018 (http://dx.doi.org/10.4230/LIPIcs.CSL.2018.4); list of changes given in Section 1.5 of the paper; v3: small corrections throughout the paper, no major change

Modelling and analysis of biochemical signalling pathway cross-talk

Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical in producing the correct signal-response relationship. Formal models of signalling pathways and cross-talk in particular can aid understanding and drive experimentation. We define an approach to modelling based on the concept that a pathway is the (synchronising) parallel composition of instances of generic modules (with internal and external labels). Pathways are then composed by (synchronising) parallel composition and renaming; different types of cross-talk result from different combinations of synchronisation and renaming. We define a number of generic modules in PRISM and five types of cross-talk: signal flow, substrate availability, receptor function, gene expression and intracellular communication. We show that Continuous Stochastic Logic properties can both detect and distinguish the types of cross-talk. The approach is illustrated with small examples and an analysis of the cross-talk between the TGF-b/BMP, WNT and MAPK pathways

Carnap: an Open Framework for Formal Reasoning in the Browser

This paper presents an overview of Carnap, a free and open framework for the development of formal reasoning applications. Carnap’s design emphasizes flexibility, extensibility, and rapid prototyping. Carnap-based applications are written in Haskell, but can be compiled to JavaScript to run in standard web browsers. This combination of features makes Carnap ideally suited for educational applications, where ease-of-use is crucial for students and adaptability to different teaching strategies and classroom needs is crucial for instructors. The paper describes Carnap’s implementation, along with its current and projected pedagogical applications