Grant Malcolm

A hidden agenda

Our experts consider a hot topic of the day.

Spatio-logical processes in intracellular signalling

Classical models of intracellular signalling describe how small changes in a cells external environment can bring about major changes in cellular activity. Recent findings from experimental biology indicate that many intracellular signalling systems show a high level of spatial organisation. This permits the modification, by protein kinase or protein phosphatase action, of specific subsets of intracellular proteins - an attribute that is not addressed in classical signalling models. Here we use ideas and concepts from computer science to describe the information processing nature of intracellular signalling pathways and the impact of spatial heterogeneity of their components (e.g. protein kinases and protein phosphatases) on signalling activity. We argue that it is useful to view the signalling ecology as a vast parallel distributed processing network of agents operating in heterogeneous microenvironments, and we conclude with an overview of the mathematical and semantic methodologies that might help clarify this analogy between biological and computational systems.

Software Engineering with OBJ

This is an introduction to the philosophy and use of OBJ, emphasizing its operational semantics, with aspects of its history and its logical semantics. Release 2 of OB13 is described in detail, with many examples. OBJ is a wide spectrum first-order functional language that is rigorously based on (order sorted) equationallogic and parameterized programming, supporting a declarative style that facilitates verification and allows OBJ to be used as a theorem prover. Order sorted algebra provides a notion of subsort that rigorously supports mUltiple inheritance, exception handling and overloading. Parameterized programming gives powerful support for design, verification, reuse, and maintenance, using two kinds of module: objects to encapsulate executable code, and in particular to define abstract data types by initial algebra semantics; and (loose) theories to specify both syntactic and semantic properties of modules. Each kind 4 SOFTWARE ENGINEERING WITH OBl of module can be parameterized, where actual parameters may be modules. For parameter instantiation, a view binds the formal entities in an interface theory to actual entities in a module, and also asserts that the target module satisfies the semantic conditions of the interface theory. Module expressions allow complex combinations of already defined modules, including sums, instantiations, and transformations; moreover, evaluating a module expression actually constructs the described software (sub)system from the given components. Default views can greatly reduce the effort of instantiating modules, by allowing obvious correspondences to be left out. We argue that first-order parameterized programming includes much of the power of higher-order programming, in a form that is often more convenient. Although OBI executable code normally consists of equations that are interpreted as rewrite rules, OBJ3 objects can also encapsulate Lisp code, e.g., to provide efficient built-in data types, or to augment the system with new capabilities; we describe the syntax of this facility, and provide some examples. In addition, OBI provides rewriting modulo associative, commutative and/or identity equations, as well as user-definable evaluation strategies that allow lazy, eager, and mixed evaluation strategies on an operator-by-operator basis; memoization is also available on an operator-by-operator basis. In addition, OBJ3 supports the application of equations one at a time, either forwards or backwards; this is needed for equational theorem proving. Finally, OBI provides user-definable mixfix syntax, which supports the notational conventions of particular application domains.

Hidden coinduction: behavioural correctness proofs for objects

This paper unveils and motivates an ambitious programme of hidden algebraic research in software engineering. We begin with an outline of our general goals, continue with an overview of results, and conclude with a discussion of some future plans. The main contribution is powerful hidden coinduction techniques for proving behavioural correctness of concurrent systems, and several mechanical proofs are given using OBJ3. We also show how modularization, bisimulation, transition systems, concurrency and combinations of the functional, constraint, logic and object paradigms fit into hidden algebra.

Signs and Representations: Semiotics for User Interface Design

Goguen has proposed the use of semiotics to study the ways in which information is mediated in computer systems, particularly in user interfaces. His algebraic semiotics provides a formal tool for studying the systematic use of signs in computer systems, and for presenting formal comparisons of different interface designs. The formal elements of algebraic semiotics make it a kind of algebraic engineering for sign systems, and introduces an engineering rigour to interface design.

More Higher Order Programming in OBJ

This paper discusses the use of OBJ3’s parameterized modules for higher order programming, giving examples beyond those in [8, 3, 4] and showing some capabilities that may seem surprising. We also discuss parameterized views, which are not yet implemented, but which we hope soon will be. We assume familiarity with [8], which appears as the first paper in this book.

Developing Algebraic Models of Protein Signalling Agents

This chapter considers a number of ways in which individual molecules in protein signalling systems can be thought of as computational agents. We begin with a general discussion of some of the ways proteins can be viewed from an information processing point of view. The degree of computational prowess shown by many proteins, such as enzymes and transcription factors is discussed; specifically in terms of a number of ‘cognitive’ capacities. We review some of the proteins involved in signalling that make use of transfer of phosphate groups (kinases and phosphatases) and focus attention on the Yeast MAP Kinase cascades. An algebraic approach to modelling certain aspects of protein interactions is introduced. We begin with a simple algebraic model which we describe in some depth, using yeast signalling pathways as an example; we then describe techniques and tools which promise more sophisticated models.