Related papers: A Minimal OO Calculus for Modelling Biological Sys…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. We enrich this calculus with a type discipline to guarantee the soundness of reduction rules with respect…
In this paper, we introduce the problem of rewriting finite formal languages using syntactic macros such that the rewriting is minimal in size. We present polynomial-time algorithms to solve variants of this problem and show their…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are…
Capture calculus has recently been proposed as a solution to effect checking, achieved by tracking the captured references of terms in the types. Boxes, along with the box and unbox operations, are a crucial construct in capture calculus,…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
We introduce a new definition of a model for a formal mathematical system. The definition is based upon the substitution in the formal systems, which allows a purely algebraic approach to model theory. This is very suitable for applications…
We introduce a taxonomy of objects for EO programming language. This taxonomy is designed with a few principles in mind: non-redundancy, simplicity, and so on. The taxonomy is supposed to be used as a navigation map by EO programmers. It…
We consider the global minimization of a particular type of minimum structured optimization problems wherein the variables must belong to some basic set, the feasible domain is described by the intersection of a large number of functional…
We describe a process calculus featuring high level constructs for component-oriented programming in a distributed setting. We propose an extension of the higher-order pi-calculus intended to capture several important mechanisms related to…
A type system is introduced for a generic Object Oriented programming language in order to infer resource upper bounds. A sound andcomplete characterization of the set of polynomial time computable functions is obtained. As a consequence,…
Verifying properties of object-oriented software requires a method for handling references in a simple and intuitive way, closely related to how O-O programmers reason about their programs. The method presented here, a Calculus of Object…
We use a labelled deduction system based on the concept of computational paths (sequences of rewrites) as equalities between two terms of the same type. We also define a term rewriting system that is used to make computations between these…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
We propose to use orthologic as the basis for designing type systems supporting intersection, union, and negation types in the presence of subtyping assumptions. We show how to extend orthologic to support monotonic and antimonotonic…
Various formal languages have been proposed in the literature for the individual-based modelling of ecological systems. These languages differ in their treatment of time and space. Each modelling language offers a distinct view and…
Rewriting is a formalism widely used in computer science and mathematical logic. The classical formalism has been extended, in the context of functional languages, with an order over the rules and, in the context of rewrite based languages,…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…