Beta-binders for Biological Quantitative Experiments (original) (raw)

Formal Executable Descriptions of Biological Systems

2005

The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems.

An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra

Computational Methods in Systems Biology, 2007

The aim of this work is twofold. First, we propose an high level textual modelling language, which is meant to be biologically intuitive and hence easily usable by life scientists in modelling intra-cellular systems. Secondly, we provide an automatic translation of the proposed language into Beta-binders, a bio-inspired process calculus, which allows life scientists to formally analyse and simulate their

PML: Toward a high-level formal language for biological systems

2007

Documentation of knowledge about biological pathways is often informal and vague, making it difficult to efficiently synthesize the work of others into a holistic understanding of a system. Several researchers have proposed solving this problem by modeling pathways using formal languages, which have a precise and consistent semantics. While precise, many of these languages may be too low-level to model feasibly complex pathways.

Constraint Based Languages for Biological Reactions

Abstract. In this paper, we study the modelization of biochemical reaction by using concurrent constraint programming idioms. In particular we will consider the stochastic concurrent constraint programming (sCCP), the Hybrid concurrent constraint programming languages (Hcc) and the Biochemical Abstract Machines (BIOCHAM).

Language Based Techniques for Systems Biology

In this dissertation it is argued that techniques rooted in the theory and practice of programming languages, language based techniques if you will, constitute a strong basis for the investigation of models of biological systems as formalised in a process calculus. In particular it is argued that Static Program Analysis provides a useful approach to the study of qualitative properties of such models. In support of this claim a number of static program analyses are developed for Regev’s BioAmbients – a bio-inspired variant of Cardelli’s Ambient Calculus that incorporates all features of Milner’s π-alculus.

Quantitative and Probabilistic Modeling in Pathway Logic

2007 IEEE 7th International Symposium on BioInformatics and BioEngineering, 2007

This paper presents a study of possible extensions of Pathway Logic to represent and reason about semiquantitative and probabilistic aspects of biological processes. The underlying theme is the annotation of reaction rules with affinity information that can be used in different simulation strategies. Several such strategies were implemented, and experiments carried out to test feasibility, and to compare results of different approaches. Dimerization in the ErbB signalling network, important in cancer biology, was used as a test case.

Process Calculi Abstractions for Biology

Natural Computing Series, 2009

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntaxdriven rules.

A Translation of Beta-binders in a Prioritized Pi-calculus

Electronic Notes in Theoretical Computer Science, 2009

A translation of Beta-binders in pi@ is presented. Beta-binders is a bio-inspired formalism that allows the modelling of processes wrapped into boundaries. No notion of enclosing compartment can instead be found in pi@, a dialect of the pi-calculus where actions are associated with a priority value driving their execution and where channel names can have a composite structure. As recently shown, pi@ is a suitable language for encoding both Bio-Ambients and Brane Calculi, two of the most well-known formalisms for modelling biological scenarios. The translation provided here, which comes together with results about the operational correspondence of Beta-binders processes and their encodings, goes in the direction of assessing pi@ as a platform for investigating the relative expressive power of various bio-inspired languages.

A Stochastic Semantics for BioAmbients

Lecture Notes in Computer Science, 2007

We consider BioAmbients, a calculus for specifying biological entities and for simulating and analysing their behaviour. We extend BioAmbients to take quantitative information into account by defining a stochastic semantics, based on a simulation stochastic algorithm, to determine the actual rate of transitions.

Languages for Biological Models: Importance, Implications and Challenges-A Work In Progress

lukechurch.net

In this paper we outline a new kind of challenge for the Psychology of Programming research community: how do we build programming languages to support modelling biological systems? We argue that such systems tend to be tightly coupled, partially understood and highly complex, and as such rather similar to modern software. We consider design challenges of such systems, including designing for reverse engineering, how to assist social processes and the importance of translucent abstractions. Finally, we consider how answers to these challenges may assist in the design of other domain specific languages.