Modular modelling of signalling pathways and their crosstalk

Signalling pathways are well-known abstractions that explain the mechanisms whereby cells respond to signals. Collections of pathways form networks, and interactions between pathways in a network, known as cross-talk, enables further complex signalling behaviours. While there are several formal modelling approaches for signalling pathways, none make cross-talk explicit; the aim of this paper is to define and categorise cross-talk in a rigorous way. We define a modular approach to pathway and network modelling, based on the module construct in the PRISM modelling language, and a set of generic signalling modules. Five different types of cross-talk are defined according to various biologically meaningful combinations of variable sharing, synchronisation labels and reaction renaming. The approach is illustrated with a case-study analysis of cross-talk between the TGF-β, WNT and MAPK pathways

Ten virtues of structured graphs

This paper extends the invited talk by the first author about the virtues of structured graphs. The motivation behind the talk and this paper relies on our experience on the development of ADR, a formal approach for the design of styleconformant, reconfigurable software systems. ADR is based on hierarchical graphs with interfaces and it has been conceived in the attempt of reconciling software architectures and process calculi by means of graphical methods. We have tried to write an ADR agnostic paper where we raise some drawbacks of flat, unstructured graphs for the design and analysis of software systems and we argue that hierarchical, structured graphs can alleviate such drawbacks

Introduction to the 28th International Conference on Logic Programming Special Issue

We are proud to introduce this special issue of the Journal of Theory and Practice of Logic Programming (TPLP), dedicated to the full papers accepted for the 28th International Conference on Logic Programming (ICLP). The ICLP meetings started in Marseille in 1982 and since then constitute the main venue for presenting and discussing work in the area of logic programming

Dagstuhl News January - December 2000

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic

Dagstuhl News January - December 1999

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic