PIC PIC

Project no. FP6-NEST-2003-1-12789
ESIGNET
Evolving Cell Signalling Networks in Silico

Specific Targeted Research Project
Sixth Framework Programme Priority

Deliverable number 3.1
Cell Signalling Networks: State of the Art Report
Due date of deliverable: April 2006
Actual submission date: April 2006

Start date of project: 2005-09-01 Duration: 36 months

Dublin City University Revision: 1

Project co-funded by the European Commission within the Sixth Framework Programme (2002-2006)
Dissemination Level
PU Public X
PP Restricted to other programme participants (including the Commission Services)
RERestricted to a group specified by the consortium (including the Commission Services)
COConfidential, only for members of the consortium (including the Commission Services)

ESIGNET Members

The first contact is the Coordinator of ESIGNET, Dr Jon Rowe based at the School of Computer Science, University of Birmingham.

The University of Birmingham

Technical University Eindhoven

Dublin City University

Friedrich Schiller University, Jena

Abstract

The overall goal of the ESIGNET project is to study the computational properties of Cell Signaling Networks (CSN) by evolving them using methods from evolutionary computation, and to re-apply this understanding in developing new ways to model and predict real CSNs.

In this report we describe the current state of the art in the field. As this project is highly interdisciplinary, we present a thematic bibliography involving papers from different scientific fields: Biology, Mathematics, Computer Science and Engineering. The various distinguished themes relevant to our project are: Evolution of CSNs, Mathematical analysis of CSNs, Modelling CSNs: concept and example, Reverse engineering of biochemical networks, Synthetic Biology, Real CSNs and Verification of CSN behaviour.

An objective is to develop open-source software packages for scientific use. In this optic, we review the existing computing tools available that might be useful. Main publication resources and research groups concerned in the field are also presented. Finally a glossary of biologigal terms is given as a reference.

Contents
1 Introduction
2 Bibliography
3 Online Databases and Tools
4 Software
5 Publication
6 Selected Research Groups
7 Conclusion
8 Acknowledgements
A Glossary