Call for Papers

Systems Biology Workshop at ECAL 2005

organised by Jan T. Kim

Aims and Scope

Systems biology involves modelling and simulating the complex dynamic interactions between genes, transcripts, proteins, metabolites and cells using integrated systems-based approaches. Encompassing proteomics, transcriptomics, metabolomics and functional genomics, systems biology uses computational and mathematical models to analyse and simulate networks, pathways and the spatial and temporal relationships that give rise to cause and effect in living systems. Such work is of great importance to a better understanding of disease mechanisms, pharmaceutical drug discovery and drug target validation.

from the Introduction to the Systems Biology Journal

Artificial Life is a field of study devoted to understanding life by attempting to abstract the fundamental dynamical principles underlying biological phenomena, and recreating these dynamics in other physical media — such as computers — making them accessible to new kinds of experimental manipulation and testing.

from the preface of Artificial Life II

According to the definitions quoted above, Systems Biology and Artificial Life both involve computer modelling of living systems, and both aim at revealing mechanisms that underlie biological processes and phenomena. Systems Biology is closely associated with analysing "postgenomic" data, coming from novel, high-throughput methods such as microarrays, mass spectroscopy etc. On the other hand, Artificial Life embraces computational models as objects of experimentation. The Systems Biology and Artificial Life communities can mutually benefit from each other. Artificial Life models can be tested using biological data from high-throughput measurements, Systems Biology methods can be evaluated using Artifical Life models, and modelling approaches can be compared and finally be integrated to arrive at advanced models of biological systems.

The Systems Biology workshop at the ECAL 2005 will focus on bringing the Systems Biology and the Artificial Life communities closer together in order to enable such synergies. To achieve this, it will provide an introduction into Systems Biology which is accessible to a general Artificial Life audience, and presentations of research from (the intersection of) Systems Biology and Artificial Life. The workshop intends to bridge gaps and difficulties that result from differences in technical jargon, to increase the awareness of Systems Biology progress in the Artificial Life community, and to give Systems Biology researchers an opportunity to discuss their work under Artificial Life perspectives.

Topics of interest include, but are not limited to

  • Modelling of biological processes in evolutionary biology, ecology, developmental biology, immunology, cell biology and molecular biology
  • Using pattern recognition / machine learning to analyse data from molecular biology
  • Platforms for computational modelling of living systems
  • Applications of Systems Biology in the design of biological and of technical systems
  • Complexity and its emergence in biological processes
  • Self-organization in living systems (cells, organisms, swarms, ecosystems, ...)
  • Dynamics of information in living and life-like systems
  • ...

Developing and strengthening links between Systems Biology and Artificial Life is a major focus of the Systems Biology Workshop at the European Conference on Artificial Life. Therefore, contributions that are accessible and relevant to both fields are especially encouraged. Examples of such work includes generic computational and mathematical modelling approaches and tools, approaches to parameterise such model based on "post-genomic" data sets, application of bio-inspired techniques for analysing such data sets, and more. Furthermore, we also solicit reviews of research in Systems Biology and Artificial Life that are suitable for providing a common basis, enabling communication and collaboration among the communities.

Important Dates

29. May 2005Extended deadline for submissions
15. June 2005Notification of acceptance
22. June 2005Final camera-ready copies due
6. September 2005Systems Biology Workshop at ECAL 2005


All accepted contributions will be published in the ECAL 2005 Workshop Proceedings, which will be provided on CD to all ECAL 2005 workshop participants. In addition, papers accepted for the Workshop will be considered for publication in a special issue of Artificial Life devoted to Systems Biology.


Papers should be formatted according to the instructions for authors provided at the ECAL 2005 website. In addition to full papers, extended abstracts, which must provide reviewers with a self-contained description of content to be presented, are also acceptable.

Publication in the special issue of Artificial Life on Systems Biology is subject to an additional review process.

As specified in the ECAL 2005 instructions for authors, papers have to be submitted as PDF files. Further technical details on the submission process will be posted here in the future.


This workshop is part of the workshop programme at ECAL 2005. Please refer to the ECAL 2005 website for registration details.

Programme Committee

  • J. Andrew Bangham, University of East Anglia
  • Mark A. Bedau, Reed College
  • Dennis Bray, University of Cambridge
  • Peter Dittrich, University of Jena
  • Roland Eils, University of Heidelberg
  • Andrew Finney, University of Hertfordshire
  • Jan T. Kim, University of East Anglia (organiser)
  • Christopher Krause, University of Lübeck
  • Winfried Kurth, Brandenburg University of Technology
  • Thomas Martinetz, University of Lübeck
  • Wolfgang Marwan, University of Magdeburg
  • Eric Minch, Merck Research Laboratories
  • Vincent Moulton, University of East Anglia
  • Chrystopher Nehaniv, University of Hertfordshire
  • Rintaro Saito, Keio University
  • Herbert Sauro, Keck Graduate Institute
  • Markus Schwehm, University of Tübingen
  • Masaru Tomita, Keio University
  • Claus O. Wilke, Keck Graduate Institute
  • Katsuyuki Yugi, Institute for Advanced Biosciences, Keio University

Last change: Thu Jan 26 17:01:16 2006 by Jan T. Kim (