Call for Papers - International Workshop on Computational Methods in Systems Biology 2004 (CMSB’04) Organized by Genoscope, Evry – Génopole, Evry – CNRS – University of Paris VII – BioPathways Consortium

Hotel Meridien Montparnasse, Paris, France 26-28 May, 2004

Deadline : March 1st, 2004

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Molecular biology has traditionally focused mainly on the properties of individual molecules as isolated entities or as components of simple systems. Biological molecules in living systems, however, participate in very complex networks, including regulatory networks for gene expression, intracellular metabolic networks and both intra- and intercellular communication networks. Recent progress in high-throughput data-production technologies – e.g. sequencing allowing the systematic identification of genes and proteins, microarrays or expression proteomics providing large amounts of experimental data on the end-effects of regulation, etc...,– is allowing biologists to progressively root their view of biological function into a detailed understanding of the structure, dynamics and design principles underlying macromolecular networks.

This ambitious research program is sometimes named "systems biology" or “integrative biology”, to emphasize the shift towards a more global view than the gene-centric approach typical of molecular biology, one that focuses on how components work together as a system; it has been characterized in a variety of ways, however, e.g. sometimes with a heavy emphasis on simulation or quantitative approaches. It is also closely related to some parts of the research agenda of the computational biology / bioinformatics community. An essential common denominator is the methodological necessity of an 'experiments -> modelling -> prediction -> experiments' loop. The complexity of signalling, regulatory and metabolic processes taking place within a cell have motivated a series of attempts at modelling these processes to facilitate system description, help simulate or analyze their dynamical behaviour. These attempts have spanned a large spectrum of formalisms, from discrete to continuous, from systems of deterministic or stochastic differential equations to process algebra, Petri-nets, Boolean networks, logical formalisms, state-charts, rewriting systems, constraint programming languages or hybrid automata.

Simultaneously, the view of cellular mechanisms as computational processes has been gaining acceptance, not only for its relevance as a metaphor, but also because of the added explanatory value of concepts such as syntax vs semantics, abstraction, the relationship between a specification and an implementation, and of the promised analytical power of formal tools such as verification techniques or model-checking. As the field matures, it is becoming increasingly obvious that there is probably no 'one-size fits all' formal language for molecular biology, but rather several modelling paradigms, each with its strengths and weaknesses relatively to specific analytical goals. Theoretical arguments supporting one representation over others or actual biological analyses conducted using a formal language and associated formal methods are still lacking. Also, while a model of a biological system should ideally have explanatory or predictive value, and could have applications in understanding the causes of genetic diseases or developing new drugs, most modelling attempts are still far from this degree of maturity.

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The CMSB (Computational Methods in Systems Biology) conference series was established in 2003 by Corrado Priami and several colleagues (see the CMSB’03 web site and the proceedings TOC) to help catalyze the convergence between modellers – physicists, mathematicians, and theoretical computer scientists from fields such as language design, concurrency theory or program verification – and biologists interested in a systems-level understanding of cellular processes.

In order to reflect the complementary scientific motivations underlying existing work in the field, CMSB’04 is soliciting original research articles (including significant works-in-progress) and surveys of current research in either of the following two thematic tracks :

Track A : Formal models for biological systems analysis

This track focuses on theoretical or applied contributions that are motivated by a biological question and can demonstrate either actual or potential usefulness towards answering that question.

Topics of interest in this track include : - Formal models for regulatory, signalling or metabolic networks - Formal methods to analyse biomolecular systems - Qualitative or quantitative analyses of biomolecular systems - Simulation techniques for Systems Biology - Theoretical comparisons between different formal models of cellular processes - Applications of formal techniques to reverse-engineering of biological networks - Methods to predict biological network behavior from incomplete information - Detailed case-studies on how a biological question was successfully addressed using formal models

Note that, since many formal languages are expressive enough to allow for some representation of biological networks, describing a representation of, e.g., signalling networks at a given level of detail in a given language and advocating the use of that language does not necessarily constitute in itself a novel contribution to the field. The introduction of a formal model should be supported by theoretical arguments on the model and/or on the analyses that it enables, by comparisons with other network models, and/or by examples of representation and analysis of a biological system.

Track B : Models of computation inspired by biological processes

This track focuses on contributions that take inspiration from cellular processes to lay down the plans for new computing techniques and paradigms, to study their theoretical properties and applications. Similar motivations led to the definition of neural networks and genetic algorithms, which were neither motivated by biological research nor faithful models of biological systems, but gave birth to a huge field for non-standard programming solutions. The motivation of this track is computational rather than biological.

Topics of interest in this track include : - Definition and study of theoretical properties of biologically-inspired formal languages - Biologically-inspired extensions to concurrency theory, constraint programming or logical methods - Biologically-inspired equivalences - Quantitative formal languages - Models of Self-assembly - Models including symbolic evolution and learning - ODE as a programming language

SUBMISSION GUIDELINES

Authors are invited to submit original research papers or survey papers of no more than 12 pages in .ps or .pdf format. All submissions will be reviewed by the program committee. Accepted papers will be included in the proceedings, which will be published by Springer in the new Lecture Notes in Bioinformatics Series.

We also accept poster proposals in the form of a text-only abstract describing the poster contents.

Papers and posters should be submitted online via the submission page on the CMSB’04 web site (http://www.biopathways.org/CMSB04/). Papers should be formatted according to LNCS guidelines (http://www.springer.de/comp/lncs/authors.html).

IMPORTANT DATES

* March 1, 2004 Submission deadline for papers and demos * March 24, 2004 Notification of acceptance * April 5, 2004 Camera-ready version due * May 26-28, 2004 CMSB’04 Workshop in Paris

PROGRAM COMMITTEE

Gordon Plotkin , University of Edinburgh, (UK) Corrado Priami, University of Trento (IT) Luca Cardelli, Microsoft Research Cambridge (UK) Vincent Danos (co-chair), University of Paris VII (FR) Gilles Bernot, University of Evry (FR) Alexander Bockmayr , Henri Poincaré University, Nancy (FR) François Fages, INRIA Rocquencourt (FR) Walter Fontana, Santa Fe Institute (US) François Kepes, CNRS / Epigenomics Program, Evry (FR) Kurt Kohn, National Cancer Institute, NIH, US Marta Kwiatkowska, University of Birmingham (UK) Nicolas Le Novère, European Bioinformatics Institute (UK) Pat Lincoln, Stanford Research International (US) Satoru Miyano, University of Tokyo (JP) Eric Neumann, Beyond Genomics, Cambridge,US Bernard Palsson, UCSD (US) Vijay Saraswat, Penn State University (US) Vincent Schachter (co-chair), Genoscope (FR) Birgit Schoeberl , MIT (US) Adelinde Uhrmacher, University of Rostock (D) Alfonso Valencia, CNB-CSIC (SP)

CONTACT INFORMATION Conference website :(http://www.biopathways.org/CMSB04/ Contact email : cmsb04@genoscope.cns.fr