Algorithmic Bioprocesses

3 - 7 December 2007

Venue: Lorentz Center@Oort

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Algorithmic Bioprocesses (foundations, experiments, applications)

The spectacular progress in Information and Communication Technology (ICT) is very much supported by the evolution of computer science which designs and develops the instruments needed for this progress: computers, computer networks, software methodologies, etc. Since ICT has such a tremendous impact on our everyday life, so does computer science. However, there is much more to computer science than ICT: it is the science of information processing, and as such it is a fundamental science for other scientific disciplines.

On the one hand, the only common denominator for research done in all so diverse areas of computer science is thinking about various aspects of information processing. Therefore, frequently used (mostly in Europe) term “Informatics” is much better than “Computer Science” – the latter stipulates that a specific instrument, viz., computer, is the main research topic of our discipline. On the other hand, one of the important developments of the last century for a number of other scientific disciplines is the adoption of Information and Information Processing as their central notions and thinking habits – biology and physics are prime examples here. For these scientific disciplines informatics provides not only instruments but also a way of thinking. One of the Grand Challenges of informatics is to understand the world around us in terms of information processing.

An important example of interdisciplinary research towards such an understanding is the interplay between biosciences and informatics. As an illustration of this research, this workshop will focus on algorithmic bioprocesses, especially including algorithmic self-assembly and RNA folding, algorithmic foundations for biochemical reactions, and algorithmic nature of developmental processes.

We next discuss these focus topics.

Algorithmic self-assembly. Self-assembly is a bottom-up method of constructing superstructures by spontaneous self-ordering of substructures by their selective affinity. It plays central role in molecular computing and in nanoscience in general. Both theoretical and experimental aspects of self-assembly will be covered in the workshop. The three main topics for the workshop are:

Models of self-assembly processes Experimental self-assembly Computing with self-assembly

RNA folding. RNA folding plays important role in both the biology of the cell and in the engineering of molecules. Understanding RNA folding also plays an important role in molecular computing. There is quite a number of computational models for representing the secondary structure of RNA and quite efficient algorithms exist for predicting the secondary RNA structures. It is planned that the workshop reviews the basic methods based on alignment techniques, free energy folding, and grammatical models.

Algorithmic foundations for biochemical reactions. The goal here is to build a foundational, algorithmic understanding of the interaction between components of a cell. As a matter of fact on an abstract level one can see the functioning of a living cell as an interaction between huge number of biochemical reactions (biological components) – this is the point of view of systems biology. In a nutshell it requires the understanding of the information processing that takes place both within and between components.

Algorithmic nature of developmental processes. We have chosen three examples of algorithmic research in this area which will be presented at the workshop.

Computational modeling and insights into C.elegans vulval development using visual languages developed in computer science such as statecharts and live sequence charts to develop a formal dynamic model. Discovering the logic functions of the genomic cis-regularity code in sea urchins. To construct functional maps of the cell, and in particular cis-regulatory maps one is using here logic functions, obtaining in this way the “wiring” of the biological computer that guides the development of the embryo of urchin. Algorithmic botany. This is concerned with modeling, simulation and visualization of plants. It is based on models initially developed in computer science which together with the developed powerful software for simulation and visualization underlies the “virtual laboratory” for performing simulated experiments.

Important feature of the workshop is its interdisciplinarity. As a matter of fact through this workshop we want to demonstrate a multitude of links (mutual feedbacks) between informatics and biosciences. It is planned that a considerable proportion of talks will be of a survey/tutorial character reflecting on the achievements and challenges of this area of interdisciplinary research.

The central themes of the workshop are:

The state of the art of each of the focus themes will presented at the workshop. What has been achieved thus far from the biological and from the computer science points of view? The potential and limitations of the algorithmic methods in the study of bioprocesses. The role of interdisciplinarity in the research themes of the workshop. How does the study of bioprocesses influence our understanding of the notion of computation? Stating challenging, but still realistic, research goals and specific research questions for each of the focus themes. Transferring/modifying existing (computer science) models into the realm of biology versus constructing new models.

    Anne Condon, University of Britisch Columbia  

    Arto Salomaa, Turku Centre for Computer Science  

    David Harel, Weizmann Institute of Science  

    Erik Winfree, Caltech  

    Joost Kok, LIACS  

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