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Algorithmic Bioprocesses |
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Algorithmic Bioprocesses 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:
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.
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:
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