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Workshop Report
Workshop on Constraint Based Methods for Bioinformatics
(WCB'07)
Rolf Backofen1, Alessandro Dal Palù2, Sebastian Will1
1Albert-Ludwigs Universität
2Università di Parma
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Editor: Enrico Pontelli
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PDF Version available HERE.
Workshop Web Page: http://www.bioinf.uni-freiburg.de/Events/WCB07
There is a vivid interest in producing new solutions and tools to the
challenging biological problems, since an improvement and/or solution
of one of them can provide significant benefits in medicine,
agriculture, and industry.
To pick out only a few examples, Bioinformatics tackles problems related to
- recognition, analysis, and organization of DNA sequences
- biological systems simulations (for metabolic or regulatory networks)
- prediction of the spatial conformation of a biological polymer, given its sequence of monomers (in particular for proteins and RNA).
The methods to tackle Bioinformatics problems span across various
areas, such as semantics of concurrent processes, string and substring
matching, optimization techniques, just to cite a few. Many of
Bioinformatics hard problems can be naturally formalized by applying
the state-of-the-art techniques of constraint programming. Among
the successfully tackled problems in the area are:
- the fundamental bioinformatics problem of sequence alignment can be solved by recent inference based constraint methods,
- biological systems simulations can be easily designed using concurrent constraint programming, and
- the constrained-based prediction of protein conformations promoted the development of new search strategies, new constraint solvers, and general symmetry breaking.
The WCB'07 workshop, colocated with ICLP'07 in Porto, Portugal, was
organized with the aim of sharing new theoretical and practical results
in the area and to discuss new challenging problems for the declarative
programming and constraint community. The workshop is the
successor of the \emph{Constraints and Bioinformatics/Biocomputing}
workshops colocated with CP'97 and CP'98, and of the WCB workshops at
CP/ICLP'05 in Sitges, Spain and at CP'06 in Nantes, France.
The workshop featured the presentations of seven contributed papers.
Among the discussed topics were the simulation and analysis of
biological systems, constraints for protein folding and pedigree
analysis. The interest of the constraint community in bioinformatics is
witnessed by the number of participants (16), which is still remarkable
since the workshop ran in parallel to other extremely exciting
workshops.
Finally, the workshop enjoyed a lively discussion on promoting the
popularity of biological problems among constraint programmers. Some
the proposals are:
starting a constraint programming contest on biologically motivated
problems and collecting a catalog of challenging bioinformatics
problems that are predestined for constraint techniques. Due to the
lasting interest the series of WCB workshops will be continued in 2008.
Additional information, in particular the workshop proceedings, can be found at http://www.bioinf.uni-freiburg.de/Events/WCB07/.
Finally, we acknowledge the PC members, the external referees, all the
participants, and the ICLP workshop chair Agostino Dovier.
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