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{\Large  Call for Participation} \\
{\LARGE  \bf The Fourth DIMACS International \\
Algorithm Implementation Challenge:\\ \vspace{.3cm}}
{\LARGE \bf Two Problems in Computational Biology:\\
Fragment Assembly and Genome Rearrangements\\ }

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In conjunction with its Special Year on Mathematical Support for
Molecular Biology, the
Center for Discrete Mathematics and Theoretical Computer Science
(DIMACS) invites participation in an international Implementation Challenge
focussed on two problems from Computational Molecular Biology: 
Fragment Assembly and Genome Rearrangments.
The Implementation Challenge will take place between September 1994 and
August 1995.  Participants are invited to carry out research 
projects related to these problem areas and to present research papers 
at a DIMACS workshop to be held in September 1995.  A
refereed workshop proceedings will be published.
\vspace {-.3cm}
\paragraph{Research Projects.} 

There still is a large gap in Computational Molecular Biology between
biological application and algorithmic work aimed at answering
biological questions. It is the goal of this implementation
challenge to help bridge this gap. {\bf Fragment Assembly} 
is the problem of reconstructing a DNA sequence
knowing only the sequences of many overlapping fragments of it.
{\bf Genome Rearrangments} is the problem of comparing two orders
of genes under the assumption that one order is transformed into another
by a series of rearrangments. For both problems there
exist algorithms and software that in the case of fragment assembly is
widely used. Many forms of contributions are conceivable.
Participants may wish to implement algorithms or use
existing implementations for 
evaluation; participants may develop new algorithms, implement them and
compare to existing ones; participants may formalize the underlying 
biological problem in a new manner and subsequently show the merits of the
resulting algorithms and implementation over existing ones.
Work on other problems from computational molecular 
biology than the suggested ones (for instance the problem
of constructing phylogenies) may be acceptable as well.
The advisory committee is not presently in a position to
provide test instances for such problems, but can arrange
for DIMACS to serve as a clearing house if participants
wish to provide their own.

\vspace {-.3cm}
\paragraph{DIMACS Support.} 

The advisory committee will provide benchmark instances and evaluation 
criteria for the problems. The committee offers the participants
advice and support in their projects throughout the duration of the
implementation challenge. DIMACS 
facilities will provide a clearing-house for exchange of 
programs and data and for communication among researchers.
DIMACS can provide neither financial support for research projects nor 
machine cycles for the experiments.  

{\small\vspace {-.3cm}
\paragraph{How to Participate.} 
Challenge materials will be available via anonymous
ftp from dimacs.rutgers.edu. A document giving general
information on the challenge and the topics will be available 
September 30, 1994. We expect most communication with respect to the
Challenge to take place over the Internet. 
Participants should submit an abstract of their
project.

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\paragraph{Advisory Committee.}  
Ellson Chen, Applied Biosystems,
Sorin Istrail, Sandia National Laboratory,
David Johnson, AT\&T Bell Laboratories,
John Kececioglu, UC Davis,
Joachim Messing, Rutgers University,
Joseph Nadeau, Jackson Laboratory,
Pavel Pevzner, Pennsylvania State University,
Peter Rice, Sanger Center,
Martin Vingron, German National Research Center for Computer Science 
(Coordinator),
Michael Waterman, University of Southern California.}
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