August 26, 2012
St. Petersburg, Russia
http://bioinf.spbau.ru/be2012/
recombbe2012@gmail.com
OVERVIEW
The Fourth Annual RECOMB Conference on Bioinformatics Education (RECOMB-BE)
will be held in St. Petersburg, Russia, August 26, 2012. The conference follows
the first three RECOMB-BE meetings (see "ADDITIONAL RESOURCES" below).
RECOMB-BE 2012 will consist of invited presentations, oral presentations
selected from submitted educational problems, and discussion panels, all of
which focus on improving bioinformatics education. RECOMB-BE will immediately
precede the RECOMB Satellite Conference on Open Problems in Algorithmic
Biology (RECOMB-AB), which also will be held in St. Petersburg,
August 27-29, 2012 (http:// bioinf.spbau.ru/ab2012).
Saint Petersburg (formerly known as Leningrad) is Russia's second largest city.
The large historic center of Saint Petersburg, threaded with canals dotted with
baroque bridges, is a UNESCO World Heritage site. Its Hermitage Museum, housed
in the former palace of the Russian tsars, displays one of the world's greatest
collections of art.
INVITED SPEAKERS
Michael Brudno (University of Toronto)
Uri Keich (University of Sydney)
Chris Lee (University of California-Los Angeles)
PROGRAM COMMITTEE
Pavel Pevzner (University of California-San Diego) (Co-chair)
Ron Shamir (Tel Aviv University) (Co-chair)
Phillip Compeau (University of California-San Diego)
Ran Libeskind-Hadas (Harvey Mudd College)
Glenn Tesler (University of California-San Diego)
Nikolay Vyahhi (St. Petersburg Academic University)
GOALS
The goals of RECOMB-BE 2012 are twofold: to showcase best practices of teaching
algorithmic bioinformatics and to demonstrate and discuss a novel learning
framework (ROSALIND) for students to understand bioinformatics problems through
programming within a guided feedback environment.
While biology has been transformed into a computational science in the
last decade, the biological curriculum remains largely unchanged with
respect to computational issues. The question: "How should we teach
bioinformatics to biology students?" has become of the utmost importance,
as many universities have not only founded undergraduate bioinformatics
programs but are considering the addition of new computational courses to
the standard biology curriculum—a change that would represent a dramatic
paradigm shift in biology education.
ROSALIND
The usual process of learning bioinformatics requires the solution of
computational problems of varying difficulty that are extracted from real
challenges of molecular biology. In an attempt to make this learning
experience as effective as possible, we have founded ROSALIND, an independent
programming and testing environment that will host a resource of
self-contained bioinformatics problems. The ROSALIND website will check
solutions to these problems automatically and will provide interested students
with an intellectually stimulating way to learn the key concepts and
algorithms of bioinformatics online. By its innovative approach,
ROSALIND also promises to facilitate improvements in standard bioinformatics
education by providing a vital teaching aid.
ROSALIND is inspired by Project Euler (http://projecteuler.net/) ,
Google Code Jam contests (http://code.google.com/codejam/) ,
and free online courses from Stanford University
(http://www.class-central.com/) .
The project's name commemorates Rosalind Franklin, whose X-ray crystallography
facilitated the discovery of the double helix by Watson and Crick. We hope that
ROSALIND will inspire a new generation of bioinformatics students, including
biologists who want to develop vital programming skills at their own pace in a
unique environment, and also programmers who have never been exposed to the
intriguing computational problems generated by molecular biology.
BIOINFORMATICS FOR BIOLOGISTS TEXTBOOK PROJECT
The participants of previous RECOMB-BE meetings formed the Bioinformatics
Education Alliance, a group of sixteen leading bioinformaticians who have
recently collaborated to produce a textbook, called Bioinformatics for
Biologists (B4B). The first edition of B4B was published by Cambridge
University Press in 2011. Please see the B4B website for more details:
http://cseweb.ucsd.edu/~ppevzner/B4B/
B4B is an open project that will be continuously expanded by new chapters.
Therefore, RECOMB-BE invites submissions of proposals for new chapters; accepted
chapters will be included in the second edition of B4B.
SUBMISSIONS
We invite submissions in two areas: Bioinformatics Education Problems and
Bioinformatics for Biologists Chapter Proposals.
Bioinformatics Education Problems should be submitted via the RECOMB-BE website
and must be received by May 7, 2012. Each submission should cover a single
educational bioinformatics problem and ideally comprise the following sections:
Title.
Problem introduction and statement. The problem should be well formulated and
self-contained, both biologically and computationally, so that an independently
motivated student will be able to understand the problem formulation without
much previous exposure to the field. We encourage the use of figures and
tables as illustrative aids. The introduction to the problem should
be concluded
with a "problem statement" that requests the solution of a particular
instance of
the problem.
Draft of expected solution. Authors should provide an outline of how
students are
expected to solve this problem and should indicate any major tricks
and pitfalls.
Draft of expected checking process. Authors should also provide a
detailed method
describing how solutions will be tested for correctness. Should the answer be
checked literally (e.g., integer solution calculating edit distance) or by
applying a more sophisticated algorithm, such as when multiple optimal
solutions
exist (e.g., sequence of sorting reversals).
Optional Dataset. If the problem instance requires a dataset to process, please
provide an example of such a dataset (1MB limit).
We expect a wide variety of problems: from classical exercises for the
bioinformatics novice to advanced puzzles for graduate students.
Problems can be
canonical, novel, or anything in between, although ROSALIND
universally encourages
originality of exposition.
We allow multiple submissions within the same problem environment,
including simple
and difficult versions of the same problem. For example, an author may provide
brute-force and dynamic programming solutions for the same
problem (see http://projecteuler.net/problem=18, which is a brute-force
introduction to http://projecteuler.net/index.php?section=problems&id=67).
Multiple submissions should be provided separately with a corresponding note.
RECOMB-BE imposes no explicit restrictions on format, length, or notation, as
we encourage contributors to choose the style they feel is the most
appropriate,
and we are willing to consider a variety of formats; however, we
anticipate that
each problem introduction and statement will be at most 2 pages long
(and ideally less than a page), not including figures. The conference website
contains two sample problem submissions that illustrate the range of difficulty
levels that we intend ROSALIND's problems to cover.
"Pairwise Alignment," by Nikolay Vyahhi, St. Petersburg Academic University
"Signed Reversal Distance," by Phillip Compeau, UC-San Diego
Authors of selected problems will be invited for short oral presentations and
discussion as well as asked to submit a joint paper for consideration in
PLOS Computational Biology (within the Education Article category).
Furthermore, accepted problems will be integrated into the growing
ROSALIND website,
which will be launched in advance of RECOMB-BE.
Bioinformatics for Biologists (B4B) Chapter Proposals should be
submitted via the
RECOMB-BE website and must be received by May 7, 2012. Each submission in this
category should constitute a brief description of the proposed chapter.
Authors of selected proposals will be invited for oral or poster presentations
at RECOMB-BE 2012. In addition, these authors will be asked to submit a
full-length chapter shortly after RECOMB-BE for the second edition of B4B.
Proposals should cover a single biological problem and focus on didactic ways
to convey the computational ideas needed to address it. Submissions that focus
either solely on computational topics or solely on biological topics
will not be
considered. We anticipate that each chapter proposal will be 1-2 pages long.
KEY DATES
Submission deadline Monday, May 7, 2012
Notification of acceptance Friday, May 18, 2012
Request for visa Friday, May 25, 2012
Registration period To be announced
Arrival: Saturday, August 25, 2012
Conference: Sunday, August 26, 2012
Followed by RECOMB-AB: August 27-29, 2012
ORGANIZING COMMITTEE
Phillip Compeau (University of California-San Diego)
Alexander Kulikov (St. Petersburg Academic University)
Nikolay Vyahhi (St. Petersburg Academic University)
RECOMB-BE SUPPORT
RECOMB-BE is supported by the Howard Hughes Medical Institute (HHMI),
the International Society for Computational Biology (ISCB), and the
Ministry of Education and Science of the Russian Federation.
ABOUT RECOMB
The RECOMB International Conference on Research in Computational Molecular
Biology was founded in 1997 to provide a scientific forum for theoretical
advances in computational biology and their applications in molecular biology
and medicine. The conference arose from the need to advance research on the
mathematical and computational side of molecular biology. The 16th Annual
RECOMB conference (RECOMB 2012) will be held April 21-24, 2012 in
Barcelona, Spain.
The conference website is found at http://recomb2012.crg.cat/.
The RECOMB Satellites Series was founded by Pavel Pevzner in 2001.
Today, it consists of eight focused meetings covering various specialized
aspects of bioinformatics: RECOMB Comparative Genomics, RECOMB
Regulatory Genomics,
RECOMB Computational Cancer Biology, RECOMB Computational Proteomics,
RECOMB Systems Biology, RECOMB Massively Parallel Sequencing,
RECOMB Algorithmic Biology, and of course RECOMB Bioinformatics Education.
ADDITIONAL RESOURCES
Past RECOMB Bioinformatics Education Conferences
2009, 2010, 2011
RECOMB Algorithmic Biology 2012:
http://bioinf.spbau.ru/ab2012
Bioinformatics for Biologists
http://cseweb.ucsd.edu/~ppevzner/B4B/
Project Euler
http://projecteuler.net/
Google Code Jam
http://code.google.com/codejam/
Class Central
http://www.class-central.com/
SUBSCRIPTION INFORMATION
***To unsubscribe from future RECOMB satellite conference mailings,
please send an
E-mail to Phillip Compeau at pcompeau@math.ucsd.edu.
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