[BiO BB] NESCent Computational Phyloinformatics Course July 24 - Aug 4

Hilmar Lapp hlapp at gmx.net
Fri Mar 28 00:47:19 EDT 2008

Computational Phyloinformatics: A Course at NESCent.
24 July - 4 August 2008


Course Director: William Piel (piel at treebase.org)
Course Administrator: Jory Weintraub (jory at nescent.org)
Organizing Committee: Hilmar Lapp, William Piel, Todd Vision, Jory

Computational Phyloinformatics is a 10-day summer course sponsored by
and held at the National Evolutionary Synthesis Center (NESCent) in
Durham, North Carolina (USA) that aims to give students practical
knowledge and hands-on skills in phyloinformatics.

Biologists are faced with ever-larger datasets, more complex
evolutionary models, and more elaborate analytical methods. Seldom is
it sufficient to run a dataset through an off-the-shelf program on a
desktop PC; increasingly, biologists need to write scripts to
interface with internet services and databases, build analytical
pipelines, customize analyses, and distribute computation over
multiple processors.  This course is designed for graduate students,
postdocs, and researchers in phylogenetics interested in receiving
practical, hands-on training in the use of Perl, Java, or R for
phyloinformatics applications.

The course is divided into three parts:

- Part I: A tutorial review of either Perl, Java, or R (while
optional, this part is strongly recommended).

- Part II: Students have the choice of pursuing (1) a Perl track, with
focus on BioPerl and Bio::Phylo; (2) a Java track, with focus on how
to write a Mesquite module and program workflows that utilize Mesquite
modules; or (3) an R track, with a focus on comparative phylogenetic
analysis using the libraries Ape, Ouch, and Phylobase.

- Part III: Students choose between (1) a database track (with focus
on SQL, BioSQL and database queries of phylogenetic trees); (2) a
HyPhy track (with focus on scripting molecular evolution hypothesis
tests in a phylogenetic framework); or (3) an advanced R track (with
focus on automating analyses using vectorized calculations, advanced
plotting and animations, and the R-LaTex document system using Sweave).

Students in all tracks will learn how to write basic phylogenetic or
comparative analysis scripts, parse NEXUS files, traverse and compute
over trees, and make practical use of phylogenetic software
libraries.  These skills will be learned in a biological context,
touching on a diverse array of topics (depending on the track) such as
alignment of large numbers of sequences, ancestral state
reconstruction, testing for positive selection, etc.

James Balhoff, Marguerite Butler, R. Todd Jobe, Hilmar Lapp, Darin
London, David Maddison, Spencer Muse, Jeff Oliver, Brian O'Meara,
William Piel, Sergei L. Kosakovsky Pond, Ryan Scherle, Todd Vision,
Rutger Vos

Biology: A solid understanding of phylogenetics - for example, having
already taken the Workshop on Molecular Evolution (http:// 
) or equivalent coursework or experience.
Computing: Prior experience with Perl, Java, or R; or careful study of
the suggested reading materials (see web site). Students should have
experience with basic Unix shell commands. All students are expected
to bring their own Mac OSX computer (a limited number of loaners are
available upon request).

Tuition is $600.00. Accommodation is $50/night for a single occupancy
apartment, $26/night for double occupancy apartment in housing
provided at Duke University (students are also free to make their own
housing arrangements). Travel awards of up to $450 each are available
to subsidize travel expenses for applicants from underrepresented

Apply through the course website (http://www.nescent.org/courses/2008/ 
). You will be asked to provide a resume, two references, a brief
description of your computational and phylogenetic background, and
your reasons for taking the course. Applications are due by April 15,
2008. International students may wish to apply for Travel Awards from
the Society of Systematic Biologists (due date: March 31, 2008, see
website for details).

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