[BiO BB] Computational Phyloinformatics Course at NESCent

Hilmar Lapp hlapp at gmx.net
Thu Apr 5 17:36:52 EDT 2007

Computational Phyloinformatics: A Course at NESCent. 9 - 19 July 2007

The National Evolutionary Synthesis Center (Durham, NC, USA)


Computational Phyloinformatics is a new course 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 to give graduate students, post-docs, and
researchers in phylogenetics who have an interest in writing programs
and scripting analyses the skills needed to tackle the grand
challenges posed by the Assembling the Tree of Life program, Evo-
Devo, Metagenomics, Phylogenomics, and other emerging research areas.
Students will learn how to build and compute with phylogenetic
databases; they will learn "power-user" skills for scripting analyses
in Mesquite and HyPhy. Students choose between either a Java- or a
Perl-based environment for learning how to write basic phylogeny
programs: parsing NEXUS files; traversing and computing over trees;
and making practical use of phylogenetic libraries (e.g. PAL, JEBL,
BioJava; BioPerl, Bio::Phylo, CIPRES interface). These skills will be
learned in a biological context, touching on a diverse array of
topics such as automated base calling, ancestral state and continuous
character reconstruction, model selection, parametric bootstrapping,

Organizer: William Piel (william.piel at yale.edu)
Hilmar Lapp
David Maddison
Wayne Maddison
Jeff Oliver
Sergei L. Kosakovsky Pond
Stephen Smith
Arlin Stoltzfus
Rutger Vos

Biology: A solid understanding of phylogenetics -- for example,
having already taken the Workshop on Molecular Evolution (http://
www.molecularevolution.org/) or equivalent coursework or experience.

Computing: Prior experience with either Perl or Java; or, having read
and studied the recommended books on either language (see web site).
Students will be using Mac OSX computers in the course, so should
have experience with basic Unix shell commands.

Tuition is $500.00.  Housing is $440 for single occupancy, $220 for
double occupancy in housing provided at Duke University.  Travel
awards of up to $620 each are available to subsidize travel expenses
for applicants from underrepresented groups.

Students may apply through the website (www.nescent.org/
summer_course).  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, 2007.  International students may
wish to apply for Travel awards from the Society of Systematic
Biologists (due date: March 31, 2007, see website for details).

William Piel <william.piel at yale.edu>

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