[Mesquitelist] Mesquite and Java in the Computational Phyloinformatics course
hlapp at duke.edu
Mon Apr 14 15:49:13 PDT 2008
The deadline for the Computational Phyloinformatics Summer Course has
just been extended by one week. Note that this course has a track on
writing Mesquite modules or workflows that utilize Mesquite modules,
taught by David Maddison.
Deadline Extension for Computational Phyloinformatics.
24 July - 4 August 2008
In response to requests from our applicants, we are extending the
application deadline for our course on Computational Phyloinformatics
to Tuesday of next week, April 22. 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.
This course trains students, post-docs, faculty, and researchers in
phylogenetic computational thinking: instead of being locked in to
using point-and-click off-the-shelf software, we show you how to
write your own scripts and programs to customize calculations,
implement new statistical analyses, or devise pipelines for high-
Writing and distributing your own Mesquite module, pipelining data
through BioPhylo, refining evolutionary models in HyPhy, archiving
and querying your lab's productivity in a database, and designing
comparative statistical analyses in R: these are not difficult tasks,
but there are no textbooks to get you started -- yet the explosion of
phyloinformatic data means that the cutting-edge researcher has to be
comfortable with computational tools. That's where we come in. This
hands-on course gets you over the learning curve: we help you with
the installations, show you what libraries to use, and get you
comfortable with writing your own programs.
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,
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 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
HOW TO APPLY
Apply through the course website (http://www.nescent.org/courses/2008/
comphy). 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.
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
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