[BiO BB] Deadline extended for Computational Phyloinformatics Summer Course

Hilmar Lapp hlapp at gmx.net
Mon Apr 14 23:40:42 EDT 2008

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- 
throughput phylogenetics.

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,  
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 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/ 
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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