Computational Phyloinformatics: A Course at NESCent. 24 July - 4 August 2008
http://www.nescent.org/courses/2008/comphy/ Course Director: William Piel ([EMAIL PROTECTED]) Course Administrator: Jory Weintraub ([EMAIL PROTECTED]) Organizing Committee: Hilmar Lapp, William Piel, Todd Vision, Jory Weintraub 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. SYNOPSIS 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. INSTRUCTORS 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 PREREQUISITES 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). FEES 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 groups. 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. 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). _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
