Society of Systematic Biologists

Course Contacts: Wang Xiaoling training@genomics.org.cn and William Piel (piel@treebase.org) Organizing Committee: Li Zhuo, Wang Xiaoling, Hilmar Lapp, William Piel, Todd Vision

Computational Phyloinformatics (http://www.nescent.org/courses/2010/comphy/) is an 11-day intensive summer course co-sponsored by BGI-Shenzhen and the U.S. National Evolutionary Synthesis Center (NESCent), and will take place at the BGI-Shenzhen genomics institute in Yah Tian District, Shenzhen, China, August 5-17, 2010. The venue is in proximity to beaches, national forests, and holiday resorts. The course aims to give students practical knowledge and hands-on programming skills in phyloinformatics.

Synopsis Biologists are faced with ever-larger datasets, more complex evolutionary models, and increasingly elaborate analytical methods. Seldom is it sufficient to run a dataset with 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 and SQL for phyloinformatics applications.

The course is divided into three parts:

• Part I: A tutorial review of of Perl, including object oriented programming and building packages
• Part II: Introduction and practical use of BioPerl and Bio::Phylo, (e.g. scripting for large tree inference engines, automating model testing, supertree assembly, rate smoothing and branch calibration, tree traversal, etc).
• Part III: Introduction to database design; computing and querying nested sets and transitive closure; topological querying of both large trees (e.g. NCBI) and large collections of trees (e.g. TreeBASE).

Students 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 such as analysis of large datasets, automation of supertree assembly, querying for topological patterns in large collections of trees, etc.

Instructors Darin London, William Piel, Rutger Vos

Prerequisites Biology: A solid understanding of phylogenetics (e.g. familiarity with MP, ML, BI, NJ, substitution models, tree searching, bootstrapping, etc) -- for example, having already taken the Workshop on Molecular Evolution (http://www.molecularevolution.org/), Bodega Applied Phylogenetics Workshop (http://bodegaphylo.wikispot.org/), or equivalent coursework or experience.

Computing: Prior experience with Perl 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 either their own Mac OSX computer or a LINUX computer; otherwise LINUX computers will be provided.

Fees Full tuition is ¥6,800 (~$US 996), and includes lunches, coffee, computer equipment, and an outing on one of two free days. Students are free to find their own accommodation, but shuttle service is offered to/from the recommended hotels: Pattaya Hotel and East Coast Blue Club Hotel, located near Dameisha beach.

How to apply Apply through the course website. You will be asked to provide a resume and a motivation statement (including a self-assessment of your skills, experience, and knowledge of both phylogenetics and computing). Applications are due by April 5 2010.