[Bioperl-l] Computational Phyloinformatics: A BGI-Shenzhen and NESCent Course, 5/8 - 17/8 '10

Rutger Vos rvos at interchange.ubc.ca
Wed Apr 21 07:18:25 EDT 2010

Dear bioperlers,

the National Evolutionary Synthesis Center (http://www.nescent.org)
and BGI-Shenzhen (formerly Beijing Genomics Institute,
http://www.genomics.cn/) are organizing a course in Computational
Phyloinformatics 5 August - 17 August 2010, in Shenzhen, PRC. The
course will have a very strong (Bio)Perl component, which is why I
thought it appropriate to post to this list. There are still spots
available for graduate students and postdocs who can come to Shenzhen,
so please help us reach them by forwarding the announcement below to
any suitable channels, thank you!

Computational Phyloinformatics: A BGI-Shenzhen and NESCent Course
5 August - 17 August 2010


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

Computational Phyloinformatics 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.  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.

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.

Darin London, William Piel, Rutger Vos

Biology: A solid understanding of phylogenetics (maximum parsimony,
maximum likelihood, bayesian inference, neighbor-joining, substitution
models) – 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.

Full tuition is ¥6,800 (~$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.

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

Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
United Kingdom
Tel: +44 (0) 118 378 7535

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