[BioRuby] 10 days left to register: workshop phylogenetic pipelines, August 1-11

[Rutger Vos]

COMPUTATIONAL PHYLOINFORMATICS
August 1 2011 through August 11 2011
Bioinformatics Center of Kyoto University
Application Deadline:  May 31, 2011

http://academy.nescent.org/wiki/Computational_phyloinformatics

Computational Phyloinformatics is an 11-day international course
(August 1-11, 2011) co-organized by the Computational Biology Research
Center (CBRC/AIST), the Bioinformatics Center of Kyoto University, the
Database Center for Life Science (DBCLS/JST), and the National
Evolutionary Synthesis Center (NESCent).  This course, which will take
place at Kyoto University directly following the SMBE Meeting
(http://smbe2011.com/), aims to give participants practical knowledge
and hands-on skills in phyloinformatics.

The venue in Kyoto is completely unaffected by the unfortunate events
in Fukushima and the power shortages in Tokyo. We encourage biologists
from other countries to participate in the SMBE meeting and/or this
special international course, in solidarity with the scientific
community of Japan in their effort to return to normalcy and to help
minimize any negative impacts that the earthquake may have on
scientific activities in Japan.

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, faculty, and researchers in phylogenetics interested in
receiving practical, hands-on training in the use of Perl and SQL for
workflows and applications in phyloinformatics.

The course is divided into four parts:

PART I: A tutorial review 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, genomic-scale data mining and acquisition, supertree
assembly, rate smoothing and branch calibration, tree traversal, etc).

PART III: Introduction and practical use of BioRuby for molecular
evolution and functional genomics  (e.g. scripting multiple sequence
alignment, gene duplication inference, tree inference, etc.).

PART IV: Introduction to SQL and database design; computing and
querying nested sets and transitive closure; querying both large trees
(e.g. NCBI) and large collections of trees (e.g. TreeBASE).

Participants  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. Participants will leave the course with a
full set of installations and libraries on their computer ready to
build phyloinformatic workflows for their own research projects, as
well as continued access to a 50+ page wiki "textbook" containing
step-by-step instructions, problem sets, and examples.

INSTRUCTORS AND COURSE ORGANIZERS
Christian Zmasek, Karen Cranston, Rutger A. Vos, Susumu Goto, Toshiaki
Katayama, William H. Piel

APPLICATION DEADLINE
May 31, 2011

TUITION
¥40,000 (~$500)

Participants are responsible for their own travel costs, including
transportation and accommodation -- see the website for more
information. International participants will benefit by combining
attendance with the 2011 SMBE meeting. A limited number of travel
scholarships from NESCent are available for US-based students.
Preference will be given to students from under-represented
minorities.

SUBSIDIES AND SCHOLARSHIPS
A limited number of travel scholarships from NESCent are available for
US-based students. Preference will be given to students from
under-represented minorities.

The Asia-Pacific Bioinformatics Network (APBioNet) is happy to provide
travel assistance for a limited number of students/early career
researchers from the Asia-Pacific region. Applicants are requested to
contact Dr Asif Khan, APBioNet Secretariat: asif -$- bic.nus.edu.sg
(replace -$- with @) for details.

PREREQUISITES

BIOLOGY: A good 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 or careful study of the
suggested reading materials in advance of the class (see web site).
Participants should have some experience with basic Unix shell
commands.

EQUIPMENT: Participants are expected to bring their own Mac OSX
computer or a LINUX computer, else they will be provided with an iMac.
Participants who cannot bring their own computer and will be using a
supplied iMac, should consider bringing their own portable
firewire/usb drive so that they can also leave the course with a full
suite of phyloinformatic software tools.

-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading, RG6 6BX, United Kingdom
Tel: +44 (0) 118 378 7535
http://rutgervos.blogspot.com