Kyoto 2011

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Computational Phyloinformatics [1] is an 11-day intensive summer workshop co-sponsored by the Bioinformatics Center of Kyoto University, DBCLS/JST, NESCent, and the Phyloinformatics Research Foundation, Inc., and will take place at the Bioinformatics Center in Kyoto, Japan following the SMBE 2011 meeting. The workshop aims to give biologists practical knowledge and hands-on programming skills in phyloinformatics. Although originally scheduled to take place in Tokyo, the course has since been moved to Kyoto because of the anticipated risk of power shortages. Kyoto is unaffected by the effects of the earthquake and there is no risk of contamination from the Fukushima nuclear power plants.

Contents

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 four 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 and practical use of BioRuby for molecular evolution and functional genomics (e.g. gene duplication inference, scripting sequence alignment and tree inference)
  • Part IV: 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 various data 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, scripting multiple sequence alignment processing, gene duplication inference, querying for topological patterns in large collections of trees, etc.

Instructors and Course Organizers

  • Christian Zmasek (Sanford-Burnham Medical Research Institute; Functional Genomics with BioRuby)
  • Karen Cranston (NESCent Training Coordinator)
  • Rutger A. Vos (University of Reading; Phyloinformatics with BioPerl and Bio::Phylo)
  • Susumu Goto (Bioinformatics Center, KEGG laboratory)
  • Toshiaki Katayama (Human Genome Center, University of Tokyo)
  • William H. Piel (Yale Peabody Museum; Phyloinformatics with SQL)

Application and Registration

To register, please visit the registration page. You will be asked to provide a motivation statement (including a self-assessment of your skills, experience, and knowledge of both phylogenetics and computing). For questions or comments, please contact Rutger Vos (r.a.vos <at> reading.ac.uk) or William Piel (william.piel <at> yale.edu).

Important Dates

Deadlines

  • Application Deadline: May 31, 2011
  • Acceptance Notification: June 5, 2011

We will continue to accept students after the deadline, but subject to availability

Syllabus

The course wiki with detailed syllabus is here: https://www.nescent.org/comphy2011/Main_Page

  • Sunday 31 July: Arrival Day
  • Monday 1 August: Part I - Unix Refresher
  • Tuesday 2 August: Part I - Perl refresher
  • Wednesday 3 August: Part II - PhyloInformatic workflow design
  • Thursday 4 August: Part II - PhyloInformatic workflow design
  • Friday 5 August: Part II - PhyloInformatic workflow design
  • Saturday 6 August: Part II - PhyloInformatic workflow design
  • Sunday 7 August: Day off
  • Monday 8 August: Part III - Functional Genomics with BioRuby
  • Tuesday 9 August: Part IV - SQL Refresher
  • Wednesday 10 August: Part IV - Databasing Trees
  • Thursday 11 August: Part IV - Databasing Trees
  • Friday 12 August: Departure Day

Daily Schedule

  • 08:00 - 09:00 Coffee, check email
  • 09:00 - 10:30 Session 1
  • 10:30 - 10:45 Coffee break
  • 10:45 - 12:15 Session 2
  • 12:15 - 13:30 Lunch break
  • 13:30 - 15:00 Session 3
  • 15:00 - 15:30 Coffee break
  • 15:15 - 16:45 Session 4
  • 16:45 - 19:30 R&R and dinner
  • 19:30 - 21:00 Optional evening sessions or software installation

Venue

Location

Bioinformatics Center, Kyoto University, Gokasho, Uji, Kyoto 611-­‐0011 JAPAN

Map campus.jpg

Travel

We suggest that international participants arrive in Kansai Airport in Osaka and take the bullet train to Kyoto.

Student Pre-Requisites

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, Bodega Applied Phylogenetics Workshop, or equivalent coursework or experience.

Computing

Prior experience with Perl or reading some suggested materials: There are numerous books on perl, though many focus on CGI scripting and do not encourage best practices in terms of modularity and object-oriented design. A good beginner book is Mastering Perl for Bioinformatics by James Tisdal ISBN: 0596003072. Also consider reading Perl How To Program, by H.M. Deitel, P.J. Deitel, T. Nieto and D.C. McPhie ISBN:0130284181. Students should have experience with basic Unix shell commands. Students should introduce themselves to SQL by reading an introductory book on the subject.

Equipment

Each student is strongly encouraged to bring her or his own Apple Macintosh iBook, MacBook (or equivalent) running OSX 10.4, 10.5, or 10.6 with Apple’s developer package (XCode) installed; or a computer running Linux with a working wireless card installed, superuser control, Perl, PostgreSQL, and DBD/DBI installed with a functioning CPAN installer. Bringing your own computer has the advantage that you will leave the course with a machine loaded and fully configured with a working set of phyloinformatic libraries, programs, and modules. If you cannot bring one, an iMac computer will be provided, but in that case you should bring a portable self-powered Mac-compatible hard drive with USB and Firewire ports with Firewire 400 cables (e.g. the Iomega® eGo™ or WD My Passport Studio). This hard drive will allow you to leave the course with a full suite of phyloinformatic software.

Tuition Costs

Tuition: ¥40,000 (~$500)

Students are responsible for their own travel costs, including transportation and accommodation.

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.

Accommodation

Participants are asked to find their own accommodation.

Hotels Near Campus in Uji City

Hotels In Kyoto

Participants may prefer to stay in Kyoto to enjoy the nightlife in the evenings. Kyoto to Uji is about ~30 min by train (JR line or Keihan line).

Premium Hotels

Medium Class

Budget

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