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Computational Phyloinformatics July 9-19 2009
An International Collaboration between Instituto Gulbenkian de Ciência and NESCent
This year, Computational Phyloinformatics will be traveling to the Instituto Gulbenkian de Ciência, near Lisbon, Portugal. The IGC is one of Portugal's top research institutes that focuses on the genetic basis of development and evolution of complex systems. Please consult the main IGC GTPB course page here.
The course will provide a hands-on instruction in phyloinformatics using Perl (BioPerl and Bio::Phylo) and SQL (Postgres and BioSQL).
Phylogenetics is key to studying evolution, systematics, comparative genomics, and bioinformatics — phylogenies are now ubiquitous in the biological literature. However, with the growth in computational power and DNA sequencing, and with ever more complex substitution models and analytical methods, it is less and less practical to run simple, one-shot analyses on a personal computer with an off-the-shelf program. As a result, we increasingly rely on custom-scripted analyses or custom-designed computational pipelines, and often on large compute machines or clusters. While books and courses on phylogenetics are common, it is harder to find information on how to script large-scale and complex analyses, or how to write your own scripts and programs.
This course aims to address this gap by introducing these skills in a practical, hands-on setting at the Instituto Gulbenkian de Ciência, near the mouth of the Tagus river in Oeiras, Portugal. This year's course will focus on hands-on training in Perl and SQL and will be structured to accommodate students with less prior programming experience.
The course is divided into three parts:
- Part I: Students bring their programming skills up to par with a review and tutorial in Perl, starting with "hello world" and ending with object oriented programming.
- Part II: Students learn how to do large-scale phyloinformatics, such as writing scripts to automate the assembly of a large supertree and then recalibrate its branch lengths using BioPerl and Bio::Phylo
- Part III: Students learn to design a database, write queries in SQL, store and query trees, and use bindings between BioPerl and BioSQL.
Students will learn how to write basic phylogenetic or comparative analysis scripts: parsing NEXUS files; traversing and computing over trees; and making practical use of phylogenetic libraries. These skills will be learned in a biological context, touching on a diverse array of topics.
| When: | July 9 - July 19 2009 |
| Where: | Instituto Gulbenkian de Ciência Rua da Quinta Grande, 6 |
| Application Deadline: | June 8 2009 (but rolling admissions remain open) |
| Target Students: | The course is intended for graduate students, post-docs, and researchers in biology who are interested in developing skills in phyloinformatics |
| Prerequisites: | Biology: A solid understanding of phylogenetics — for example, having already taken the Workshop on Molecular Evolution or equivalent coursework or experience. |
| Computing: Prior experience with Perl or having studied books or tutorials on Perl prior to the course starting; and prior experience with basic operations in unix. We will offer two days of review to bring everyone up to speed, but the onus is on the students to have studied Perl ahead of time. |
