National Evolutionary Synthesis Center (NESCent)
Published June 18, 2015 | Version v1
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The Computational Phyloinformatics Summer Course wikis

Authors/Creators

  • 1. Naturalis
  • 2. Yale-NUS, Singapore
  • 3. National Evolutionary Synthesis Center (NESCent)
  • 4. University of Hawaii
  • 5. University of North Carolina at Chapel Hill
  • 6. University of California at San Diego
  • 7. Duke University
  • 8. Oregon State University
  • 9. North Carolina State University
  • 10. University of Tennessee at Knoxville

Description

These are snapshots of the 2008-2012 course wikis for the Computational Phyloinformatics Summer Courses. (There was no course wiki for the 2007 course.)

Computational Phyloinformatics Summer Course

Computational Phyloinformatics is an 10 to 14-day intensive summer workshop established at NESCent, but often co-sponsored and hosted at other institutions. The workshop aims to give biologists practical knowledge and hands-on programming skills in phyloinformatics. The curriculum changes form year to year, but has included PERL (BioPerl, BioPhyo), SQL (BioSQL, TreeBASE), JAVA (JEBL, PAL, Mesquite), R (Ape), HyPhy, and BioRuby.

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 scripting languages for solving phyloinformatics problems. 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. Participants leave the course with their laptops filled with working software and programming libraries to apply them to their own research projects.

Current and Prior Workshops

  • NESCent, Durham, NC, USA, 2007
  • NESCent, Durham, NC, USA, 2008
  • Instituto Gulbenkian, Lisbon, Portugal, 2009
  • BGI-Shenzhen, China, 2010
  • Kyoto, Japan, 2011
  • Moscow, Russia, 2012

Notes

Instructions on how to import the dump into a MediaWiki instance can be found at MediaWiki: https://www.mediawiki.org/wiki/Manual:Importing_XML_dumps. Every dump consists of two files, an .xml.gz and a .tar.gz. The .xml.gz is processed by importDump.php, the .tar.gz is processed by importImages.php, as per the above documentation.

Files

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