From NESCent Informatics Wiki

Contents 1 Project Summary 2 Author 3 Abstract 4 Source Code 5 Links 6 Project Plan 6.1 Week 1 (May 24 - May 30) 6.2 Week 2 (May 31 - June 6) 6.3 Week 3 (June 7 - June 13) 6.4 Week 4 (June 14 - June 20) 6.5 Week 5 (June 21 - June 27) 6.6 Week 6 (June 28 - July 4) 6.7 Week 7 (July 5 - July 11) 6.8 Week 8 (July 12 - July 18) 6.9 Week 9 (July 19 - July 25) 6.10 Week 10 (July 26 - August 1) 6.11 Week 11 (August 2 - August 8) 6.12 Week 12 (August 9 - August 15) 7 Notes

Project Summary

I've written up a project summary for my google of code here:

File:Interoperable rec summary.pdf

Author

My name is Daniel Packer and I study computer science and bioinformatics at Hunter College. My email address is [dp] [at] [danielpacker] [dot] [org].

My GSOC blog posts are here.

Abstract

The goals of this project are:

• Standardize the XML encoding of gene tree reconciliation data by extending an existing standard
• Implement this encoding in a standard bioinformatics library (BioPerl)
• Modify the iPlant GTR database to support import and export of GTR trees using the new encoding
• If time permits, modify the iPlant tree visualization tool so that it internally uses the new encoding
• If time permits, use iPlant's taxa resolution abilities to populate imported and exported data with taxonomic name strings

Source Code

• My github repository for GSOC

Links

• iPlant: https://pods.iplantcollaborative.org/wiki/display/iptol/1.0+Architecture
• BioPerl::TreIO: http://doc.bioperl.org/releases/bioperl-1.4/Bio/TreeIO.html
• PhyloXML: http://www.phyloxml.org/
• NeXML: http://www.nexml.org/
• Prime: http://prime.sbc.su.se/primetv/
• TreeBeST: http://treesoft.sourceforge.net/treebest.shtml

Project Plan

NOTE: this is based on the original project plan from my application and will be updated as I have more information.

Week 1 (May 24 - May 30)

• Deliverables Planned
  • Write the XML data type definition for the GTR extensions so we can validate GTR input files.
• Progress Reported
  • Communicate with mentors about code repository and blog
  • Update project template wiki page
  • First blog post (reflections on what's ahead this summer)
  • Establish iPlant and NESCent wiki access

Week 2 (May 31 - June 6)

• Deliverables Planned
  • Post code repository and homepage to project template wiki page

(done by EOD today)

• • Check out iPlant source for review
  • Commit skeletal BioPerl TreeIO module
  • Review mentor's recommendations and thoughts on XML representations
  • Commit a preliminary tree reconciliation DTD
  • Continue to read relevant papers and learn more about tree

reconciliation (on my own time)

• • Tree reconciliation working group meeting (tomorrow, Tues 2PM)
  • Further define communication plan (schedule, method) with my

mentors, especially James Estill

Week 3 (June 7 - June 13)

• Extend BioPerl::TreeIO module to generate GTR XML. James Estill has a BioPerl::TreeIO module that consumes PRIME data, so I can use his module to bootstrap this.

Week 4 (June 14 - June 20)

• Extend BioPerl::TreeIO module to support parsing and consumption of GTR XML.

Week 5 (June 21 - June 27)

• Set up skeletal functions in iPlant database and tests for GTR XML export via BioPerl.

Week 6 (June 28 - July 4)

• Give iPlant database the ability to produce GTR XML via BioPerl. This will let us export the iPlant data in a portable way.

Week 7 (July 5 - July 11)

• Set up skeletal functions in iPlant graphical interface and tests for internal use of GTR XML instead of the JSON data it's using now.

Week 8 (July 12 - July 18)

• Implement internal use of GTR XML within iPlant graphical interface.

Week 9 (July 19 - July 25)

• Use iPlant's internal taxa resolution system to export and import fully resolved data trees.

Week 10 (July 26 - August 1)

• Continue implementing taxa resolution.

Week 11 (August 2 - August 8)

• Code revisions, bug fixes.

Week 12 (August 9 - August 15)

• Code revisions, bug fixes.

Notes

See my notes page.