View source for PhyloSoC: Interoperable exchange of gene tree reconciliation maps

= 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 [http://danielpacker.org/tag/gsoc 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 =
* [https://github.com/danielpacker/TreeRecXML 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 [[PhyloSoC:_Interoperable_exchange_of_gene_tree_reconciliation_map:notes | notes page]].

[[Category:GSoC proposals]]
[[Category:Bioinformatics]]
[[Category:Phyloxml]]
[[Category:PhyloSoC]]