Difference between revisions of "PhyloSoC:Build a Mesquite Package to view Phenex-generated Nexml files"

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Project Blog: [http://gsoc09mesquite.wordpress.com/ Wordpress GSoC blog]
Project Blog: [http://gsoc09mesquite.wordpress.com/ Wordpress GSoC blog]
Source Code: (link coming)
Source Code: [http://code.google.com/p/mesquitegsoc09/ Google code]

Revision as of 09:34, 27 May 2009


Student: Kasia Hayden, Bennington College, khayden@bennington.edu

Mentors: Peter Midford (primary), Jim Balhoff


Build a Mesquite Package to view Phenex-generated Nexml files

Project Blog: Wordpress GSoC blog

Source Code: Google code


Extend Mesquite's capabilities to represent character matrices by allowing for the addition of ontology terms produced by Phenex in the Nexml format. Mesquite currently supports the Nexml file format and by the end of this project would be able to display Phenex's files directly in Mesquite, and depending on the speed of development, would display chained ontology concepts in graphical format with the use of a library like GraphViz.


Dates Description Completed
Week 1 (5/23 – 5/29) Investigate xml beam space parser (Dig it out of Nexml tree, figure out how it works) No
Week 2 (5/30 - 6/5) Validate that xml parser works with Phenoscape. Figure out how annotation panels work in Mesquite. No
Week 3 (6/6 - 6/12) Build a module in Mesquite (Take a tree or matrix and return the number of its fields) No
Week 4 (6/13 - 6/19) Test Phenoscape data No
Week 5 (6/20 - 6/26) fill No
Week 6 (6/27 - 7/3) First release, user testing, collect/prioritize bug list No
Week 7 (7/4 - 7/10) Midterm evaluations written/submitted, clean up first release's code/documentation No
Week 8 (7/11 - 7/17) fill No
Week 9 (7/18 - 7/24) fill No
Week 10 (7/25 - 7/31) fill No
Week 11 (8/1 - 8/7) fill No
Week 12 (8/8 - 8/16) Finish coding, improve documentation and wiki No
Final Week (8/17 - 8/24) Write final evaluation No