View source for PhyloSoC:BioPerl integration of the NeXML exchange standard and Bio::Phylo toolkit

2009 Google Summer of Code Project

== Title ==


BioPerl integration of the NeXML exchange standard and Bio::Phylo toolkit

== Authors ==

'''Student''': [http://www.bioperl.org/wiki/User_talk:Chmille4 Chase Miller]

'''Mentors''': [http://www.bioperl.org/wiki/User:Majensen Mark A. Jensens] (primary) [http://rutgervos.blogspot.com/ Rutger Vos]

== Project Blog ==

http://gsocnexml.blogspot.com/

== Abstract ==


This project will integrate the NeXML exchange standard into BioPerl, facilitating the adoption of this standard and easing the transition from the overworked NEXUS standard. A wrapper will be used to allow BioPerl native access to the preferred NeXML parser (Bio::Phylo), allowing Bio::Phylo and NeXML to co-evolve without being encumbered by BioPerl. Additionally, test cases and example sets will be developed that target real world uses.

== Background ==

Phylogenetic trees, like all visual data representations, require special consideration to represent the complete structure in a linear non-visual data format.  The current accepted standard is the NEXUS file format, which is a highly expressive and popular file format.  However, it has become increasingly cumbersome to use due to three main reasons: “(i) deficiencies in the standard itself, (ii) variable level of support for standard feature in current software, and (iii) an extremely high incidence of illegal files (a byproduct of the fact that most parsers are ‘forgiving’ of errors)” <sup>[https://www.nescent.org/wg_evoinfo/NEXUS_Problems 1]</sup>.  These problems have sparked a transition away from the NEXUS standard to a more flexible, extensible, and strictly defined standard.  One candidate is the NeXML exchange standard, which, in addition to satisfying the goals of being more extensible and more strictly defined, leverages the power of pre-existing XML tools and capabilities (such as parser libraries, web service toolkits, and serialization) to make a more robust product <sup>[http://docs.google.com/Present?docid=dc3k7mhr_8g9j2j7ct 2]</sup>.  One of the current barriers of adopting the NeXML standard into wider use is the lack of support for NeXML in popular programming tools.  One way to lower the entrance barrier for use of the new NeXML standard is to incorporate the preferred NeXML parser (Bio::Phylo) into BioPerl - a popular bioinformatics framework.  However, the NeXML standard is rapidly evolving and would be hampered by having to interact directly with the large BioPerl project.  To circumvent these potential pitfalls, a lightweight dynamic wrapper will be created around Bio::Phylo.  In this way BioPerl users will be given access to the full suite of functionality provided by Bio::Phylo without encumbering the future development of the NeXML standard or the Bio::Phylo module.  To facilitate the use of the newly designed wrapper and the NeXML standard, test cases and example sets will be developed that target real world uses.  This project will be an important step in the transition away from an overworked standard to the more powerful and extensible NeXML exchange standard, inherently increasing productivity along the way.

== Project Plan ==


==='''May 23rd - June 5th'''===

NeXML to BioPerl Objects - write modules for reading nexml files into BioPerl objects. The following mod

*Bio::Phylo::Matrices::Datum to Bio::Seq - Implement the Bio::SeqIO::nexml::next_seq() method, which will override the Bio::SeqIO::next_seq() method, giving native support for reading nexml files.

*Bio::Phylo::Matrices::Matrix to Bio::Align - Implement the Bio::AlignIO::nexml::next_aln() method, which will override the Bio::AlignIO::next_seq() method, giving native support for reading nexml files

*Bio::Phylo::Forest::Tree to Bio::Tree - Implement the Bio::TreeIO::nexml::next_tree() method, which will override the Bio::TreeIO::next_seq() method, giving native support for reading nexml files

==='''June 6th - June 12th'''===

BioPerl Objects to NeXML
*Write module to allow BioPerl objects to write data to a Nexml file.
Bio::Seq to Bio::Phylo::Matrices::Datum
*Create a Bio::SeqIO::nexml.pm module that overwrites the write_seq() method using the code from  the Bio::Phylo::Matrices::Datum->new_from_bioperl() method
Bio::Align to Bio::Phylo::Matrices::Matrix
*Create a Bio::AlignIO::nexml.pm module that overwrites the write_aln() method using the code from the Bio::Phylo::Matrices::Matrix->new_from_bioperl() method
Bio::Tree to Bio::Phylo::Forest::Tree
*Create a Bio::TreeIO::nexml.pm module that overwrites the write_tree() method using the code from the Bio::Phylo::Forest::Tree->new_from_bioperl() method

==='''June 13th - June 19th'''===

Finish Modules
*Finish coding the nexml.pm modules (Bio:SeqIO:nexml, Bio:AlignIO:nexml, and Bio:TreeIO:nexml) adding any extra wrapper code that might be neccessary
*'''Milestone''' - Testable nexml.pm modules

==='''June 20th - June 26th'''===

Regression testing
*Develop tests using Bioperl's [http://www.bioperl.org/wiki/HOWTO:Writing_BioPerl_Tests test suite], which uses the [http://search.cpan.org/~mschwern/Test-Simple-0.86/lib/Test/Tutorial.pod Test::More] module

==='''June 27th - July 3rd'''===

Test Data Sets
*Generate test data sets that will be used for both benchmarking and test use cases

==='''July 4th - July 10th'''===

Benchmark
*Use BioPerl to query large data sets from GenBank

Validation
*Use the online NeXML validator at http://www.nexml.org to check the NeXML produced by the new modules

Potential Cases
*Set of test NeXML files produced at the NESCent Database Interoperability Hackathon (http://dbhack1.googlecode.com/svn/trunk/data/nexml/)
*Datasets with many sequences
*Datasets with very long sequences
*More...

Start Midterm evaluation

==='''July 11th - July 17th'''===

Use Cases
*Generate real world examples based on test data sets with detailed documentation that will walk someone step by step through the new wrapper and the functionality of Bio::Phylo from a BioPerl perspective

==='''July 18th - July 24th'''===

Code Optimization
*Optimize code based on results from benchmark

==='''July 25th - July 31st'''===

Incorporate new module into BioPerl
*BioPerl-dev – the repository for experimental packages
*BioPerl-live – the repository for modules slated for core releases (Only will go here if BioPerl Core Devs think that it works well and is useful enough to be packaged as part of the core)

==='''August 1st - August 7th'''===

Debugging and Testing

==='''August 8th - August 10th'''===

Finish documentation and wrap up

==='''August 17th - August 24th'''===

Begin and finish final evaluations

== Deliverables ==
*Native NeXML integration into BioPerl
*Full Bio::Phylo functionality from within BioPerl
*Example files and test cases to facilitate adoption of NeXML