BioPerl Project UpdateJason Stajich

(on behalf of BioPerl developers)

BioPerl

Since ~1995

10s of developers over the years

2002 Publication cited ~500 times

DeObfuscator

Interface to search available methods in objects

Dave Messina and Laura Kavanaugh

http://bioperl.org/cgi-bin/deob_interface.cgi

Search class names by string or Perl regex (examples: Bio::SeqIO, seq, fasta$)

Submit Query

OR select a class from the list:

sort by methodsort by method

Welcome to the BioPerl Deobfuscator [ bioperl-live ] what is it?

Bio::Align::AlignI An interface for describing sequence alignments.

Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment

Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments

Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances)

Bio::Align::StatisticsI Calculate some statistics for an alignment

Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects

Bio::AlignIO Handler for AlignIO Formats

Bio::AlignIO::arp ARP MSA Sequence input/output stream

Bio::AlignIO::bl2seq bl2seq sequence input/output stream

Bio::AlignIO::clustalw clustalw sequence input/output stream

Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle)

methods for Bio::SimpleAlign

Method Class Returns Usage

accession Bio::SimpleAlign An acc string $myalign->accession("PF00244")

add_seq Bio::SimpleAlign nothing$myalign->add_seq($newseq); it - just adds it to the hashes.

add_SeqFeature Bio::SimpleAlign nothing$feat->add_SeqFeature($subfeat); $feat->add_SeqFeature($subfeat,'EXPAND')

add_tag_value Bio::AnnotatableI not documented See add_Annotation

addSeq Bio::SimpleAlign not documented not documented

all_gap_line Bio::SimpleAlign string $line = $align->all_gap_line()

annotation Bio::SimpleAlign Bio::AnnotationCollectionI object $ann = $aln->annotation or $aln->annotation($ann)

average_percentage_identity Bio::SimpleAlignThe average percentage identity of the alignment

$id = $align->average_percentage_identity

Gratuitous Statistics

975 modules in core, 375 in run

600,000+ lines of code/POD

Lots of emails go through the list!

Phylo-HackathonHosted at National Evolutionary Synthesis Center (www.nescent.org)

Several BioPerl participants focusing on interfacing with phylogenetics and molecular evolution software

Generated more documentation for existing BioPerl related evolutionary tools

Evolutionary ToolsPopulation Genetics tests and processing code

McDonald-Kreitman, Tajima’s D, LD

Phylogenetics

Tree parsing and manipulation

Simple NJ tree building

Tree Drawing

More Evolutionary Interfaces

Parsing and running of PAML for Ka, Ks rates and model testing

PhastCons & PhyloFast interfaces

NJTree (TreeFam software) running and parsing of NHX results

Interface to HyPhy for relative rates, model testing, and Ka/Ks testing

BioSQL support

Had been for storing sequence, features, annotations

Postgresql and mysql schemas

New support for phylogenetic trees and topological queries

Perl modules in bioperl-db package

GFF3 Support

Bio::DB::SeqFeature is interface for RDBMS for GFF3 storage

Backend for Gbrowse

Postgresql, Mysql, and Flatfile (BDB) implementations

Documentation

Two years since we started the BioPerl Wiki and reorganized documentation

Have expanded HOWTOs and user guides

Tracking project needs and progress to wiki

Education

BioPerl instruction through courses at NESCent (Phyloinformatics)

Programming for Biology course at CSHL

Several workshops at universities

Release schedule

1.4 was released in Dec 2004!

1.5.1 and 1.5.2 have come out and are in CPAN as ‘unstable’

Plans afoot for 1.6 release

In late 2007

1.6 release needs

Remove broken code for auto feature to string generation

Full Bio::FeatureIO support or removal

Tidy GFF/GFF3 and Genbank parsing

Other Admin news

Plan to migrate from CVS to SVN in August (George Hartzell)

Do we reorg to different logical components (Core w/ sequences)

Major Kudos

Project Management & Leadership

Sendu Bala - Cambridge Univ

Chris Fields - Univ of Illinois, Urbana-Champaign

More Kudos

Nathan Haigh - Sheffield Univ

Hilmar Lapp - NESCent

Torsten Seeman - Monash University

Dave Messina - Washington Univ St Louis

Mauricio Herrera Cuadra - Facultad de Estudios Superiores Iztacala, UNAM