Title: BioPerl Project Update Author: Jason Stajich

1. BioPerl Project
Update
Jason Stajich
(on behalf of BioPerl developers)

2. BioPerl
Since ~1995
10s of developers over the years
2002 Publication cited ~500 times

3. DeObfuscator
Interface to search available methods
in objects
Dave Messina and Laura Kavanaugh
http://bioperl.org/cgi-bin/
deob_interface.cgi

4. Welcome to the BioPerl Deobfuscator what is it?
[ bioperl-live ]
Search class names by string or Perl regex (examples: Bio::SeqIO, seq, fasta$)
Submit Query
OR select a class from the list:
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)
sort by method
methods for Bio::SimpleAlign
Method Class Returns Usage
accession Bio::SimpleAlign An acc string $myalign->accession(quot;PF00244quot;)
$myalign->add_seq($newseq); it - just adds it to the
add_seq Bio::SimpleAlign nothing
hashes.
$feat->add_SeqFeature($subfeat);
add_SeqFeature Bio::SimpleAlign nothing
$feat->add_SeqFeature($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)
The average percentage identity of the
average_percentage_identity Bio::SimpleAlign $id = $align->average_percentage_identity
alignment

5. Gratuitous
Statistics
975 modules in core, 375 in run
600,000+ lines of code/POD
Lots of emails go through the list!

6. Phylo-Hackathon
Hosted 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

7. Evolutionary Tools
Population Genetics tests and
processing code
McDonald-Kreitman, Tajima’s D, LD
Phylogenetics
Tree parsing and manipulation
Simple NJ tree building
Tree Drawing

8. 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

9. 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

10. GFF3 Support
Bio::DB::SeqFeature is interface for
RDBMS for GFF3 storage
Backend for Gbrowse
Postgresql, Mysql, and Flatfile (BDB)
implementations

11. 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

12. Education
BioPerl instruction through courses
at NESCent (Phyloinformatics)
Programming for Biology course at
CSHL
Several workshops at universities

13. 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

14. 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

15. Other Admin news
Plan to migrate from CVS to SVN in
August (George Hartzell)
Do we reorg to different logical
components (Core w/ sequences)

16. Major Kudos
Project Management & Leadership
Sendu Bala - Cambridge Univ
Chris Fields - Univ of Illinois,
Urbana-Champaign

17. 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