0
BioPerl Project
      Update
          Jason 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-b...
Welcome to the BioPerl Deobfuscator                                                                                     wh...
Gratuitous
       Statistics

975 modules in core, 375 in run

600,000+ lines of code/POD

Lots of emails go through the l...
Phylo-Hackathon
Hosted at National Evolutionary
Synthesis Center (www.nescent.org)

Several BioPerl participants focusing
...
Evolutionary Tools
Population Genetics tests and
processing code

  McDonald-Kreitman, Tajima’s D, LD

Phylogenetics

  Tr...
More Evolutionary
    Interfaces
Parsing and running of PAML for Ka,
Ks rates and model testing

PhastCons & PhyloFast int...
BioSQL support

Had been for storing sequence,
features, annotations

Postgresql and mysql schemas

New support for phylog...
GFF3 Support

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

Backend for Gbrowse

Postgresql, Mysql, and Fla...
Documentation

Two years since we started the
BioPerl Wiki and reorganized
documentation

Have expanded HOWTOs and user gu...
Education

BioPerl instruction through courses
at NESCent (Phyloinformatics)

Programming for Biology course at
CSHL

Seve...
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 ...
1.6 release needs

Remove broken code for auto feature
to string generation

Full Bio::FeatureIO support or
removal

Tidy ...
Other Admin news


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

Do we reorg to different logical
component...
Major Kudos

Project Management & Leadership



Sendu Bala - Cambridge Univ

Chris Fields - Univ of Illinois,
Urbana-Champ...
More Kudos
Nathan Haigh - Sheffield Univ

Hilmar Lapp - NESCent

Torsten Seeman - Monash University

Dave Messina - Washin...
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BioPerl Project Update

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Title: BioPerl Project Update
Author: Jason Stajich

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Transcript of "BioPerl Project Update"

  1. 1. BioPerl Project Update Jason Stajich (on behalf of BioPerl developers)
  2. 2. BioPerl Since ~1995 10s of developers over the years 2002 Publication cited ~500 times
  3. 3. DeObfuscator Interface to search available methods in objects Dave Messina and Laura Kavanaugh http://bioperl.org/cgi-bin/ deob_interface.cgi
  4. 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. 5. Gratuitous Statistics 975 modules in core, 375 in run 600,000+ lines of code/POD Lots of emails go through the list!
  6. 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. 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. 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. 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. 10. GFF3 Support Bio::DB::SeqFeature is interface for RDBMS for GFF3 storage Backend for Gbrowse Postgresql, Mysql, and Flatfile (BDB) implementations
  11. 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. 12. Education BioPerl instruction through courses at NESCent (Phyloinformatics) Programming for Biology course at CSHL Several workshops at universities
  13. 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. 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. 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. 16. Major Kudos Project Management & Leadership Sendu Bala - Cambridge Univ Chris Fields - Univ of Illinois, Urbana-Champaign
  17. 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
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