[Bioperl-l] bioperl-1.5.0 released

Nathan Haigh nathanhaigh at ukonline.co.uk
Wed Jan 26 03:59:54 EST 2005


Would it be helpful for me to make the ppd file for bioperl-run 1.4 so people can install it easily using PPM?


Nathan


> -----Original Message-----
> From: Jason Stajich [mailto:jason.stajich at duke.edu]
> Sent: 25 January 2005 20:21
> To: nathanhaigh at ukonline.co.uk
> Cc: Bioperl list
> Subject: Re: [Bioperl-l] bioperl-1.5.0 released
> 
> I just don't have the time to do this right now. It has not really been
> tested for all tests passing.
> 
> if someone else wants to volunteer to work on validating it for release
> that would be great.
> 
> -jason
> On Jan 25, 2005, at 12:59 PM, Nathan Haigh wrote:
> 
> > Will there also be 1.5 releases for bioperl-run etc?
> >
> > Nathan
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at portal.open-bio.org
> >> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Jason
> >> Stajich
> >> Sent: 25 January 2005 02:37
> >> To: 'bioperl-l at bioperl.org' List; bioperl-announce-l at bioperl.org
> >> Subject: [Bioperl-l] bioperl-1.5.0 released
> >>
> >> Bioperl 1.5.0 Developer's release is available for download.
> >> ===============================================
> >>
> >>   http://bioperl.org/DIST/bioperl-1.5.0.tar.bz2
> >> 425ac55ecbb4339b7b532ba6d429bb40
> >>   http://bioperl.org/DIST/bioperl-1.5.0.tar.gz
> >> 172472f0675de9a583432e21c9b1b5fc
> >>   http://bioperl.org/DIST/bioperl-1.5.0.zip
> >> 3febcd2445a7393c65981a6f9f13a9ed
> >>
> >> We'll update the website to reflect this new release.
> >>
> >> The odd-numbered releases are called developer releases and are not
> >> deposited on CPAN.  Please note that the API in 1.5.0 may change
> >> before
> >> the 1.6.0 release. which will be consider a stable API.  We may do
> >> another developer release before 1.6.0 goes out.
> >>
> >> Lots of people have contributed to this release, I apologize for not
> >> naming them all.  I'll try to cover some: thanks to Aaron Mackey for
> >> getting this release started, Brian Osborne for extensive
> >> documentation
> >> improvements, Nathan Haigh for volunteering to make a PPM of the
> >> release and Barry Moore and Nathan answering many of the windows
> >> related questions, Allen Day & Scott Cain & Steffen Grossmann for the
> >> work on FeatureIO, GFF3, and SeqFeature::Annotated, Chris Mungall for
> >> the work with Unflattener to merge GenBank annotations into GFF3
> >> objects.
> >>
> >> Please see the AUTHORS file for a complete list of contributors.
> >>
> >> Jason Stajich on behalf of the Bioperl developers.
> >>
> >>
> >> Here is the info from the Changes file.
> >> 1.5 Developer release
> >>
> >>      o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
> >>        provide Jukes-Cantor and Kimura pairwise distance methods,
> >>        respectively.
> >>
> >>      o Bio::AlignIO support for "po" format of POA, and "maf";
> >>        Bio::AlignIO::largemultifasta is a new alternative to
> >>        Bio::AlignIO::fasta for temporary file-based manipulation of
> >>        particularly large multiple sequence alignments.
> >>
> >>      o Bio::Assembly::Singlet allows orphan, unassembled sequences to
> >>        be treated similarly as an assembled contig.
> >>
> >>      o Bio::CodonUsage provides new rare_codon() and probable_codons()
> >>        methods for identifying particular codons that encode a given
> >>        amino acid.
> >>
> >>      o Bio::Coordinate::Utils provides new from_align() method to
> >> build
> >>        a Bio::Coordinate pair directly from a
> >>        Bio::Align::AlignI-conforming object.
> >>
> >>      o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
> >>        Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
> >>        web service using standard Pubmed query syntax, and retrieve
> >>        results as XML.
> >>
> >>      o Bio::DB::GFF has various sundry bug fixes.
> >>
> >>      o Bio::FeatureIO is a new SeqIO-style subsystem for
> >>        writing/reading genomic features to/from files.  I/O classes
> >>        exist for BED, GTF (aka GFF v2.5), and GFF v3.  Bio::FeatureIO
> >>        classes only read/write Bio::SeqFeature::Annotated objects.
> >>        Notably, the GFF v3 class requires features to be typed into
> >> the
> >>        Sequence Ontology.
> >>
> >>      o Bio::Graph namespace contains new modules for manipulation and
> >>        analysis of protein interaction graphs.
> >>
> >>      o Bio::Graphics has many bug fixes and shiny new glyphs.
> >>
> >>      o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
> >>        indexing for HMMER reports and FASTA qual files, respectively.
> >>
> >>      o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
> >>        new objects that can be placed within a
> >> Bio::Map::MapI-compliant
> >>        genetic/physical map; Bio::Map::Physical provides a new
> >> physical
> >>        map type; Bio::MapIO::fpc provides finger-printed clone mapping
> >>        import.
> >>
> >>      o Bio::Matrix::PSM provide new support for postion-specific
> >>        (scoring) matrices (e.g. profiles, or "possums").
> >>
> >>      o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
> >>        be instantiated without explicitly using Bio::OntologyIO.  This
> >>        is possible through changes to Bio::Ontology::OntologyStore to
> >>        download ontology files from the web as necessary.  Locations
> >> of
> >>        ontology files are hard-coded into
> >>        Bio::Ontology::DocumentRegistry.
> >>
> >>      o Bio::PopGen includes many new methods and data types for
> >>        population genetics analyses.
> >>
> >>      o New constructor to Bio::Range, unions().  Given a list of
> >>        ranges, returns another list of "flattened" ranges --
> >>        overlapping ranges are merged into a single range with the
> >>        mininum and maximum coordinates of the entire overlapping
> >> group.
> >>
> >>      o Bio::Root::IO now supports -url, in addition to -file and -fh.
> >>        The new -url argument allows one to specify the network address
> >>        of a file for input.  -url currently only works for GET
> >>        requests, and thus is read-only.
> >>
> >>      o Bio::SearchIO::hmmer now returns individual Hit objects for
> >> each
> >>        domain alignment (thus containing only one HSP); previously
> >>        separate alignments would be merged into one hit if the domain
> >>        involved in the alignments was the same, but this only worked
> >>        when the repeated domain occured without interruption by any
> >>        other domain, leading to a confusing mixture of Hit and HSP
> >>        objects.
> >>
> >>      o Bio::Search::Result::ResultI-compliant report objects now
> >>        implement the "get_statistics" method to access
> >>        Bio::Search::StatisticsI objects that encapsulate any
> >>        statistical parameters associated with the search (e.g.
> >> Karlin's
> >>        lambda for BLAST/FASTA).
> >>
> >>      o Bio::Seq::LargeLocatableSeq combines the functionality already
> >>        found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
> >>
> >>      o Bio::SeqFeature::Annotated is a replacement for
> >>        Bio::SeqFeature::Generic.  It breaks compliance with the
> >>        Bio::SeqFeatureI interface because the author was sick of
> >>        dealing with untyped annotation tags.  All
> >>        Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
> >>        compliant, and accessible through Bio::Annotation::Collection.
> >>
> >>      o Bio::SeqFeature::Primer implements a Tm() method for primer
> >>        melting point predictions.
> >>
> >>      o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
> >>        InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
> >>
> >>      o Bio::Taxonomy::Node now implements the methods necessary for
> >>        Bio::Species interoperability.
> >>
> >>      o Bio::Tools::CodonTable has new reverse_translate_all() and
> >>        make_iupac_string() methods.
> >>
> >>      o Bio::Tools::dpAlign now provides sequence profile alignments.
> >>
> >>      o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
> >>
> >>      o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
> >>        parsers.
> >>
> >>      o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
> >>        for designing small inhibitory RNA.
> >>
> >>      o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
> >>        methods based on a distance matrix.
> >>
> >>      o Bio::Tree::Statistics provides an assess_bootstrap() method to
> >>        calculate bootstrap support values on a guide tree topology,
> >>        based on provided bootstrap tree topologies.
> >>
> >>      o Bio::TreeIO now supports the Pagel (PAG) tree format.
> >>
> >> --
> >> Jason Stajich
> >> jason.stajich at duke.edu
> >> http://www.duke.edu/~jes12/
> >> ---
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> >>
> >>
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> >
> >
> >
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
> ---
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> 

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