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'ontology-overhaul-start'.

svn path=/bioperl-live/tags/ontology-overhaul-start/; revision=5638
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1 parent e4ca546 commit e7c0f160035fca42514bb4e6d633ea180480c417 nobody committed Feb 28, 2003
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-=head1 PRIMARY AUTHORS AND MAJOR CONTRIBUTORS TO BIOPERL
-
-=head2 Releases co-ordinated and submitted by bioperl core devs.
-
-=over
-
-=item * Ewan Birney <birney at ebi.ac.uk>
-
-=item * Chris Dagdigian <dag at sonsorol.org>
-
-=item * Hilmar Lapp <hilmarl at yahoo.com>
-
-=item * Heikki Lehvaslaiho <heikki at ebi.ac.uk>
-
-=item * Jason Stajich <jason at bioperl.org>
-
-=item * Lincoln Stein <stein at cshl.org>
-
-=back
-
-=head2 Previous Bioperl Coordinators:
-
-=over
-
-=item * Steven Brenner <brenner at compbio.berkely.edu>
-
-=item * Georg Fuellen <fuellen at alum.mit.edu>
-
-=item * Steve Chervitz <sac at bioperl.org>
-
-=back
-
-=head2 Major Contributors
-
-(Feel free to add descriptions of which modules you are responsible
-for if you see fit)
-
-=over
-
-=item * Kris Boulez <kris.boulez at algonomics.com>
-
-=item * David Block <dblock at gnf.org>
-
-=item * Tim Bunce <Tim.Bunce at pobox.com> Code optimizations
-
-=item * Brad Chapman <chapmanb at arches.uga.edu>
-
-=item * Steve Chervitz <sac at bioperl.org>
-
-=item * Michele Clamp <michele at sanger.ac.uk>
-
-=item * Tony Cox <avc at sanger.ac.uk>
-
-=item * James Cuff <james at sanger.ac.uk>
-
-=item * Andrew Dalke <dalke at acm.org>
-
-=item * Allen Day <allenday at ucla.edu>
-
-=item * James Diggans <JDiggans at genelogic.com>
-
-=item * Arne Elofsson <arne at sbc.su.se>
-
-=item * Mark Fiers <M.W.E.J.Fiers at plant.wag-ur.nl>
-
-=item * Georg Fuellen <fullen at bioperl.org>
-
-=item * James Gilbert <jgrg at sanger.ac.uk>
-
-=item * Ed Green <ed at compbio.berkeley.edu>
-
-=item * Roger Hall <roger at iosea.com>
-
-=item * Ian Holmes <ihn at fruitfly.org>
-
-=item * Shawn Hoon <shawnh at fugu-sg.org>
-
-=item * Joseph Insana <insana at ebi.ac.uk> - Bio::LiveSeq
-
-=item * Nicolas Joly <njoly at pasteur.fr>
-
-=item * Ian Korf <ikorf at sapiens.wustl.edu>
-
-=item * Arek Kasprzyk <arek at ebi.ac.uk>
-
-=item * Catherine Letondal <letondal at pasteur.fr>
-
-=item * Aaron Mackey <amackey at virginia.edu>
-
-=item * Brad Marshall <bradmars at yahoo.com>
-
-=item * Chad Matsalla <bioinformatics1 at dieselwurks.com>
-
-=item * Chris Mungall <cjm at fruitfly.bdgp.berkeley.edu>
-
-=item * Brian Osborne <brian_osborne at cognia.com>
-
-=item * Jong Park
-
-=item * Matthew Pocock <matthew_pocock at yahoo.co.uk>
-
-=item * Lorenz Pollack <lorenz at ist.org> -- BPlite porting
-
-=item * Richard Resnick -- original Bio::Seq
-
-=item * Todd Richmond <todd at andrew2.stanford.edu>
-
-=item * Peter Schattner <schattner at alum.mit.edu>
-
-=item * Martin Senger <senger at ebi.ac.uk> -- Biblio
-
-=item * Allen Smith <allens at cpan.org> -- Bio::Matrix and Bio::SimpleAlign fixes
-
-=item * Arne Stabenau <stabenau at ebi.ac.uk>
-
-=item * Elia Stupka <elia at fugu-sg.org>
-
-=item * Gert Thijs <gert.thijs at esat.kuleuven.ac.be>
-
-=item * Charles Tilford <tilfordc at bms.com>
-
-=item * Paul-Christophe Varoutas
-
-=item * Andrew G. Walsh <paeruginosa at hotmail.com>
-
-=item * Kai Wang <tumorimmunology at yahoo.com>
-
-=item * Mark Wilkinson <mwilkinson at gene.pbi.nrc.ca>
-
-=item * Helge Weissig <helgew at sdsc.edu>
-
-=item * Alex Zelensky <alex_zelensky at mac.com> - Bioperl-DB
-
-=back
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-# $Id: BUGS,v 1.4 2002-12-31 13:09:05 birney Exp $
-
-Known Bugs
-
-Bioperl 1.2
-===========
-
- * The searchio.t test is failing on cygwin installations (and
- nowhere else). We need a developer who works with cygwin to
- help us out here. We suspect something to do with temporary file
- opening.
-
-
-Bioperl 0.9.0
-=============
- * Bio::Tools::Blast continues to cause problems for some people. As
- it is not actively maintained there are a slew of reported bugs for
- it that have not been fixed.
-
- * Bio::Tools::Run::Alignment::TCoffee - t_coffee binary does not get
- all parameters it needs when aligning (two) two DNA sequences
- (jitterbug #966).
-
- * Bio::Tools::Run::ClustalW and t/ClustalW will report errors for
- clustalw versions 1.8x due to a bug in clustalw.
-
- * Bio::DB::GenBank continues to have intermittent errors. Bio::DB::GDB
- is also unreliable at times and one can safely ignore errors from
- these during a make test.
- Bio::DB::GenBank is unable to download whole contig files as well
- as NCBI ref seqs like NT_* numbers unless the -format flag is
- passed in and specified as 'fasta' in the constructor.
- get_Stream_by_batch() also has intermittent errors which are being
- tracked down.
-
-Bioperl 0.7.2
-=============
-
- * NCBI has changed some of the cgi scripts for retrieving sequences
- online which as resulted in some of the DB methods from not working
- consistently. We are addressing these in the 0.9.x and 1.0 series
- of releases. We recommend using the Bio::DB::EMBL object that is
- part of the later releases.
-
- Additionally RefSeq Contigs are not properly downloaded, please see
- the bioperl list archives for information about potential
- workarounds and ongoing development effort to address these.
-
-Bioperl 0.7.1
-=============
- * Bio::Tools::BPlite does not parse and set frame properly for
- tblastx reports (Jitterbug bug # 978).
-
- * Bio::Tools::BPlite interface needs to be updated to fix parsing
- more than bl2seq report report (Jitterbug bug #940), this has been
- fixed on the main code trunk and will be part of the next major
- bioperl release.
-
- * If File::Temp is not installed, tempdirs are not cleaned up
- properly. This is fixed on main code trunk with the introduction
- of rmtree method in Bio::Root::IO, however, it is best to install
- File::Temp when running 0.7 branch code.
-
- * Bio::Tools::Blast does not allow users to run blast, instead use
- Bio::Tools::Run::StandAloneBlast to run local blasts. To submit
- jobs to a remote blast server like NCBI a module
- Bio::Tools::Run::RemoteBlast has been written but is part of the
- main trunk code and must be obtained through CVS until the next
- major bioperl release.
-
-Bioperl 0.7
-===========
- * Bio::Tools::BPlite doc error lists
- code synopsis code as
- my $parser = new BPlite(\*FH);
- should be
- my $parser = new Bio::Tools::BPlite(\*FH);
-
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