[Biojava-l] BioJava Boot Camp

[Robert Stones]

Where and where will be the next BioJava bootcamp in th UK?

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> Today's Topics:
> 
>    1. North American BioJava Bootcamp August 18-22 in Montreal
>       (Sylvain Foisy)
>    2. genbank contig stuff (Matthew Pocock)
>    3. Re: genbank contig stuff (Matthew Pocock)
>    4. Re: Remove features from a sequence (Matthew Pocock)
>    5. Re: Remove features from a sequence (Keith James)
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 26 Jun 2003 13:20:31 -0400
> From: Sylvain Foisy <sylvain.foisy at bioneq.qc.ca>
> Subject: [Biojava-l] North American BioJava Bootcamp August 18-22 in
>         Montreal
> To: <biojava-l at biojava.org>
> Message-ID: <BB20A39F.3908%sylvain.foisy at bioneq.qc.ca>
> Content-Type: text/plain; charset="ISO-8859-1"
> 
> Hi,
> 
> BioneQ, the Quebec Bioinformatics Network, is organizing the first North
> American BioJava Bootcamp from August 18th to 22nd. We have invited Matthew
> Pocock to come to Montreal to present the material that has been presented
> to the European Bootcamps for quite some time now. On the agenda
> (preliminary):
> 
> -Sequence I/O and manipulations;
> -BLAST and FASTA parsing;
> -Using databases with BioJava;
> -Intro to Sequence GUI.
> 
> The bootcamp will be at the Universite de Montreal and the registration fee
> is $250US. If you are interested, use the following link to register:
> 
> http://132.204.90.239/bioneq/biojava_workshop.jsp
> 
> Please paste in your CV for evaluation of programming experience/knowledge.
> Places are quite limited (20) so register soon.
> 
> Cordially
> 
> Sylvain
> 
> ===================================================================
> Sylvain Foisy, Ph. D.
> Directeur - operations / Project Manager
> BioneQ - Reseau quebecois de bio-informatique
> U. de Montreal / Genome-Quebec
> 
> Adresse postale:
> 
> Departement de biochimie
> Pavillon principal
> 2900, boul. Édouard-Montpetit
> Montréal (Québec) H3T 1J4
> 
> Tel: (514) 343-6111 x.4066
> Courriel: sylvain.foisy at bioneq.qc.ca
> ===================================================================
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 26 Jun 2003 19:48:05 +0100
> From: Matthew Pocock <matthew_pocock at yahoo.co.uk>
> Subject: [Biojava-l] genbank contig stuff
> To: biojava-l <biojava-l at biojava.org>
> Message-ID: <3EFB3FE5.5070004 at yahoo.co.uk>
> Content-Type: text/plain; charset=us-ascii; format=flowed
> 
> Hi,
> 
> Has anybody looked at supporting genbank records with CONTIG blocks
> rather than sequences in them?
> 
> Matthew
> --
> BioJava Consulting LTD - Support and training for BioJava
> http://www.biojava.co.uk
> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 26 Jun 2003 19:57:50 +0100
> From: Matthew Pocock <matthew_pocock at yahoo.co.uk>
> Subject: [Biojava-l] Re: genbank contig stuff
> To: Matthew Pocock <matthew_pocock at yahoo.co.uk>
> Cc: biojava-l <biojava-l at biojava.org>
> Message-ID: <3EFB422E.8060903 at yahoo.co.uk>
> Content-Type: text/plain; charset=us-ascii; format=flowed
> 
> Sory - I fired that off without thinking much.
> 
> I just downloaded the genbank file NT_010783 from the ncbi. Our parsers
> spewed lots of errors about features not being within the range 1..0,
> and after a little poking arround in the code, I found that a zero
> length sequence was being generated. In despiration, I looked at the
> physical genbank file. Instead of sequences, it contains a CONTIG
> section with a single big join() describing how to build it from other
> entries.
> 
> Has anybody modified our genbank parser to process entries like this? To
> be honest, I'm not quite sure where to start.
> 
> Matthew
> 
> ------------------------------
> 
> Message: 4
> Date: Fri, 27 Jun 2003 10:29:30 +0100
> From: Matthew Pocock <matthew_pocock at yahoo.co.uk>
> Subject: Re: [Biojava-l] Remove features from a sequence
> To: "Schreiber, Mark" <mark.schreiber at agresearch.co.nz>
> Cc: biojava-l at biojava.org
> Message-ID: <3EFC0E7A.2030206 at yahoo.co.uk>
> Content-Type: text/plain; charset=us-ascii; format=flowed
> 
> Done. SimpleFeatureHolder wraps it's features() iterator using
> ListUtils.nonRemoveIterator(). All in cvs.
> 
> Matthew
> 
> ps Developers may wish to use this wrapper method in other places
> 
> >>So, on balance, I guess we should throw NotImplementedException on
> >>remove(). Unless somebody has a bright idea?
> 
> ------------------------------
> 
> Message: 5
> Date: 27 Jun 2003 11:50:47 +0100
> From: Keith James <kdj at sanger.ac.uk>
> Subject: Re: [Biojava-l] Remove features from a sequence
> To: Matthew Pocock <matthew_pocock at yahoo.co.uk>
> Cc: biojava-l at biojava.org
> Message-ID:
>         <sc4k7b7iyk8.fsf at maul.i-did-not-set--mail-host-address--so-shoot-me>
> Content-Type: text/plain; charset=us-ascii
> 
> >>>>> "Matthew" == Matthew Pocock <matthew_pocock at yahoo.co.uk> writes:
> 
>     Matthew> Done. SimpleFeatureHolder wraps it's features() iterator
>     Matthew> using ListUtils.nonRemoveIterator(). All in cvs.
> 
> Thanks! I'll go on a hunt for other places where this needs to be
> used...
> 
> Keith
> 
> --
> 
> - Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
> - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -
> 
> ------------------------------
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> End of Biojava-l Digest, Vol 6, Issue 29
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