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Bioperl 1.3 - Perl Modules for Biology
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If you're new to Bioperl, you should start reading F<bptutorial.pl>, an
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overview of the Bioperl toolkit.
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In the style of the perl documentation, core Bioperl documentation has
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been split up into the following sections:
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bioperl Bioperl overview (this document)
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biodatabases How to use databases with Bioperl
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biodesign A guide for authoring a Bioperl module
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bptutorial.pl Bioperl tutorial for beginners
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http://www.pasteur.fr/recherche/unites/sis/formation/bioperl
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=head2 References for Individual Modules
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For ease of maintenance and coordination amongst contributors, bioperl
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code is maintained in a modular form, as is the documentation. Refer to
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the documentation for individual modules by using perldoc, i.e.
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to get documentation for the Bio::Seq object.
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Bioperl is the product of a community effort to produce Perl code which is
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useful in biology. Examples include Sequence objects, Alignment objects
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and database searching objects. These objects not only do what they are
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advertised to do in the documentation, but they also interact - Alignment
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objects are made from the Sequence objects, Sequence objects have access
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to Annotation and SeqFeature objects and databases, Blast objects can be
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converted to Alignment objects, and so on. This means that the objects
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provide a coordinated and extensible framework to do computational
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Bioperl development focuses on Perl classes, or code that is used to
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create objects representing biological entities. There are scripts
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provided in the scripts/ and examples/ directories but scripts are not the
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main focus of the Bioperl developers. Of course, as the objects do most of
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the hard work for you, all you have to do is combine a number of objects
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together sensibly to make useful scripts.
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The intent of the Bioperl development effort is to make reusable tools
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that aid people in creating their own sites or job-specific applications.
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The bioperl.org website at http://bioperl.org also attempts to maintain
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links and archives of standalone bio-related Perl tools that are not
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affiliated or related to the core Bioperl effort. Check the site for
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useful code ideas and contribute your own if possible.
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The Bio::Perl module is designed to flatten the learning curve for
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newcomers to Perl/Bioperl. This is a good place to start if you want
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some simple functionality. We have a cookbook tutorial in
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bptutorial.pl which has embedded documentation. Start there if
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learning-by-example suits you most, or examine the Bioperl online
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http://www.pasteur.fr/recherche/unites/sis/formation/bioperl. Make
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sure to check the documentation in the modules as well - there are
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over 900 modules in Bioperl, and counting, and there's detail in the
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modules' documentation that will not appear in the general
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The Bioperl modules are distributed as a tar file that expands into a
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standard perl CPAN distribution. Detailed installation directions
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can be found in the distribution INSTALL file. Installing on windows
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using ActiveState Perl is covered in the INSTALL.WIN file.
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The Bioperl modules can now interact with local flat file and relational
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databases. To learn how to set this up, look at the biodatabases.pod
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documentation ('perldoc biodatabases.pod' should work once Bioperl has
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The bioperl-db, bioperl-run, bioperl-gui, corba-server, bioperl-ext,
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bioperl-pipeline, bioperl-microarray and corba-client packages are
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installed separately from Bioperl. Please refer to their respective
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documentation for more information.
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=head1 GETTING STARTED
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A good place to start is by reading and running the cookbook script,
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The distribution I<scripts/> directory has working scripts for use
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with Bioperl, check the self-described examples/ directory as well.
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A list and brief description of all these scripts is found
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in bioscripts.pod. You are more than welcome to contribute your script!
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If you have installed Bioperl in the standard way, as detailed in the
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INSTALL in the distribution, these scripts should work by just running
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them. If you have not installed it in a standard way you will
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have to change the 'use lib' to point to your installation (see INSTALL
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=head1 GETTING INVOLVED
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Bioperl is a completely open community of developers. We are not
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funded and we don't have a mission statement. We encourage
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collaborative code, in particular in Perl. You can help us in many
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different ways, from just a simple statement about how you have used
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Bioperl to doing something interesting to contributing a whole new object
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hierarchy. See http://bioperl.org for more information. Here are
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some ways of helping us:
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=head2 Asking questions and telling us you used it
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We are very interested to hear how you experienced using Bioperl. Did
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it install cleanly? Did you understand the documentation? Could you
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get the objects to do what you wanted them to do? If Bioperl was useless
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we want to know why, and if it was great - that too. Post a message to
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B<bioperl-l@bioperl.org>, the Bioperl mailing list, where all the developers
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Only by getting people's feedback do we know whether we are providing
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=head2 Writing a script that uses it
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By writing a good script that uses Bioperl you both show that Bioperl
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is useful and probably save someone elsewhere writing it. If you
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contribute it to the 'script central' at http://bioperl.org then other
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people can view and use it. Don't be nervous if you've never done this
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sort of work, advice is freely given and all are welcome!
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We know that there are bugs in there. If you find something which you are
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pretty sure is a problem, post a note to bioperl-bugs@bioperl.org and
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we will get on it as soon as possible. You can also access the bug
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system through the web pages.
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=head2 Suggest new functionality
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You can suggest areas where the objects are not ideally written and
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could be done better. The best way is to find the main developer
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of the module (each module was written principally by one person,
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except for Seq.pm). Talk to him or her and suggest changes.
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=head2 Make your own objects
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If you can make a useful object we will happily include it into the
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core. Probably you will want to read a lot of the documentation
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in L<Bio::Root>, talk to people on the Bioperl mailing list,
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B<bioperl-l@bioperl.org>, and read biodesign.pod. biodesign.pod provides
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documentation on the conventions and ideas used in Bioperl, it's definitely
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worth a read if you would like to be a Bioperl developer.
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=head2 Writing documentation
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We appreciate good documentation. It's what tells the world what's in
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Bioperl, it's what instructs the user, it's what describes the rationale
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and inner workings of the package. Feel free to contribute.
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=head1 ACKNOWLEDGEMENTS
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Bioperl owes its early organizational support to its association with
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the award-winning VSNS-BCD BioComputing Courses; some students of the
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1996 course (Chris Dagdigian, Richard Resnick, Lew Gramer, Alessandro
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Guffanti, and others) have contributed code and commentary. Georg
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Fuellen, the VSNS-BCD chief organizer was one of the early driving forces
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behind Bioperl. Steven Brenner, who was an early adopter of Perl for
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bioinformatics provided some of the early work on Bioperl. Lincoln Stein
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has long provided guidance and code.
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Bioperl was then taken up by people developing code at the large
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genome centres. In particular Steve Chervitz at Stanford, Ian Korf at
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the Genome Sequencing Centre (St. Louis) and Ewan Birney at the Sanger
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Centre (Cambridge UK). All of the C code XS extensions were
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provided by Ewan Birney. Bioperl is used in anger at these sites,
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indicating that is both useful and that it works.
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Jason Stajich and Hilmar Lapp joined Bioperl for the drive towards a
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0.7 release over 2000 and the first part of 2001, which includes a
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revised feature location model, richer feature objects (in particular
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genes) and more and better tools. Peter Schattner and Lorenz Pollak
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contributed serious chunks of code, being the AlignIO and bptutorial
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scripts and the BPLite port to Bioperl respectively. At this time
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Bioperl was being used in absolute earnest by the Ensembl group which
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shook out a number of problems in the code base. Additional
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compatibility with the Sequence Workbench (Bioperl-gui, Mark
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Wilkinson and David Block) and Biocorba (Jason Stajich, Brad Chapman
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and Alan Robinson) and finally Game-XML (Brad Marshall) provided more
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From 2001-2002 we saw the developer ranks swell and contributions
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increase with folks volunteering everything from bibliographic modules
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(Martin Senger) to new SCF chromatogram file parsers (Chad Matsalla
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and Aaron Mackey) to a new relational database and Bioperl layer for
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fast access to feature data (Lincoln Stein) as well as graphical
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rendering of sequences with features (Lincoln Stein). In early 2002
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Open-Bioinformatics foundation was formally incorporated as a
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non-profit organization (see http://www.open-bio.org) in the early
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part of 2002. We also participated in the 1st Bio-Hackathon that
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February which drew developers from several Open-Bio projects to
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lovely Cape Town, South Africa and the hospitality of the co-sponsor
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Electric Genetics (O'Reilly and Associates also co-sponsored the
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event, and AstraZeneca contributed to the sponsorship). In early May
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we released bioperl 1.0 as an effort to put a stamp of completeness on
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the toolkit and submitted a paper detailing the efforts thus far (see
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the FAQ). In late 2002 we released a developer release 1.1 for
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testing purposes and released bioperl 1.2 at the beginning of 2003.
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Current server hardware for bioperl.org (and other open-bio.org hosted
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projects) is provided by Sun. A previous server was provided by Compaq
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Computer Corporation. The compaq donation was facilitated by both the
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Pharmaceutical Sales and High Performance Technical Computing (HPTC)
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The Bioperl servers reside in Cambridge, Massachusetts USA with
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colocation facilities and Internet bandwidth donated by Genetics
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Institute. In particular Dr. Steven Howes, Kenny Grant &
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Rich DiNunno have made significant efforts on our behalf.
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Copyright (c) 1996-2003 Georg Fuellen, Richard Resnick, Steven E. Brenner,
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Chris Dagdigian, Steve Chervitz, Ewan Birney, James Gilbert, Elia Stupka,
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and others. All Rights Reserved. This module is free software; you can
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redistribute it and/or modify it under the same terms as Perl itself.
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