Remove Bio::Microarray from branch (still in development on trunk). May return later...

[bioperl-live.git] / README

# $Id$

This is the README file for the Bioperl central distribution.

o Version

 This is Bioperl version 1.5.2 from CVS HEAD

o Getting Started
 
 Thanks for downloading this distribution!

 Please see the the INSTALL or INSTALL.WIN documents for installation
 instructions.

 For tutorials see the Bioperl Tutorial.pl
 (http://www.bioperl.org/wiki/Bptutorial.pl) or the HOWTO documents and
 tutorials online at http://bioperl.org. To look at example code browse the
 scripts/ and examples/ directories

 For people starting out with Perl and Bioperl, look at the Bio::Perl module (go
 "perldoc Bio::Perl" from within this directory). This module is designed to
 flatten the learning curve for newcomers.

 For a list of OS's and versions that are known to support Bioperl see the
 PLATFORMS file.
 
 For info on Bioperl read on!

o About Bioperl

 Bioperl is a package of public domain Perl tools for computational molecular
 biology.

 Our website, http://bioperl.org, provides an online resource of modules,
 scripts, and web links for developers of Perl-based software for life science
 research.

o Contact info

 Bioperl developers: bioperl-l@bioperl.org

 There's quite a variety of tools available in Bioperl, and more are added all
 the time. If the tool you're looking for isn't described in the documentation
 please write us, it could be undocumented or in process.

 Project website : http://bioperl.org Project FTP server : bioperl.org
 (anonymous FTP ok)

 Bug reports : http://bugzilla.open-bio.org/

 Please send us bugs, in particular about documentation which you think is
 unclear or problems in installation. We are also very interested in functions
 which don't work the way you think they do!

 Please see the AUTHORS file for the complete list of bioperl developers and
 contributors.

o About the directory structure

 The bioperl directory structure is organized as follows:

 Bio/ - Bioperl modules models/ - DIA drawing program generated OO UML for
 bioperl classes
                   (These are quite out-of-date)
 t/ - Perl built-in tests. Tests are divided into subdirectories generally
                   based on the specific classes being tested
 t/data/ - Data files used for the tests - provides good data
                   examples for those new to bioinformatics data.
 scripts/ - Useful production-quality scripts with POD documentation examples/ -
 Scripts demonstrating the many uses of Bioperl maintenance/ - Bioperl
 housekeeping scripts

o Documentation

 The Bioperl Tutorial (http://www.bioperl.org/wiki/Bptutorial.pl) contains
 useful information for new and existing Bioperl users. This file also contains
 a number of useful scripts that the student of Bioperl may want to examine.

 Individual *.pm modules have their own embedded POD documentation as well. A
 complete set of hyperlinked POD, or module, documentation is available at
 http://www.bioperl.org.

 Remember that 'perldoc' is your friend. You can use it to read any file
 containing POD formatted documentation without needing any type of translator.
 
 If you used the Build.PL installation, and depending on your platform, you may
 have documentation installed as man pages, which can be accessed in the usual
 way.

 There is also an online course written at the Pasteur Institute. See
 http://www.pasteur.fr/recherche/unites/sis/formation/bioperl.

 Useful documentation in the form of example code can also be found in the
 examples/ and scripts/ directories. The current collection includes scripts
 that run BLAST, index flat files, parse PDB structure files, make primers,
 retrieve ESTs based on tissue, align protein to nucleotide sequence, run
 GENSCAN on multiple sequences, and much more! See bioscripts.pod for a complete
 listing.

o Releases
  
 Bioperl releases are always available from the website http://www.bioperl.org
 or by FTP from ftp://bioperl.org (note that we've had trouble with our new
 network setup which is not allowing FTP to support passive mode properly, use
 http://www.bioperl.org/DIST to get a listing of the distribution directory).
 Each release is tested with the test suite and cross-tested on a number of
 different platforms. See the PLATFORMS file for more information on a specific
 platform. All efforts are made to release a bug-free package, however most
 major bugs in a release will be documented in the BUGS file. See the Changes
 file for a listing of what features have been added or what APIs have changed
 between releases.

 Bioperl formerly used a numbering scheme to indicate stable release series vs.
 development release series. A release number is a three digit number like
 1.2.0. The first digit indicates the major release - the idea being that all
 the API calls in a major release are reasonably consistent. The second number
 is the release series. This is probably the most important number.
 
 From the 1.0 release until the 1.6 release, even numbers (1.0, 1.2 etc)
 indicated stable releases. Stable releases were well tested and recommended for
 most uses. Odd numbers (1.1, 1.3 etc) were development releases which one would
 only use if one were interested in the latest and greatest features. The final
 number (e.g. 1.2.0, 1.2.1) is the bug fix release. The higher the number the
 more bug fixes has been incorporated. In theory you can upgrade from one bug
 fix release to the next with no changes to your own code (for production cases,
 obviously check things out carefully before you switch over).
 
 The 1.6 release will be the last release series to utilize the alternating
 'stable'/'developer' convention. Starting immediately after the 1.6 branch, we
 will start splitting BioPerl into several smaller easier-to-manage
 distributions, including a developer distribution for cutting-edge (in
 development) code, untested modules, and alternative implementations.

o Caveats, warnings, etc

 When you run the tests ("./Build test") some tests may issue warnings messages
 or even fail. Sometimes this is because we didn't have anyone to test the test
 system on the combination of your operating system, version of perl, and
 associated libraries and other modules. Because Bioperl depends on several
 outside libraries we may not be able to test every single combination so if
 there are warnings you may find that the package is still perfectly useful. See
 the PLATFORMS file for reports of specific issues.
 
 If you install the bioperl-run system and run tests when you don't have the
 program installed you'll get messages like 'program XXX not found, skipping
 tests'. That's okay, Bioperl is doing what it is supposed to do. If you wanted
 to run the program you'd need to install it first.
 
 Not all scripts in the examples/ directory are correct and up-to-date. We need
 volunteers to help maintain these so if you find they do not work, submit a bug
 report to http://bugzilla.open-bio.org and consider helping out in their
 maintenance.

 If you are confused about what modules are appropriate when you try and solve a
 particular issue in bioinformatics we urge you to look at the Bioperl Tutorial
 or the HOWTO documents first.

o A simple module summary

 Here is a quick summary of many of the useful modules and how the toolkit is
 laid out:

 All modules are in the Bio/ namespace,
 - Perl is for newbies and gives a functional interface to the main parts of the
   package
 - Seq is for Sequences (protein and DNA).
   o Bio::PrimarySeq is a plain sequence (sequence data + identifiers)
   o Bio::Seq is a PrimarySeq plus it has a Bio::Annotation::Collection
     and Bio::SeqFeatureI objects attached (via Bio::FeatureHolderI).
   o Bio::Seq::RichSeq is all of the above plus it has slots for
     extra information specific to GenBank/EMBL/SwissProt files.
   o Bio::Seq::LargeSeq is for sequences which are too big for
     fitting into memory.
 - SeqIO is for reading and writing Sequences, it is a front end module for
   separate driver modules supporting the different sequence formats
 - SeqFeature - start/stop/strand annotations of sequences
   o Bio::SeqFeature::Generic is basic catchall
   o Bio::SeqFeature::Similarity a similarity sequence feature
   o Bio::SeqFeature::FeaturePair a sequence feature which is pairwise
     such as query/hit pairs
 - SearchIO is for reading and writing pairwise alignment reports like BLAST or
   FASTA
 - Search is where the alignment objects are defined
   o Bio::Search::Result::GenericResult is the result object (a blast query
     is a Result object)
   o Bio::Search::Hit::GenericHit is the Hit object (a query will have 0->
     many hits in a database)
   o Bio::Search::HSP::GenericHSP is the High-scoring Segment Pair
     object defining the alignment(s) of the query and hit.
 - SimpleAlign is for multiple sequence alignments
 - AlignIO is for reading and writing multiple sequence alignment formats
 - Assembly provides the start of an infrastructure for assemblies and
   Assembly::IO IO converters for them
 - DB is the namespace for all the database query objects
   o Bio::DB::GenBank/GenPept are two modules which query NCBI entrez
     for sequences
   o Bio::DB::SwissProt/EMBL query various EMBL and SwissProt
     repositories for a sequences
   o Bio::DB::GFF is Lincoln Stein's fast, lightweight feature and
     sequence database which is the backend to his GBrowse system (see
     www.gmod.org)
   o Bio::DB::Flat is a fast implementation of the OBDA flat-file
     indexing system (cross-language and cross-platform supported by O|B|F
     projects see http://obda.open-bio.org).
   o Bio::DB::BioFetch/DBFetch for OBDA, Web (HTTP) access to remote
     databases.
   o Bio::DB::InMemoryCache/FileCache (fast local caching of sequences
     from remote dbs to speed up your access).
   o Bio::DB::Registry interface to the OBDA specification for remote
     data sources
   o Bio::DB::Biblio for access to remote bibliographic databases.
   o Bio::DB::EUtilities is the initial set of modules used for generic
     queried using NCBI's eUtils.
 - Annotation collection of annotation objects (comments, DBlinks, References,
   and misc key/value pairs)
 - Coordinate is a system for mapping between different coordinate systems such
   as DNA to protein or between assemblies.
 - Index is for locally indexed flatfiles with BerkeleyDB
 - Tools contains many miscellaneous parsers and function for different
   bioinformatics needs
   o Gene prediction parser (Genscan, MZEF, Grail, Genemark)
   o Annotation format (GFF)
   o Enumerate codon tables and valid sequences symbols (CodonTable, IUPAC)
   o Phylogenetic program parsing (PAML, Molphy, Phylip)
 - Map genetic and physical map representations
 - Structure - parse and represent protein structure data
 - TreeIO is for reading and writing Tree formats
 - Tree is the namespace for all the associated Tree objects
   o Bio::Tree::Tree is the basic tree object
   o Bio::Tree::Node are the nodes which make up the tree
   o Bio::Tree::Statistics is for computing statistics for a tree
   o Bio::Tree::TreeFunctionsI is where specific tree functions are implemented
     (like is_monophyletic and lca)
 - Bio::Biblio is where bibliographic data and database access objects are kept
 - Variation represent sequences with mutations and variations applied so one
   can compare and represent wild-type and mutation versions of a sequence.
 - Root, basic objects for the internals of Bioperl

o Upgrading from an older version
 
 If you have a previously installed version of bioperl on your system some of
 these notes may help you.

 Some modules have been removed because they have been superceded by new
 development efforts. They are documented in the DEPRECATED file that is
 included in the release. In addition some methods, or the Application
 Programming Interface (API), have changed or been removed. You may find that
 scripts which worked with bioperl 1.4 may give you warnings or may not work at
 all (although we have tried very hard to minimize this!). Send an email to the
 list and we'll be happy to give you pointers.