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	BioPerl - BioPerl
		Officially organized in 1995 and existing informally for several years prior, the BioPerl project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.
		BioPerl is released under the Perl Artistic License.
		Bioperl is the product of a community effort to produce Perl code which is useful in biology.
	www.bioperl.org /wiki/BioPerl (499 words)

	Bioinformatics.Org: BioPerl 1.0 Release
		Bioperl was developed by a loose collaboration of individuals worldwide, similar to the open development ethos in Linux or Apache.
		Bioperl was started in 1995, during the Perl4 heydays as young bioinformatics researchers started to share ideas about how to use this language in biology.
		Bioperl is used in both small academic labs through to enterprise level computing in large pharmaceutical companies.
	bioinformatics.org /forum/forum.php?forum_id=827 (523 words)

	Main Page - Bioperl.info
		BioPerl project is to provide easy programming modules to Biological community to enhance the development of science and technology.
		Throughout the period (and in the future) bioperl has been a natural consequence of many people who had the vision of sharing (an honest and true sharing rather than some empty echos with selfish interest to enhance their fame, influence etc).
		Bioperl and Biojava were not a mere technical advancement but they represent the nature of human beings: biological information objects.
	bioperl.net (438 words)

	ScienceCareers.org \| Bioperl: Open-Source Bioinformatics Tools: Stajich: 10 September 2004
		Bioperl is a tool kit for building applications in Perl as opposed to an already written suite of tools like EMBOSS.
		Bioperl offers a set of reusable components that can be used like building blocks to construct applications for bioinformatics analysis.
		Contributions to Bioperl are typically made by submitting a bug report or patch to the mailing list or the project's bug-tracking server.
	sciencecareers.sciencemag.org /career_development/previous_issues/articles/3220/bioperl_open_source_bioinformatics_tools (874 words)

	BioPerl
		The Bioperl project is open to all and we invite suggestions and participation from the larger bioinformatics community.
		The main people at bioperl are not computer scientists but self taught biologists who learned perl and programming generally because they had problems that they wanted to solve.
		Bioperl is all about being able to do interesting things and sharing the ability to get through the tedium of bioinformatics.
	www.biosino.org /bioinformatics/1024-2.htm (585 words)

	BioperlTutorial - a tutorial for Bioperl
		Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
		Although interface objects are not of much direct utility to the casual Bioperl user, being aware of their existence is useful since they are the basis to understanding how bioperl programs can communicate with other bioinformatics projects and computer languages such as Ensembl and biopython and biojava.
		Bioperl map objects can be used to describe any type of biological map data including genetic maps, STS maps etc. Map I/O is performed with the MapIO object which works in a similar manner to the SeqIO, SearchIO and similar I/O objects described previously.
	www.bioperl.org /Core/Latest/bptutorial.html (13894 words)

	bioperl-pipeline- Main page
		The bioperl pipeline framework is a flexible workflow system that complements the bioperl package in providing job managment facilities for high throughput analysis.
		One main feature of the bioperl pipeline is the flexibility in allowing the retrieval of multiple data inputs from a variety of input formats and databases.
		Data may be retrieved as long as the adaptors for the database is written and the data format is handled by the bioperl object layer.
	www.fugu-sg.org /bioperl-pipeline/bioperl-pipeline-about.html (639 words)

	So - we are always looking forward to people posting on the guts list
		Bioperl is a coordinated project which has a number of design features which allow it to be well used and extensible as well as collaborate with other packages.
		The biggest problem often in reusing a code base like Bioperl is that it requires both the people using it and the people contributing to it to change their attitude towards code.
		Bioperl is a truly collaborative project (the core code is the product of about 15 individuals) and anyone will be only contributing some part of it in the future.
	cpan.uwinnipeg.ca /htdocs/bioperl/biodesign.html (2561 words)

	Fink - Package Database - Package bioperl-pm581
		Bioperl is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications.
		On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER.
		Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
	pdb.finkproject.org /pdb/package.php/bioperl-pm581 (114 words)

	Morten/Bioperl - BINF - Bioinformatics Centre (Site not responding. Last check: 2007-10-31)
		Bioperl and the ensembl-api are large packages with many useful functions.
		Install bioperl and the ensembl-api on your computer by following the procedure described on the ensembl website.
		If you want you can look at the tutorials about bioperl or ensembl-api, but the basic stuff will also be covered during the course.
	www.binf.ku.dk /Morten/bioperl (551 words)

	[No title]
		It is very easy to write programs using the bioperl modules, as alot of the complex processing happens in the modules and not in the part of the program which you have to write.
		Bioperl is not a new version of perl, it just extends the standard perl for biological objects #!/usr/local/bin/perl These use lines actually import the bioperl modules.
		Bio::Seq is the bioperl main sequence object; Bio::SeqIO is the bioperl support for sequence input/output into files use Bio::Seq; use Bio::SeqIO; These two lines create two SeqIO streams: one for reading in sequences and one for outputting sequences.
	web.mit.edu /seven/share/bioperl-0.7.1/biostart.pod (708 words)

	Bioperl: LSR RFI
		Bioperl grew out of a recognition of the fact that Perl is being used with increasing frequency in bioinformatics for a variety of common information processing tasks.
		The Bioperl developers appreciate the power of the object-oriented approach and have implemented a variety of objects ("bio-objects") that encapsulate key data and behaviors of biological entities.
		The Bioperl developers are eager to join the effort for developing general standards and believe that the design of bio-objects should be language-neutral.
	www.omg.org /docs/corbamed/97-11-16.html (1782 words)

	Bioperl course
		This course introduces to the bioperl modules with examples and exercises.
		The course content has been upgraded to bioperl 1.0 (differences with bioperl version 0.7 are displayed in yellow color in the diagrams).
		Correspondance between an EMBL entry and bioperl tags
	www.pasteur.fr /recherche/unites/sis/formation/bioperl (134 words)

	BioPerlTutorial - a tutorial for bioperl
		Bioperl is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications.
		Bioperl has mainly been developed and tested under various unix environments (including Linux) and this tutorial is intended primarily for unix users.
		Bioperl map objects can be used to describe any type of biological map data including genetic maps, STS maps etc. Map I/O is performed with the MapIO object which works in a similar manner to the SeqIO, SearchIO and similar I/O objects described previously.
	www.cs.huji.ac.il /course/2003/bioskill/BioPerl/bptutorial.html (12543 words)

	BioPerl - Debian Wiki (Site not responding. Last check: 2007-10-31)
		Bioperl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.
		The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl.
		Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as CVS modules in our repository.
	wiki.debian.org /BioPerl (120 words)

	Bioperl and friends (Site not responding. Last check: 2007-10-31)
		Bioperl provides hundreds of reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats, and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER.
		Consequently, Bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web or GUI based systems.
		Bioperl has a website http://bioperl.org, which is a good place to start learning about Bioperl (in particular, the "Docs" and "HOWTOs" sections).
	www-biocomp.doit.wisc.edu /bioperl.shtml (220 words)

	[Bioperl-announce-l] Bioperl 1.0 Released
		Bioperl 1.0 Release Announcement --------------------------------- I am pleased to announce the release of verision 1.0 of the Bioperl toolkit.
		Bioperl is supported by the Open Bioinformatics Foundation (www.open-bio.org) which provides infrastructure for the projects.
		Go to http://bioperl.org/survey.html to help us gauge how useful the toolkit is to your work and where we can make improvements to address new areas of computational biology and bioinformatics.
	bioperl.org /pipermail/bioperl-announce-l/2002-March/000186.html (972 words)

	Main Page - BioPerl
		See what BioPerl Users are using the toolkit for and what publications cite the toolkit.
		BioPerl db package is a subproject to store sequence and annotation data in a BioSQL relational database (bioperl-db in CVS).
		BioPerl is distributed under the Perl Artistic License.
	www.bioperl.org (456 words)

	Bioperl OSX installation
		Installing BioPerl and dependencies on OS X 10.3 is pretty easy now, making this page close to obsolete.
		Install bioperl either from source (easy) or with the Fink installer (also easy).
		The bioperl installation requires root access, which you will get using the 'sudo' command and your password.
	www.tc.umn.edu /~cann0010/Bioperl_OSX_install.html (1576 words)

	ASPN : Cared for by Peter Schattner (Site not responding. Last check: 2007-10-31)
		Bioperl is a collection of perl modules that facilitate the development of perl scripts for bio-informatics applications.
		Bioperl supports remote execution of blasts at NCBI by means of the Blast.pm object.
		Bioperl supports a set of XML flags and vocabulary words for molecular biology - called bioxml - detailed at http://www.bioxml.org/dtds/current/ The idea is that any bioxml features can be turned into bioperl Bio::Seq annotations.
	aspn.activestate.com /ASPN/CodeDoc/bioperl/bptutorial.html (9641 words)

	The Bioperl Toolkit: Perl Modules for the Life Sciences -- Stajich et al. 12 (10): 1611 -- Genome Research
		Bioperl is written purely in Perl and requires at least version 5.005 of the Perl interpreter (the current stable version
		Because the Bioperl toolkit depends on the Perl interpreter, there are a number of rare cases in which its behavior is not
		Bioperl has >20 active developers led by a core of five primary developers who ensure that standards are met, prepare code
	www.genome.org /cgi/content/full/12/10/1611 (5290 words)


		This tutorial describes Perl and Bioperl and their application to practical problems in molecular biology sequence analysis.
		The tutorial includes an overview of the principal features of Perl and Bioperl relevant to biology, followed by examples of how they can be applied to common bioinformatics tasks.
		By the end of the tutorial, participants will have a sense of what capabilities Perl and Bioperl can provide them in molecular biology research, as well as pointers to resources for acquiring the skills and knowledge they will need in order to take advantage of them.
	conferences.oreillynet.com /cs/bio2002/view/e_sess/2441 (254 words)

	Bioperl FAQ
		Bioperl is a tookit of perl modules useful in building bioinformatics solutions in perl.
		Bioperl is licensed under the same terms as Perl itself which is the Perl Artistic License.
		Bioperl is a pretty diverse collection of modules which has grown from the direct needs of the developers participating in the project.
	www.math.lsa.umich.edu /~dburns/548/bioperl-1.2/doc/faq/faq.xml (2175 words)

	UMSI: User's Guide - BioPerl
		Bioperl is a tookit of perl modules useful in building bioinformatics programs in perl.
		The collection of modules in the bioperl makes easy for developing bioinformatics applications such as sequences analysis, as well as creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (bioperl-run).
		The bioperl has been configured into the same path as perl's.
	www.msi.umn.edu /software/bioperl (113 words)

	[No title]
		Bioperl was then taken up by people developing code at the large genome centres.
		Bioperl is used in anger at these sites, indicating that is both useful and that it works.
		At this time Bioperl was being used in absolute earnest by the Ensembl group which shook out a number of problems in the code base.
	web.mit.edu /seven/share/bioperl-0.7.1/bioperl.pod (1338 words)

	Bioperl
		At beginnings 2002 Bioperl 1.0 has been finally been released after about 7 years of the creation of Bioperl group.
		Bioperl package may also include a set of database SQL utilities.
		Definitively, Bioperl is an outstanding model and a very helpful tool for designing an any-scale work in Bioinformatics.
	www.arrakis.es /~toniher/transcout/x257.htm (180 words)

	Web services for bioinformatics, Part 1
		BioPerl has several modules, each of which can be used to create an application workflow in Perl.
		BioPerl library enables use of a collection of pre-built software objects for the applications.
		Most of the standard analysis tools such as BLAST and ClustalW are already included in the BioPerl libraries, so that all the end user needs to do is simply include those modules in the workflow and make the necessary function calls.
	www.ibm.com /developerworks/webservices/library/ws-bioinfo.html (2638 words)

	Cyde Weys Musings » BioPerl is an excellent package
		Add on top of that the large number of heuristics that can (and some should) be used to improve the alignment, and it’s quite the programming project.
		BioPerl is an amazing set of modules for Perl that does just about anything one would want to do in Bioinformatics.
		This entry was posted on Sunday, March 11th, 2007 at 22:33 and is filed under Tech, Personal, Maryland.
	www.cydeweys.com /blog/index.php/2007/03/11/bioperl-is-an-excellent-package (483 words)

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