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	Biopython - BioPython
		The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
		The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world.
		The latest release is Biopython 1.42, released on 16 July 2006.
	www.biopython.org (111 words)

	Chapter 13. Biopython, continued
		One of the reasons there are so many parsers available is that Biopython relies on Martel (by Andrew Dalke), a scanner generator.
		For this purpose, we will build a simple parser for the Enzyme database, that is only able to store the enzyme ID and the references of an entry to other databases.
		In Biopython, parsing is often organized according to an event/callback model, one component, often called the scanner, generating parsing events when encountering a tag, and another component, often called the consumer, receiving and handling these events.
	www.pasteur.fr /recherche/unites/sis/formation/python/ch13.html (1149 words)

	The Scientist : Biopython Hits Version 1.3
		Hosted by the Open Bioinformatics Foundation (OBF), Biopython is an international effort to build reusable, open-source tools and libraries for bioinformaticians using an interpreted language called Python http://www.python.org.
		The clustering library is also written in C and supports biological algorithms such as hierarchical and k-means clustering, and self-organizing maps.
		Biopython programs can run on any platform for which a Python interpreter exists, including Windows, Mac OS, Linux (and other Unix variants), and OS/2.
	www.the-scientist.com /article/display/14780 (212 words)

	AgentMine.com » Blog Archive » Biopython (Site not responding. Last check: 2007-11-02)
		Biopython is a library of tools for computational biology that I have started working with.
		It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
		This entry was posted on Wednesday, November 2nd, 2005 at 1:55 pm and is filed under Bioinformatics.
	agentmine.com /blog/2005/11/02/biopython (129 words)

	Dalke Scientific Presentations at O'Reilly Bioinformatics Conference
		Biopython (www.biopython.org) is an international collaboration to collect and produce open source bioinformatics tools written in the Python programming language.
		Biopython is one of the projects developed under the umbrella of the Open Bioinformatics Foundation (
		The presentation will start with an overview of the Biopython project then show how the different aspects can be used to build a bioinformatics platform for a research group.
	www.dalkescientific.com /oreilly (252 words)

	BioProjects - SciRuby (Site not responding. Last check: 2007-11-02)
		BioRuby, Bioperl, Biopython and Bioconductor (for R) are all very popular and active opensource projects for interpreted languages.
		Biopython is also a large and serious library and chasing Bioperl.
		NOTE: this is not a Biopython vs. Bioperl comparison, nor a BioRuby versus Bioconductor comparison.
	sciruby.codeforpeople.com /sr.cgi/BioProjects (1076 words)

	JC's Project Suggestions 2003-04
		Biopython is a collection of Python modules which implement useful code for dealing with biological data (running remote database queries, manipulating biological sequences, etc).
		Biopython does not yet have all the utilities which the longer established Bioperl project has.
		The goal of this project is to extend Biopython's capabilities to better handle interacting with computer programs for aligning biological sequences.
	www-users.cs.york.ac.uk /~jc/teaching/projects/proj04.html (1000 words)

	FreshPorts -- biology/py-biopython
		The Biopython Project is an international association of developers who are providing freely available Python tools for use in areas of computational molecular biology such as bioinformatics and genomics.
		Biopython is a collection of Python packages and modules created by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language.
		Add py-biopython, is a collection of Python packages and modules created by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language.
	www.freshports.org /biology/py-biopython (356 words)

	Biopython API documentation
		Martel (now included in Biopython by default, so don't worry about adding this)
		Biopython is run by volunteers from all over the world, with many types of backgrounds.
		We are always looking for people interested in helping with code development, web-site management, technical administration, and whatever else comes up.
	www.bioinformatics.org /bradstuff/bp/api (377 words)

	Documentation - BioPython
		Documentation for Biopython modules is generated directly from source code comments using Epydoc.
		Ravinder Singh and Scott Kelley teach a Bioinformatics course using Biopython at the University of Colorado.
		Thomas wrote an applications note[1] for Bioinformatics about the Biopython PDB parser and related code dealing with crystal structures.
	biopython.org /wiki/Documentation (279 words)

	Bioinformatics - Tools, softwares & Programmes
		Biopython and biojava are open source projects with very similar goals to bioperl.
		With the development of interface objects and biocorba, it is possible to write java or python objects which can be accessed by a bioperl script, or to call bioperl objects from java or python code.
		Since biopython and biojava are more recent projects than bioperl, most effort to date has been to port bioperl functionality to biopython and biojava rather than the other way around.
	www.geocities.com /bioinformaticsweb/tools.html (1558 words)

	The Third Bit » Blog Archive » Contributing to Open Source
		I first ran into Biopython when I started working in the Botany Department at U of T. Perl is the language of (no) choice for bioinformatic projects simply because the BioPerl modules are so mature.
		When I investigated Python, I found a Biopython project had already started and was playing catch up to BioPerl.
		The problem was of course that Biopython was still quite a bit behind its older brother.
	pyre.third-bit.com /blog/archives/177.html (489 words)

	Using FASTA nucleotide files in BioPython
		This is an example Python program to calculate GC percentages for each gene in an nucleotide FASTA file - using the BioPython Fasta library.
		BioPython uses the term iterator to mean an lump of code we can use to step through the records in a file (i.e.
		I don't think this was possible in earlier version of BioPython, and the cookbook could be updated.
	www2.warwick.ac.uk /fac/sci/moac/currentstudents/peter_cock/python/fasta_n (1098 words)

	gmane.comp.python.bio.general
		I parsed a Genbank file using BioPython and got this: >>> f = rec.features[1] >>> print f type: gene location: [221:1607] ref: None:None strand: 1 qualifiers: Key: db_xref, Value: ['GeneID:911526'] Key: locus_tag, Value: ['MYPU_0010'] Key: note, Value: ['dnaA'] Note the coordinates - the feature's start position is 221 and end position is 1607, seemingly.
		Hello, I have searched through Biopython and have not been able to find an OBO file format parser (see http://www.geneontology.org/GO.format.shtml).
		While this isn't a BioPython issue per se, it might impact those trying to install the BioPython required files on the new architecture.
	blog.gmane.org /gmane.comp.python.bio.general (1252 words)

	BioMed Central \| Full text \| CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for ...
		The alignments are subsequently processed by the Bio.CAPS module, which we created and have submitted to the Biopython repository [13].
		The Bio.CAPS package can also utilize Biopython's Bio.Emboss.Primer module, a wrapper for a primer design program called Primer3 [12], so that primers may be generated using a need_primers call.
		When the user asks for CAPS markers to be created, many Biopython modules are employed in series to generate a marker set.
	www.biomedcentral.com /1471-2156/7/27 (1824 words)

	Protein Expression Supplementary Material
		The sequence analysis modules I wrote are available through Biopython but require programming skills.
		The calculation was described by Sharp and Li and is performed using the codon usage module I submitted to biopython.
		The modules I used for the article are more advanced than the modules I submitted to biopython, mostly because they are imbeded in ZODB infrastructure.
	homepage.mac.com /ybenita/research/protein/index.html (364 words)

	3D SIG ISMB Special Interest Scientific Registration List (Site not responding. Last check: 2007-11-02)
		In this direction, both in the design and implementation processes Biopython (http://www.biopython.org) modules were employed as references for code styling and file parsing modes.
		Trajectory and Frame classes model the traditional Molecular Dynamics objects with the ability to manipulate initial structure and simulation frames, and to run basic geometrical analyses directly, whereas Property and Fragment are aimed to manage internal and external processed data.
		The Biopython PDBParser and SMCRA (Structure-Model-Chain-Residue-Atom) model was employed to describe structures.
	www.weizmann.ac.il /usersfiles/3dsig/abstracts/2004/49.html (916 words)

	The Science Advisory Board - Protocols, Product Reviews, Member Forum, and Science News (Site not responding. Last check: 2007-11-02)
		Biopython is an international association of python professionals working in the area of bioinformatics.
		The site offers an incredible array or python based modules which are ready to use pieces of code to perform various tasks of analyzing biological sequences and structures.
		Biopython (Latest version 1.00a4) also incorporates interoperability with CORBA in its biopython-corba-0.3.0.
	www.scienceboard.net /resources/links.asp?linkId=276 (473 words)

	BioPython Tutorial
		On th elab machines, Biopython package is residing in “/usr/local/lib/python2.3/site-packages”.
		The first is to grab the info using the biopython blast function for dealing with blast, described above.
		do not have to use biopython scripts to fetch the data in order to be able to parse it.
	aleph0.clarku.edu /~achou/binf101_2004/biopython_notes.html (2033 words)

	Blog for dalke
		Sent another email asking if it is allowed at non-terminal elements, or inside of {}s.
		Haven't gotten any email back from people on biopython about the code I released last week.
		Biopython might count, but no one is using it yet.
	www.advogato.org /person/dalke/diary.html?start=4 (1407 words)

	[BioPython] Updates to the source tree (Site not responding. Last check: 2007-11-02)
		I was also going to try and get biopython-corba ready so it was distutils friendly, but I'm not positive how we want biopython-corba to be related to biopython.
		The way it is set up right now, the biopython-corba stuff would go in a separate directory in site-packages (Biocorba) from the main biopython package (which goes in Bio).
		The reason I thought this was a good idea is that then you can call the "biopython-lookalike" interface with code like: from Biocorba.Bio.Seq import Seq So to change Biocorba code to Biopython code, you would just have to drop the Biocorba part of the import.
	open-bio.org /pipermail/biopython/2000-May/000256.html (472 words)

	BioMed Central \| Full text \| A high level interface to SCOP and ASTRAL implemented in Python
		In the past we have successfully used this API to develop a web-based database of SCOP alignments, S4 The API described is now distributed as part of the Biopython suite for bioinformatics [5].
		Using the Biopython framework for handling FASTA files, sequences for SCOP domains can be quickly returned.
		The API is distributed as part of the Biopython suite for bioinformatics http://www.biopython.org.
	www.biomedcentral.com /1471-2105/7/10 (1493 words)

	[Tutor] Simple string processing problem (Site not responding. Last check: 2007-11-02)
		Hello Chris, Since this does look like a biologically-driving example, you may want to make sure that no one else has already done this work for you.
		BioPython is a collections of programs written for bioinformatics work in Python: http://biopython.org/ and you may want to just double check to see if someone has already done the work in parsing that data.
		If so, you should be aware that a Biopython parser does exist in the 'Bio.Clustalw' module package: http://biopython.org/docs/api/public/Bio.Clustalw-module.html And if you are willing to look at BioPython, then take a look at section 11.6.2 of: http://www.pasteur.fr/recherche/unites/sis/formation/python/ch11s06.html for an example of parsing a CLUSTALW file with BioPython.
	mail.python.org /pipermail/tutor/2005-May/038410.html (270 words)

	Python course in Bioinformatics
		What distinguishes this course from general Python introductory courses, is however the important focus on biological examples that are used throughout the course, as well as the suggested exercises drawn from the field of biology.
		The second half of the course describes the Biopython (http://www.biopython.org/) set of modules.
		This course can be considered a complement to the Biopython tutorial, and what's more often refers to it, by bringing practical exercises using these components.
	www.pasteur.fr /recherche/unites/sis/formation/python (314 words)

	Re: FC4- Biopython (Site not responding. Last check: 2007-11-02)
		I don't know of a repo with biopython and dependencies.
		I don't know about their quality; that is, whether they have Biopython's dependencies listed properly.
		Also, since Biopython uses distutils, you could probably make your own RPM from the source tarball by issuing the command "python setup.py bdist_rpm" in the source directory that setup.py is in.
	www.redhat.com /archives/fedora-list/2005-December/msg03352.html (148 words)

	Welcome to Dalke Scientific Software
		Instead, we provide robust, usable components and the expertise of how to use them so that you can solve your problems using your resources.
		Biopython is an international collaborative project to develop open source tools for bioinformatics based on the Python programming language.
		Dalke Scientific is a major supporter of Biopython.
	www.dalkescientific.com (250 words)

	Amazon.com: BioPython: Books (Site not responding. Last check: 2007-11-02)
		Get it by Thursday, December 21, if you order in the next 1 hour and 59 minutes.
		2 [18] and C with the Biopython 1.00a4 and mxTextTools 2.0.3 libraries.
		is strongly encouraged to visit http://www.open-bio.org and examine the Biojava, BioPython, and BioRuby projects, which provide similar extensions to the traditional...
	www.amazon.com /s?ie=UTF8&keywords=BioPython&tag=httpexplaguid-20&index=books&link_code=qs&page=1 (908 words)

	Peter's Python Programming Pages
		There is a Beginners Guide, and I have found searching on Google for specific questions very handy.
		I contribute to Biopython, an add-on module which provides support for lots of Bioinformatic work:
		Biopython 1.30 did not include any code for dealing with tree files - but check out the new Nexus module in BioPython 1.40b onwards from Frank Kauff and Cymon Cox, which should be a nice alternative.
	www2.warwick.ac.uk /fac/sci/moac/currentstudents/peter_cock/python (402 words)

	Flags and Lollipops - Bioinformatics Blog: Google Maps meets GBrowse
		Also visualisation related is a new paper in Bioinformatics by Leighton Pritchard from the Scottish Crop Research Institute, which describes a Bio::Graphics style package for BioPython.
		I don't use BioPython, so I can't say much more about it other than to note that the graphics in the user manual certainly look nice.
		Genome Diagram is a great package - you only need BioPython installed to use it, no BioPython knowledge required.
	www.ghastlyfop.com /blog/2006/03/google-maps-meets-gbrowse.html (484 words)

	gmane.comp.python.bio.general (Site not responding. Last check: 2007-11-02)
		Hello, I'm attempting to get sequence data from a DAS server (UCSC, DAS1) and am having what appears to be a unicode-related problem - if you have any insights or advice, I'd be grateful for the help.
		Change to All messages, whole messages, or hide cited text.
		[BioPython] Postdoctoral Position - Systems/Computational Biology (26 Oct 17:19)
	blog.gmane.org /gmane.comp.python.bio.general?set_skin=rightmenu (1252 words)

	[MMTK] ANN: Biopython.org (Call for Participation) (Site not responding. Last check: 2007-11-02)
		The Biopython Project (http://www.biopython.org/) is a new open collaborative effort to develop freely available Python libraries and applications that address the needs of current and future work in bioinformatics, including sequence analysis, structural biology, pathways, expression data, etc. When available, the source code will be released as open source (http://www.biopython.org/License.shtml) under terms similar to Python.
		This is a Call for Participation for interested people to join the project.
		We are hoping to attract people from a diverse set of backgrounds to help with code development, site maintenance, scientific discussion, etc. This project is open to everyone.
	starship.python.net /pipermail/mmtk/1999/000179.html (146 words)

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