The Biopython project is a distributed collaborative effort to develop [[Python]] libraries and applications which address the needs of current and future work in [[Bioinformatics]]. It's a project in [[OBF]] 
 
http://www.biopython.org 

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== Useful information ==

 * ViewCvs : http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biopython
 * EpyDoc : http://www.biopython.org/docs/api/public/frames.html
 * BioPythonInstall
 * [[http://www.biopython.org/wiki/html/BioPython/FrontPage.html|BioPython WikiWiki]]
 * [[http://mcdb.colorado.edu/courses/6440/index.html|BioPython Course in Colorado]]
 * [[http://biopython.org/pipermail/biopython-dev/|The Biopython-dev Archives]]

== Document in internet ==

 * BioPythonTutorial
 * PythonCourseInBioinformatics
 
== Biopython Documentation Project ==
 
 * BioPythonStudy in [[Sefiroth]]
  * BioPythonTutorial translation
  * BioPythonCodeAnalysis
  * BioPythonTip
  * BioPythonFaq
 
 * Articles
  * [[LabStoryOfMrK]]
  * MakeRdbUsingBioPython

== Example code ==

 * ReverseComplement : [[ReverseComplementBioPython.py]]
 * FastaFormat
 * PineGenomeComparisonUsingEntrez

== News (TopInsert) ==

'''2006-09''' UbuntuLinux 에 패키지로 등록되다.

'''2004-05-14''' 1.30 [[http://portal.open-bio.org/pipermail/biopython/2004-May/002078.html|릴리즈]]. 점차 다양한 모듈들이 가세되고, 기존 모듈도 꾸준히 수정되고 발전되고 있다. 이번변화를 정리하여 표현하면,
 * 새로운 모듈 및 기능들
  * Affy package added for dealing with [[Affymetrix]] cel files 
  * [[Parsing]] of [[BLAST]] [[XML]]
  * [[Parsing]] of [[Compass]] output 
  * Tm calculation module in PrimerDesign
  * lowess function for non-parameteric regression 
  * Reduced protein alphabet supported  
  * Added pgdb (PyGreSQL) support to [[BioSQL]]
 * 문서화 
  * Logistic Regression and Bio.PDB 
  * Added for converting between file formats.
  * Updates to install documentation for non-root users 
  * epydoc now used for automatic generation of documentation.
 * 속도향상 및 편리성강화
  * FastaFormat parser : allowing better speed and dealing with large data files.
  * Registry code. Now 'from Bio import db' gives you a number of new retrieval options, including [EMBL], FastaFormat, GenBank, InterPro, ProDoc and SwissProt.
  * GenBank parser uses new [[Martel]] format. GenBank retrieval now uses EUtils instead of the old non-working [Entrez] scripts. GenBank indexing uses standard Mindy indexing. Fix for valueless qualifiers in feature keys 
 * 업데이트 및 버그수정
  * Bio.PDB  
  * Ace parser (아쉬운부분... 나도 좀 기여했는데, 내얘기는 없었다. ㅡ.ㅡ;)
  * Added pgdb (PyGreSQL) support to [[BioSQL]]
  * using Py2Exe and Biopython 
  * PsiBlast parser 
  * NCBIWWW retrieval so that [[HTML]] results are returned correctly.
  * [[ClustalW]] to handle question marks in title names 
  * [[NBRF]] parsing to it accepts files produced by [[ClustalW]]
  * [[Enyzme]] module 
  * bugs in SeqUtils 
  * optional hsps in ncbiblast Martel format
  * FastaFormat parsing to allow # comment lines 
  * [[Cee]] [[Clustering]] library 
  * Fixes for breakage in the [[SCOP]] module and addition of regression tests to framework 
  * Various fixes to Bio.Wise 
  * Fix for bug in FastaReader 
  * Fix EUtils bug where efetch would only return 500 sequences.
  * Updates for [[EMBOSS]] commandlines, water and tranalign.
  * Fixes to the FormatIO system of file conversion.
  * [[C++]] code (KDTree, Affy) now compiled by default on most platforms 
 * Deprecation
  * Bio.sequtils -- use Bio.SeqUtils instead.
  * Bio.SVM -- use libsvm instead.
  * Bio.kMeans and Bio.xkMeans -- use Bio.cluster instead.
  * RecordFile -- doesn't appear to be finished code.


'''2004-02-28'''
 * new FastaFormat parser가 Brad Chapman에 의해 [[CVS]]에 커밋되다. 이번파서는 특히도 느렸던 부분을 매우 빠르게 동작하도록 바꾼것으로, MxExtension, 및 [[Cee]]코드가 쓰여져서, 특히도 거대한 파일 [[Parsing]]에 적합하다고 합니다.

'''2004-02-17''' 버젼 1.24 릴리즈
 * New parsers for [[Phred]] and Ace format files
 * New Code for dealing with [[NMR]] data 
 * New SeqUtils modules for CodonUsage, IsoelectricPoint and other [[Protein]] properties
 * New code for dealing with Wise
 * [[Entrez]]-Retrieve sequence retrieval now supported
 * Bio.Cluster updated along with documentation
 * BioSQL fixed so it now works with the current [[SQL]] schema 
 * Patches to Bio/__init__ to make it compatible with Py2Exe
 * Added __iter__ to all BioPython Iterators to make them Python 2.2 compatible (See PythonNewFunction)
 * Fixes to NCBIWWW for retrieving from [[NCBI]]
 * Retrieval of MultipleAlignment objects from [[BLAST]] records
 * Fixes to GenBank format for new tags
 * [[Parsing]] fixes in [[ClustalW]] parsed
 * FastaFormat Indexes can have a specified filename 
 * Fix to [[PROSITE]] parser

'''2003-07-27''' 버젼1.2 릴리즈
 * Andrew Dalke EUtils library for accessing [[Database]] at [[NCBI]] ([[Entrez]] programming utility)
 * Michiel de Hoon's gene expression analysis package 
 * Thomas Hamelryck's [[PDB]] package. 

'''2002-12-24''' 버젼1.1릴리즈
 * 이번버전에는 HiddenMarkovModel, NeuralNetwork, GeneticAlgorithm등이 포함됨 ([[CVS]]로 소스들을 보시면, UnitTest 코드들, 예제들이 많습니다. (지금보니깐, HiddenMarkovModel 테스트코드에 dishonest casino도 있네요. 주석내용말하길 RichardDurbin's BiologicalSequenceAnalysis의 예제라고 합니다. 우리들이 BSA공부할때, 지구반대편에서, 그책의 HMM내용으로 코드를 만들고 있었다고 생각하니 기분이 묘하군요)

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CategoryProgramLibrary