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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]  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]]
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 * BioPythonStudy in [Sefiroth]  * BioPythonStudy in [[Sefiroth]]
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  * [LabStoryOfMrK]   * [[LabStoryOfMrK]]
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 * ReverseComplement : [ReverseComplementBioPython.py]  * ReverseComplement : [[ReverseComplementBioPython.py]]
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  * Affy package added for dealing with [Affymetrix] cel files
  * [Parsing] of [BLAST] [XML]
  * [Parsing] of [Compass] output 		  * Affy package added for dealing with [[Affymetrix]] cel files
  * [[Parsing]] of [[BLAST]] [[XML]]
  * [[Parsing]] of [[Compass]] output
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  * Added pgdb (PyGreSQL) support to [BioSQL]   * Added pgdb (PyGreSQL) support to [[BioSQL]]
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  * 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   * 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
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  * Added pgdb (PyGreSQL) support to [BioSQL]   * Added pgdb (PyGreSQL) support to [[BioSQL]]
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  * 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 		  * 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
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  * [Cee] [Clustering] library
  * Fixes for breakage in the [SCOP] module and addition of regression tests to framework 		  * [[Cee]] [[Clustering]] library
  * Fixes for breakage in the [[SCOP]] module and addition of regression tests to framework
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  * Updates for [EMBOSS] commandlines, water and tranalign.   * Updates for [[EMBOSS]] commandlines, water and tranalign.
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  * C++ code (KDTree, Affy) now compiled by default on most platforms   * [[C++]] code (KDTree, Affy) now compiled by default on most platforms
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 * 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.  * 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.
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 * 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 parsers for [[Phred]] and Ace format files
 * New Code for dealing with [[NMR]] data
 * New SeqUtils modules for CodonUsage, IsoelectricPoint and other [[Protein]] properties
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 * [Entrez]-Retrieve sequence retrieval now supported  * [[Entrez]]-Retrieve sequence retrieval now supported
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 * BioSQL fixed so it now works with the current [SQL] schema  * BioSQL fixed so it now works with the current [[SQL]] schema
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 * Fixes to NCBIWWW for retrieving from [NCBI]
 * Retrieval of MultipleAlignment objects from [BLAST] records		  * Fixes to NCBIWWW for retrieving from [[NCBI]]
 * Retrieval of MultipleAlignment objects from [[BLAST]] records
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 * [Parsing] fixes in [ClustalW] parsed  * [[Parsing]] fixes in [[ClustalW]] parsed
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 * Fix to [PROSITE] parser  * Fix to [[PROSITE]] parser
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 * Andrew Dalke EUtils library for accessing [Database] at [NCBI] ([Entrez] programming utility)  * Andrew Dalke EUtils library for accessing [[Database]] at [[NCBI]] ([[Entrez]] programming utility)
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 * Thomas Hamelryck's [PDB] package.  * Thomas Hamelryck's [[PDB]] package.
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 * 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)  * 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)

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

Contents

  1. Useful information
  2. Document in internet
  3. Biopython Documentation Project
  4. Example code
  5. News (TopInsert)

Useful information

Document in internet

Biopython Documentation Project

Example code

News (TopInsert)

2006-09 UbuntuLinux 에 패키지로 등록되다.

2004-05-14 1.30 릴리즈. 점차 다양한 모듈들이 가세되고, 기존 모듈도 꾸준히 수정되고 발전되고 있다. 이번변화를 정리하여 표현하면,

  • 새로운 모듈 및 기능들
  • 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 CVS에 커밋되다. 이번파서는 특히도 느렸던 부분을 매우 빠르게 동작하도록 바꾼것으로, MxExtension, 및 Cee코드가 쓰여져서, 특히도 거대한 파일 Parsing에 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

CategoryProgramLibrary

BioPython (last edited 2012-08-20 13:23:05 by 182)

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