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
    • 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

CategoryProgramLibrary

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