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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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

Bhn: BioPython (last edited 2012-08-20 13:23:05 by yong27)

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