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
Useful information
ViewCvs : http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biopython
EpyDoc : http://www.biopython.org/docs/api/public/frames.html
Document in internet
Biopython Documentation Project
- Articles
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
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
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
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 (CVS로 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)