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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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| * [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] |
* [[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]] |
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| '''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, | '''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, |
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
BioPythonStudy in [Sefiroth]
- Articles
- [LabStoryOfMrK]
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
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)