News for the Biopython Project
==============================

This file contains release notes and general news 
about the biopython project.

May 14, 2004: Biopython 1.30
 Affy package added for dealing with Affymetrix cel files -- thanks to Harry 
  Zuzan.
 Added code for parsing Blast XML output -- thanks to Bertrand Frottier.
 Added code for parsing Compass output -- thanks to James Casbon.
 New melting temperature calculation module -- thanks to Sebastian Bassi.
 Added lowess function for non-parameteric regression -- thanks to Michiel.
 Reduced protein alphabet supported added -- thanks to Iddo.
 
 Added documentation for Logistic Regression and Bio.PDB -- thanks to Michiel
  and Thomas.
 Documentation added for converting between file formats.
 Updates to install documentation for non-root users -- thanks to Jakob 
  Fredslund.
 epydoc now used for automatic generation of documentation.

 Fasta parser updated to use Martel for parsing and indexing, allowing better
  speed and dealing with large data files.
 Updated to Registry code. Now 'from Bio import db' gives you a number of new
  retrieval options, including embl, fasta, genbak, 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 -- thanks to Leighton 
  Pritchard.
 Numerous updated to Bio.PDB modules -- thanks to Thomas. PDB can now parse headers
  -- thanks to Kristian Rother.
 Updates to the Ace parser -- thanks to Frank Kauff and Leighton Pritchard.

 Added pgdb (PyGreSQL) support to BioSQL -- thanks to Marc Colosimo.
 Fix problems with using py2exe and Biopython -- thanks to Michael Cariaso.
 PSIBlast parser fixes -- thanks to Jer-Yee John Chuang and James Casbon.
 Fix to NCBIWWW retrieval so that HTML results are returned correctly.
 Fix to Clustalw to handle question marks in title names -- thanks to Ashleigh 
  Smythe.
 Fix to NBRF parsing to it accepts files produced by Clustalw -- thanks to
  Ashleigh Smythe.
 Fixes to the Enyzme module -- thanks to Marc Colosimo.
 Fix for bugs in SeqUtils -- thanks to Frank Kauff.
 Fix for optional hsps in ncbiblast Martel format -- thanks to Heiko.
 Fix to Fasta parsing to allow # comment lines -- thanks to Karl Diedrich.
 Updates to the C clustering library -- thanks to Michiel.
 Fixes for breakage in the SCOP module and addition of regression tests to
  framework -- thanks to Gavin.
 Various fixes to Bio.Wise -- thanks to Michael.
 Fix for bug in FastaReader -- thanks to Micheal.
 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 -- thanks to
  Michael for some nice distutils hacks and many people for testing.
 Deprecated Bio.sequtils -- use Bio.SeqUtils instead.
 Deprecated Bio.SVM -- use libsvm instead.
 Deprecated Bio.kMeans and Bio.xkMeans -- use Bio.cluster instead.
 Deprecated RecordFile -- doesn't appear to be finished code.


Feb 16, 2004: Biopython 1.24
 New parsers for Phred and Ace format files -- thanks to Frank Kauff
 New Code for dealing with NMR data -- thanks to Bob Bussell
 New SeqUtils modules for codon usage, isoelectric points and other
  protein properties -- thanks to Yair Benita
 New code for dealing with Wise contributed by Michael
 EZ-Retrieve sequence retrieval now supported thanks to Jeff
 Bio.Cluster updated along with documentation by Michiel 
 BioSQL fixed so it now works with the current SQL schema -- thanks to Yves
  Bastide for patches
 Patches to Bio/__init__ to make it compatible with py2exe -- thanks to 
  Leighton Pritchard
 Added __iter__ to all Biopython Iterators to make them Python 2.2 compatible
 Fixes to NCBIWWW for retrieving from NCBI -- thanks to Chris Wroe
 Retrieval of multiple alignment objects from BLAST records -- thanks to 
  James Casbon
 Fixes to GenBank format for new tags by Peter
 Parsing fixes in clustalw parsed -- thanks to Greg Singer and Iddo
 Fasta Indexes can have a specified filename -- thanks to Chunlei Wu
 Fix to Prosite parser -- thanks to Mike Liang
 Fix in GenBank parsing -- mRNAs now get strand information 


Oct 18, 2003: Biopython 1.23
  Fixed distribution of files in Bio/Cluster
  Now distributing Bio/KDTree/_KDTree.swig.C
  minor updates in installation code
  added mmCIF support for PDB files

Oct 9, 2003: Biopython 1.22
  Added Peter Slicker's patches for speeding up modules under Python 2.3
  Fixed Martel installation.
  Does not install Bio.Cluster without Numeric.
  Distribute EUtils DTDs.
  Yves Bastide patched NCBIStandalone.Iterator to be Python 2.0 iterator
  Ashleigh's string coersion fixes in Clustalw.
  Yair Benita added precision to the protein molecular weights.
  Bartek updated AlignAce.Parser and added Motif.sim method
  bug fixes in Michiel De Hoon's clustering library
  Iddo's bug fixes to Bio.Enzyme and new RecordConsumer
  Guido Draheim added patches for fixing import path to xbb scripts
  regression tests updated to be Python 2.3 compatible
  GenBank.NCBIDictionary is smarter about guessing the format

Jul 28, 2003: Biopython 1.21
  Martel added back into the released package
  new AlignACE module by Bartek Wilczynski
  Andreas Kuntzagk fix for GenBank Iterator on empty files

Jul 27, 2003: Biopython 1.20
  added Andrew Dalke's EUtils library
  added Michiel de Hoon's gene expression analysis package
  updates to setup code, now smarter about dependencies
  updates to test suite, now smarter about code that is imported
  Michael Hoffman's fixes to DocSQL
  syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible
  updates in NCBIStandalone, short query error
  Sebastian Bassi submitted code to calculate LCC complexity
  Greg Kettler's NCBIStandalone fix for long query lengths
  slew of miscellaneous fixes from George Paci
  miscellaneous cleanups and updates from Andreas Kuntzagk
  Peter Bienstman's fixes to Genbank code -- now parses whole database
  Kayte Lindner's LocusLink package
  miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman
  miscellaneous BLAST fixes and updates
  Iddo added new code to parse BLAST table output format
  Karl Diedrich's patch to read T_Coffee files
  Larry Heisler's fix for primer3 output
  Bio.Medline now uses proper iterator objects
  copen now handles SIGTERM correctly
  small bugfixes and updates in Thomas Hamelryck's PDB package
  bugfixes and updates to SeqIO.FASTA reader
  updates to Registry system, conforms to 2003 hackathon OBDA spec
  Yu Huang patch to support tblastn in wublast expression

Dec 17, 2002: Biopython 1.10
  Python requirement bumped up to 2.2
  hierarchy reorg, many things moved upwards into Bio namespace
  pairwise2 replaces fastpairwise and pairwise
  removed deprecated Sequence.py package
  minor bug fix in File.SGMLStripper
  added Scripts/debug/debug_blast_parser.py to diagnoze blast parsing errors
  IPI supported by SwissProt/SProt.py parser
  large speedup for kmeans
  new registry framework for generic access to databases and parsers
  small bug fix in stringfns.split
  scripts that access NCBI moved over to new EUtils system
  new crc module
  biblio.py supports the EBI Bibliographic database
  new CDD parser
  new Ndb parser
  new ECell parser
  new Geo parser
  access to GFF databases
  new KDTree data structure
  new LocusLink parser
  new MarkovModel algorithm
  new Saf parser
  miscellaneous sequence handling functions in sequtils
  new SVDSuperimpose algorithm


Dec 18, 2001: Biopython1.00a4
  minor bug fix in NCBIStandalone.blastall
  optimization in dynamic programming code
  new modules for logistic regression and maximum entropy
  minor bug fix in ParserSupport
  minor bug fixes in SCOP package
  minor updates in the kMeans cluster selection code
  minor bug fixes in SubsMat code
  support for XML-formatted MEDLINE files
  added MultiProc.run to simplify splitting code across processors
  listfns.items now supports lists with unhashable items
  new data type for pathways
  new support for intelligenetics format
  new support for metatool format
  new support for NBRF format
  new support for generalized launching of applications
  new support for genetic algorithms
  minor bug fixes in GenBank parsing
  new support for Primer in the Emboss package
  new support for chromosome graphics
  new support for HMMs
  new support for NeuralNetwork
  slew of Martel fixes (see Martel docs)

Sept 3, 2001: Biopython1.00a3
  added package to support KEGG
  added sequtils module for computations on sequences
  added pairwise sequence alignment algorithm
  major bug fixes in UndoHandle
  format updates in PubMed  
  Tk interface to kMeans clustering

July 5, 2001: Biopython1.00a2
  deprecated old regression testing frameworks
  deprecated Sequence.py
  Swiss-Prot parser bug fixes
  GenBank parser bug fixes
  Can now output GenBank format
  can now download many sequences at a time from GenBank
  kMeans clustering algorithm
  Kabat format now supported
  FSSP format now supported
  more functionality for alignment code
  SubsMat bug fixes and updates
  fixed memory leak in listfns bug fixes
  Martel bundled and part of the install procedure
  Medline.Parser bug fixes
  PubMed.download_many handles broken IDs better


Mar 3, 2001: Biopython 1.00a1
  Refactoring of modules.  X/X.py moved to X/__init__.py.
  Can search sequences for Prosite patterns at ExPASy
  Can do BLAST searches against stable URL at NCBI
  Prosite Pattern bug fixes
  GenBank parser
  Complete Seq and SeqFeatures framework
  distutils cleanup
  compile warning cleanups
  support for UniGene
  code for working with substitution matrices
  Tools.MultiProc package for rudimentary multiprocessing stuff


Nov 10, 2000: Biopython 0.90d04
  Added support for multiple alignments, ClustalW
  BLAST updates, bug fixes, and BlastErrorParser
  Fixes for PSI-BLAST in master-slave mode
  Minor update in stringfns, split separators can be negated
  Added download_many function to PubMed
  xbbtools updates
  Prodoc parser now accepts a copyright at the end of a record
  Swiss-Prot parser now handles taxonomy ID tag


Sept 6, 2000: Biopython 0.90d03
  Blast updates:
    - bug fixes in NCBIStandalone, NCBIWWW
    - some __str__ methods in Record.py implemented (incomplete)
  Tests
    - new BLAST regression tests
    - prosite tests fixed
  New parsers for Rebase, Gobase
  pure python implementation of C-based tools
  Thomas Sicheritz-Ponten's xbbtools
  can now generate documentation from docstrings using HappyDoc


Aug17-18, 2000: Bioinformatics Open Source Conference 2000
We had a very good Birds-of-a-Feather meeting:
http://www.biopython.org/pipermail/biopython/2000-August/000360.html


Aug 2, 2000: Biopython 0.90d02 is released.
  Blast updates:
    - now works with v2.0.14
    - HSP.identities and HSP.positives now tuples
    - HSP.gaps added
  SCOP updates:
    - Lin.Iterator now works with release 50
  Starting a tutorial
  New regression tests for Prodoc

July 6, 2000: Biopython 0.90d01 is released.

February 8, 2000: Anonymous CVS made available.


August 1999
Biopython project founded.

Call for Participation sent out to relevant mailing lists, news
groups.

The Biopython Project (http://www.biopython.org/) is a new open
collaborative effort to develop freely available Python libraries and
applications that address the needs of current and future work in
bioinformatics, including sequence analysis, structural biology,
pathways, expression data, etc.  When available, the source code will
be released as open source (http://www.biopython.org/License.shtml)
under terms similar to Python.

This is a Call for Participation for interested people to join the
project.  We are hoping to attract people from a diverse set of
backgrounds to help with code development, site maintenance,
scientific discussion, etc.  This project is open to everyone.  If
you're interested, please visit the web page, join the biopython
mailing list, and let us know what you think!

Jeffrey Chang <jchang@smi.stanford.edu>
Andrew Dalke <dalke@bioreason.com>


