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

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

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>


