*****SPAM***** [Solar-general] *****SPAM***** [Biopython-announce] Biopython 1.30 release

[Diego G. Calbo Elizondo]

Sebastian, me enorgullece verte en las menciones.
Mis felicitaciones.


El mar, 18-05-2004 a las 08:42, Sebastian Bassi escribió:
> Aca mando el anuncio oficial de BioPython donde citan mi ultima
> contribución:
> 
> 
> Date: Fri, 14 May 2004 10:34:30 -0400
> From: Brad Chapman <chapmanb en uga.edu>
> To: biopython en biopython.org, biopython-announce en biopython.org
> 
> Hello all;
> I'm happy to announce a new release of Biopython 1.30, available
> today from http://biopython.org. This release contains a number of
> new modules and substantial changes to older modules. As a result of
> the changes, we've bumped up to a brand new major number. Please do
> download, test with your code, and report any bugs or problems to
> the normal lists (biopython en biopython.org or
> biopython-dev en biopython.org). The substantial changes in this
> release include:
> 
> -> Overhaul of the FASTA parser. Internally, fasta parsing now uses
> C libraries, so it is much faster and scalable to large files. The
> changes should all be internal, so that code written for the old
> Fasta parser will work with the new version.
> 
> -> Updated GenBank parser internals. In a desire to make GenBank
> parsing more flexible to the numerous updates to the format, a
> number of underlying parser details have been improved.
> 
> -> New contributed modules:
>     Affymetrix cel parsing -- Harry Zuzan
>     Compass output parsing -- James Casbon
>     Melting temperature calculation -- Sebastian Bassi
>     Reduced protein alphabets -- Iddo Friedberg
>     Blast XML output parsing -- Bertrand Frottier
> 
> -> Some duplicated and non-finished modules have been deprecated.
> For now you will get DeprecationWarnings with these modules, but
> they will eventually be removed. The effected modules are
> Bio/sequtils, Bio/kMeans, Bio/SVM and Bio/RecordFile. Please see the
> file DEPRECATED in the distribution for details of switching your
> code to use the new replacement modules.
> 
> -> The C++ code in the KDTree and Affy modules is now compiled by
> default. This has been tested on a number of platforms, but is a
> potential source of compilation errors. If you run into any problems
> compiling these C++ modules, please report them to the list.
> 
> -> A large assortment of bug fixes and updates to documentation.
> 
> A full list of changes is included below. Please download, test,
> and enjoy. Thanks much for everyone's hard work that went into
> making this release possible.
> 
> Brad
> 
> 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.
> _______________________________________________
> BioPython-announce mailing list  -  BioPython-announce en biopython.org
> http://biopython.org/mailman/listinfo/biopython-announce
> 
> 
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-- 
Diego G. Calbo Elizondo
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