Aca mando el anuncio oficial de BioPython donde citan mi ultima contribución: Date: Fri, 14 May 2004 10:34:30 -0400 From: Brad Chapman <[email protected]> To: [email protected], [email protected] 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 ([email protected] or [email protected]). 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 - [email protected] http://biopython.org/mailman/listinfo/biopython-announce
Mis mas sinceras y calidas Felicitaciones!!!! On Tue, 18 May 2004 08:42:29 -0300 Sebastian Bassi <[email protected]> wrote:
Aca mando el anuncio oficial de BioPython donde citan mi ultima contribución:
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 <[email protected]> To: [email protected], [email protected]
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 ([email protected] or [email protected]). 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 - [email protected] http://biopython.org/mailman/listinfo/biopython-announce
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participants (3)
-
Diego G. Calbo Elizondo -
Sebastian Bassi -
Vladimir di Fiore