2011-01-25  Cyrus Harmonupdate to work with new smarkup master
2011-01-25  Cyrus Harmonresurrect the ability to build the documentation
2011-01-24  Cyrus Harmonalignment improvements -- special variables for gap...
2011-01-24  Cyrus Harmononly loop (lenth residues) times when setf'ing residues...
2011-01-07  Cyrus Harmonadd alexandria dependency
2011-01-07  Cyrus Harmonpessimize code, removing speed/safety/inline declarations
2010-10-09  Cyrus Harmonfix typo and remove bio-io prefix
2010-10-09  Cyrus Harmonremove the bio-io package. just put everything in bio...
2010-10-09  Cyrus Harmonremove bogus file reference
2010-10-09  Cyrus Harmonremove some debugging declamations
2010-10-09  Cyrus Harmonfix ASDF dependencies
2010-10-09  Cyrus Harmonremoved unused res loop variable in (setf residues...
2010-06-25  Cyrus Harmonudpate taxonomy download instructions and path.
2010-06-24  Cyrus HarmonAdded gene-summary and entrez-gene parsing of gene...
2010-05-23  Cyrus Harmonbump version to 0.2.7. remove bogus asdf-related package.
2010-05-23  Cyrus Harmonreally add the NCBI_Variation DTD
2010-05-23  Cyrus Harmonupdate scratch entrez examples
2010-05-23  Cyrus Harmonadded variation DTD
2010-05-23  Cyrus Harmonudpate DTDs and fix DTD entity resolving for the case...
2010-05-23  Cyrus Harmonuse &rest and fix whitespace typo
2010-05-23  Cyrus Harmonmore version.lisp-expr removal
2010-05-23  Cyrus Harmonvarious code cleanup items
2010-05-23  Cyrus Harmonuse &rest for bio:fetch (object entrez-dictionary)
2010-05-23  Cyrus Harmonadd copyright and add some date-parsing stuff
2010-05-23  Cyrus Harmoncheck for empty node and empty node-set
2010-05-23  Cyrus Harmonadd comment about origin of the article and article...
2010-05-23  Cyrus Harmonremove bogus dependencies (ch-asdf, alexandria).
2009-07-27  Cyrus Harmonadd string-if and number-value-if
2009-07-27  Cyrus Harmonget-search-result-ids now takes :id-class arg
2009-07-27  Cyrus Harmonadd some pubmed examples
2009-07-27  Cyrus Harmonfore-name -> forenames cleanup and deal with some nil...
2009-07-27  Cyrus Harmonremove some debug declarations
2009-07-27  Cyrus Harmonsplit :cache into :use-cache-for-lookup and :cache...
2009-07-27  Cyrus Harmonadd ncbi-pmid identifier
2009-07-27  Cyrus Harmonexport some new symbols
2009-07-27  Cyrus Harmonfore-name -> forenames
2009-07-25  Cyrus Harmonadd pubmed and article lisp files
2009-07-25  Cyrus Harmonadd string-value-if
2009-07-25  Cyrus Harmonentrez pubmed parsing improvements
2009-07-25  Cyrus Harmonarticle improvements:
2009-07-25  Cyrus Harmonuse :supersede instead of :overwrite for existing files...
2009-07-25  Cyrus Harmonfix NCBI DTD's that got hosed due to using :overwrite...
2009-07-25  Cyrus Harmonforgot to add article.lisp to last commit
2009-07-25  Cyrus Harmonfirst pass at Pubmed stuff
2009-07-25  Cyrus Harmonadd new NCBI DTDs
2009-07-25  Cyrus Harmonadd some new NCBI DTDs and support multiple public...
2009-06-13  Cyrus Harmonupdate generated documentation
2009-06-13  Cyrus HarmonMerge branch 'master' of git+ssh://
2008-10-02  Cyrus Harmonformatting
2008-10-02  Cyrus Harmonformatting
2008-10-02  Cyrus Harmonprint-alignment -> alignment-results
2008-10-02  Cyrus Harmonadded a find-matches example
2008-10-02  Cyrus Harmonnewline at end of file
2008-10-02  Cyrus Harmonperformance improvements and gf's
2008-10-02  Cyrus Harmonvarious example cleanups
2008-10-02  Cyrus Harmonadded aa and rna alignment examples
2008-09-06  Cyrus HarmonMerge branch 'master' of git+ssh://
2008-09-06  Cyrus Harmonautogen'ed doc changes
2008-07-03  Cyrus Harmonversion 0.2.6
2008-07-03  Cyrus Harmon* use bio: prefixes
2008-07-03  Cyrus Harmonsplit-string-into-lines-string -> split-string-into...
2008-07-03  Cyrus Harmon* read-fasta-file arg file -> filespec
2008-07-03  Cyrus Harmon* use change-class for adjustable-seqeunces
2008-07-03  Cyrus Harmondon't explicity check for mRNA type
2008-07-03  Cyrus Harmonminor doc updates
2008-07-03  Cyrus Harmonminor documentation updates
2008-07-03  Cyrus Harmon* export write-fasta-file
2008-07-03  Cyrus Harmon* annotated-sequence no longer explicitly declares...
2008-04-21  Cyrus Harmonadd stp-document->list and stp->node-list. use in scratch.
2008-04-21  Cyrus Harmonrobustify asdf-loading of cl-bio and cl-bio-rucksack...
2008-04-21  Cyrus HarmonRevert "retrieve this for the moment, at least..."
2008-04-21  Cyrus Harmonretrieve this for the moment, at least...
2008-04-21  Cyrus Harmonprinc-to-string the object name in entrez-dictionary...
2008-04-21  Cyrus Harmonmake *tax-nodes-file* and *tax-names-file* be symbol...
2008-04-21  Cyrus Harmonadd cl-bio-taxonomy and cl-bio-entrez to the :depends...
2008-04-21  Cyrus Harmonmake the ncbi-gi id be an integer if possible.
2008-04-21  Cyrus Harmonexport some taxonomy symbols and clean up the scratch...
2008-04-20  Cyrus Harmonstart adding dictionary documentation.
2008-04-20  Cyrus Harmonexport bio-rucksack::*bio-rucksack* and use bio-rucksac...
2008-04-20  Cyrus Harmondictionary gf docstrings
2008-04-20  Cyrus Harmonadding .gitignore
2008-04-20  Cyrus Harmonstarting to add documentation about modules
2008-04-20  Cyrus Harmonnote that the cl-bio-entrez-doc has gone away, but...
2008-04-20  Cyrus Harmonadd entrez:: around some temporary entrez debugging...
2008-04-20  Cyrus Harmonremove optimize debug 3
2008-04-20  Cyrus Harmonremove xmls parsing stuff.
2008-04-20  Cyrus Harmonremove xml.lisp symbols and add generif symbols.
2008-04-20  Cyrus Harmonremove entrez/xml.lisp
2008-04-20  Cyrus Harmoncleaning up taxonomy and rucksack moves.
2008-04-20  Cyrus Harmonmoving align into its own package and fix cl-bio.asd...
2008-04-20  Cyrus Harmonmoving rucksack and taxonomy stuff into their own modules.
2008-04-19  Cyrus Harmoncl-bio 0.2.5
2008-04-19  Cyrus Harmonuse (dirname "$0") so that running from...
2008-04-19  Cyrus Harmonmake write-pdb-header a function instead of a generic...
2008-04-19  Cyrus HarmonRevert "Use bio: prefix in doc fasta examples"
2008-04-19  Cyrus Harmonuse bio: prefix in doc examples
2008-04-19  Cyrus HarmonUse bio: prefix in doc fasta examples
2008-04-19  Cyrus HarmonAdding cl-bio-entrez module
2008-03-30  Cyrus Harmon* add asdf:load-op line at the top
2008-03-30  Cyrus Harmon* export dna->rna, 3-letter-residues-string, 3-letter...