bio 1.5.1 → 1.5.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/ChangeLog

@@ -1,3 +1,144 @@
+commit 68f87dc3c4488155992f88c3cf1db27061948315
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 20 13:25:35 2018 +0900
+
+    add changes made for bioruby-1.5.2
+
+ RELEASE_NOTES.rdoc | 14 ++++++++++++++
+ 1 file changed, 14 insertions(+)
+
+commit 6b7e87abfbab88a3bb1b80227ab4b0cfaaeae26e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 20 13:24:45 2018 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit a7dbefeef20d6dea18f0bdd67df24e00c5e9ede6
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 20 13:23:31 2018 +0900
+
+    version changed to 1.5.2
+
+ lib/bio/version.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit e00134a1a31db46421b6d468ea1c1d0368bfbb6c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 20 12:55:32 2018 +0900
+
+    Bug fix: printf format syntax error about single percent character
+    
+     * Bio::Shell#seqstat: Fix format specifier syntax error.
+       Recent version of Ruby raised error: 'ArgumentError:
+       incomplete format specifier;use %% (double %) instead'.
+
+ lib/bio/shell/plugin/seq.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit df61cdba5ba3e90fda6c70cc9f880567656a5a82
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 20 07:06:08 2018 +0900
+
+    Improvement documentation
+    
+     * Improve documentation.
+     * Close https://github.com/bioruby/bioruby/pull/120 .
+
+ lib/bio/db/aaindex.rb | 79 +++++++++++++++++++++++++++++++++++++++++++++++----
+ 1 file changed, 74 insertions(+), 5 deletions(-)
+
+commit 35bcc5008c7721afb3c16467ae6dc782651f4c39
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 20 05:01:12 2018 +0900
+
+    Bug fix: Bio::Command.new_https should support proxy
+
+ lib/bio/command.rb | 18 +++++++-----------
+ 1 file changed, 7 insertions(+), 11 deletions(-)
+
+commit 88b58e94d4612f39abb14b89779ceeb533cd552e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 20 04:58:56 2018 +0900
+
+    https support for Bio::Blast::Remote::GenomeNet::Information
+
+ lib/bio/appl/blast/genomenet.rb | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+commit dfccbdf32bf819f941f2bcb4f63b2f0ce12cacfa
+Author: ramadis <rramiro.o@hotmail.com>
+Date:   Sat Jul 7 15:12:33 2018 -0300
+
+    Add https requests in command. Fix genomenet query by allowing https requests.
+
+ lib/bio/appl/blast/genomenet.rb |  2 +-
+ lib/bio/command.rb              | 14 ++++++++++++++
+ 2 files changed, 15 insertions(+), 1 deletion(-)
+
+commit d1e1358c1a5c7c7f4aa093a09d5bb45b60f7e7ee
+Author: markwilkinson <markw@illuminae.com>
+Date:   Tue Dec 12 14:13:51 2017 +0100
+
+    fixing Fasta Report parser for fasta36 -m10
+
+ lib/bio/appl/fasta/format10.rb | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+commit b9b11f66733e20e1ee6d2b5e0aab813b5b5d0000
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 13 22:13:59 2017 +0900
+
+    Suppress warning "assigned but unused variable"
+
+ lib/bio/io/flatfile/autodetection.rb | 5 +++++
+ 1 file changed, 5 insertions(+)
+
+commit 580dd6bb9344c2afd0fe60b0cf53a4b28734fbbf
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 13 22:10:53 2017 +0900
+
+    Suppress warning: "instance variable @top_strand not initialized"
+    
+     * Suppress warning: "instance variable @top_strand not initialized".
+       To do so, force to raise NoMethodError when @top_strand is not
+       initialized or is nil. This should be changed to appropriate
+       exception in the future.
+
+ lib/bio/util/sirna.rb | 2 ++
+ 1 file changed, 2 insertions(+)
+
+commit 9d7ef4e66ecdc1aadc08fda4b332a51ca7739c82
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 13 21:31:38 2017 +0900
+
+    Suppress warning in Ruby 2.4: "constant ::Fixnum is deprecated"
+
+ lib/bio/db/soft.rb                                                    | 4 ++--
+ .../util/restriction_enzyme/range/sequence_range/calculated_cuts.rb   | 2 +-
+ test/unit/bio/test_alignment.rb                                       | 4 ++--
+ 3 files changed, 5 insertions(+), 5 deletions(-)
+
+commit 2747ee11392068de88e044abf52d12a88a0624ea
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 13 21:19:12 2017 +0900
+
+    Suppress warning "parentheses after method name is interpreted as an argument list, not a decomposed argument" in Ruby 2.4
+
+ lib/bio/map.rb | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+commit 1edbd88a703d3cff0f5a29e45fa51058405ab58c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 7 22:06:32 2016 +0900
+
+    BioRuby 1.5.1 is released
+
+ ChangeLog | 690 +++++++++++++++++++++++++++++++++++---------------------------
+ 1 file changed, 385 insertions(+), 305 deletions(-)
+
 commit 917fe0d0e9910267cd54bf48c2caabe89875a299
 Author: Naohisa Goto <ng@bioruby.org>
 Date:   Wed Sep 7 22:00:56 2016 +0900
@@ -1916,11 +2057,9 @@ Date:   Fri Jun 28 15:26:20 2013 +0900
 
     rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprotkb_new_part.rb
 
- test/unit/bio/db/embl/test_uniprot_new_part.rb   | 208 -----------------------
- test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 208 +++++++++++++++++++++++
- 2 files changed, 208 insertions(+), 208 deletions(-)
- delete mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb
- create mode 100644 test/unit/bio/db/embl/test_uniprotkb_new_part.rb
+ .../bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb}  | 0
+ 1 file changed, 0 insertions(+), 0 deletions(-)
+ rename test/unit/bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb} (100%)
 
 commit 1b51d0940712a6f144f8268dc77048bc7ec7d983
 Author: Naohisa Goto <ng@bioruby.org>
@@ -1940,11 +2079,9 @@ Date:   Fri Jun 28 15:01:15 2013 +0900
 
     test_sptr.rb is renamed to test_uniprotkb.rb
 
- test/unit/bio/db/embl/test_sptr.rb      | 1807 -------------------------------
- test/unit/bio/db/embl/test_uniprotkb.rb | 1807 +++++++++++++++++++++++++++++++
- 2 files changed, 1807 insertions(+), 1807 deletions(-)
- delete mode 100644 test/unit/bio/db/embl/test_sptr.rb
- create mode 100644 test/unit/bio/db/embl/test_uniprotkb.rb
+ test/unit/bio/db/embl/{test_sptr.rb => test_uniprotkb.rb} | 0
+ 1 file changed, 0 insertions(+), 0 deletions(-)
+ rename test/unit/bio/db/embl/{test_sptr.rb => test_uniprotkb.rb} (100%)
 
 commit e1ed7fab4c0350e6866dd420a93e950c53063f38
 Author: Naohisa Goto <ng@bioruby.org>
@@ -1998,11 +2135,9 @@ Date:   Thu Jun 27 18:16:38 2013 +0900
 
     Rename lib/bio/db/embl/sptr.rb to uniprotkb.rb
 
- lib/bio/db/embl/sptr.rb      | 1456 ------------------------------------------
- lib/bio/db/embl/uniprotkb.rb | 1456 ++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 1456 insertions(+), 1456 deletions(-)
- delete mode 100644 lib/bio/db/embl/sptr.rb
- create mode 100644 lib/bio/db/embl/uniprotkb.rb
+ lib/bio/db/embl/{sptr.rb => uniprotkb.rb} | 0
+ 1 file changed, 0 insertions(+), 0 deletions(-)
+ rename lib/bio/db/embl/{sptr.rb => uniprotkb.rb} (100%)
 
 commit 2a10ded8e1502e0db5ec3b2e060f658ee53aafd0
 Author: Naohisa Goto <ng@bioruby.org>
@@ -2951,11 +3086,9 @@ Date:   Thu Aug 23 00:20:01 2012 +0900
 
     renamed ChangeLog to doc/ChangeLog-1.4.3
 
- ChangeLog           | 1478 ---------------------------------------------------
- doc/ChangeLog-1.4.3 | 1478 +++++++++++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 1478 insertions(+), 1478 deletions(-)
- delete mode 100644 ChangeLog
- create mode 100644 doc/ChangeLog-1.4.3
+ ChangeLog => doc/ChangeLog-1.4.3 | 0
+ 1 file changed, 0 insertions(+), 0 deletions(-)
+ rename ChangeLog => doc/ChangeLog-1.4.3 (100%)
 
 commit 0c20cb62ba6b253098e7198c14de1829f72474f5
 Author: Naohisa Goto <ng@bioruby.org>
@@ -2982,11 +3115,9 @@ Date:   Thu Aug 23 00:12:40 2012 +0900
 
     Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.3.rdoc
 
- RELEASE_NOTES.rdoc           | 204 -------------------------------------------
- doc/RELEASE_NOTES-1.4.3.rdoc | 204 +++++++++++++++++++++++++++++++++++++++++++
- 2 files changed, 204 insertions(+), 204 deletions(-)
- delete mode 100644 RELEASE_NOTES.rdoc
- create mode 100644 doc/RELEASE_NOTES-1.4.3.rdoc
+ RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc | 0
+ 1 file changed, 0 insertions(+), 0 deletions(-)
+ rename RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc (100%)
 
 commit 08bcabecccb271385d38a0f807e8c408def5a128
 Author: Naohisa Goto <ng@bioruby.org>

data/RELEASE_NOTES.rdoc

@@ -1,3 +1,17 @@
+= BioRuby 1.5.2 RELEASE NOTES
+
+Few bug fixes have been made to the BioRuby 1.5.2 after the version 1.5.1 is
+released.
+
+* Fixed a parser bug in Bio::Fasta::Report, FASTA output (-m 10) parser,
+  contributed by William Van Etten and Mark Wilkinson via GitHub.
+* HTTPS is used to access GenomeNet BLAST web service, contributed
+  by @ramadis via GitHub.
+* Bio::Shell#seqstat: Fix format specifier syntax error.
+* Bio::AAindex documentation fix, suggested by @kojix2 via GitHub.
+* Suppress warning messages in Ruby 2.4 and later.
+
+
 = BioRuby 1.5.1 RELEASE NOTES
 
 Few changes have been made to the BioRuby 1.5.1 after the version 1.5.0 is

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.5.1"
+  s.version = "1.5.2"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"

data/lib/bio/appl/blast/genomenet.rb

@@ -102,7 +102,7 @@ module Bio::Blast::Remote
         dbdescs = {}
         key = nil
         host = Bio::Blast::Remote::Genomenet::Host
-        http = Bio::Command.new_http(host)
+        http = Bio::Command.new_https(host)
         result = http.get('/tools/blast/')
         #p result.body
         result.body.each_line do |line|
@@ -211,7 +211,7 @@ module Bio::Blast::Remote
       end
 
       begin
-        http = Bio::Command.new_http(host)
+        http = Bio::Command.new_https(host)
         http.open_timeout = 300
         http.read_timeout = 600
         result = Bio::Command.http_post_form(http, path, form)
@@ -243,10 +243,10 @@ module Bio::Blast::Remote
         end
 
         # workaround 2005.08.12 + 2011.01.27 + 2011.7.22
-        if /\<A +HREF=\"(http\:\/\/[\-\.a-z0-9]+\.genome\.jp)?(\/tmp\/[^\"]+)\"\>Show all result\<\/A\>/i =~ @output.to_s then
+        if /\<A +HREF=\"(https?\:\/\/[\-\.a-z0-9]+\.genome\.jp)?(\/tmp\/[^\"]+)\"\>Show all result\<\/A\>/i =~ @output.to_s then
           all_prefix = $1
           all_path = $2
-          all_prefix = "http://#{Host}" if all_prefix.to_s.empty?
+          all_prefix = "https://#{Host}" if all_prefix.to_s.empty?
           all_uri = all_prefix + all_path
           @output = Bio::Command.read_uri(all_uri)
           case all_path

data/lib/bio/appl/fasta/format10.rb

@@ -94,8 +94,9 @@ class Report
     # header lines - brief list of the hits
     if list_start = data.index("\nThe best scores are") then
       data = data[(list_start + 1)..-1]
-      data.sub!(/(.*)\n\n>>>/m, '')
+      data.sub!(/(.*?)\n\n>>>/m, '')
       @list = $1
+      data.sub!(/>>><<<(.*)$/m, '')
     else
       if list_start = data.index(/\n!!\s+/) then
         data = data[list_start..-1]

data/lib/bio/command.rb

@@ -791,6 +791,16 @@ module Command
     end
   end
 
+  # Same as:
+  #   h = Bio::Command.new_http(address, port)
+  #   h.use_ssl = true
+  #   h
+  def new_https(address, port = 443)
+    connection = new_http(address, port)
+    connection.use_ssl = true
+    connection
+  end
+
   # Same as:
   #  http = Net::HTTP.new(...); http.post_form(path, params)
   # and 

data/lib/bio/db/aaindex.rb

@@ -7,12 +7,11 @@
 #              Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
 #
 # == Description
 #
 # Classes for Amino Acid Index Database (AAindex and AAindex2).
-# * AAindex Manual: http://www.genome.jp/dbget-bin/show_man?aaindex
+# * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
 #
 # == Examples
 #
@@ -40,7 +39,38 @@ require "matrix"
 
 module Bio
 
-  # Super class for AAindex1 and AAindex2
+  # == Description
+  #
+  # Bio::AAindex is the super class of Bio::AAindex1 and Bio::AAindex2,
+  # parser classes for AAindex Amino Acid Index Database.
+  # * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
+  #
+  # Except Bio::AAindex.auto, do not use this class directly.
+  # Methods of this super class is used from AAindex1 and AAindex2 classes.
+  #
+  # == Examples
+  #
+  #  # auto-detection of data format
+  #  aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")
+  #  aax2 = Bio::AAindex.auto("DAYM780301.aaindex2")
+  #
+  #  # Example of Bio::AAindex1 class
+  #  aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
+  #  aax1.entry_id
+  #  aax1.index
+  #
+  #  # Example of Bio::AAindex2 class
+  #  aax2 = Bio::AAindex2.new("DAYM780301.aaindex2")
+  #  aax2.entry_id
+  #  aax2.matrix
+  #  aax2.matrix[2,2]
+  #  aax2.matrix('R', 'A')
+  #  aax2['R', 'A']
+  #
+  # == References
+  #
+  # * http://www.genome.jp/aaindex/
+  #
   class AAindex < KEGGDB
 
     # Delimiter
@@ -136,7 +166,25 @@ module Bio
   end
 
 
-  # Class for AAindex1 format.
+  # == Description
+  #
+  # Parser class for AAindex1, Amino Acid Index Database.
+  # * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
+  #
+  # == Examples
+  #
+  #  # auto-detection of data format by using Bio::AAindex class
+  #  aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")
+  #
+  #  # parse a file and get contents
+  #  aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
+  #  aax1.entry_id
+  #  aax1.index
+  #
+  # == References
+  #
+  # * http://www.genome.jp/aaindex/
+  #
   class AAindex1 < AAindex
 
     def initialize(entry)
@@ -211,7 +259,28 @@ module Bio
   end
 
 
-  # Class for AAindex2 format.
+  # == Description
+  #
+  # Parser class for AAindex2, Amino Acid Index Database.
+  # * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
+  #
+  # == Examples
+  #
+  #  # auto-detection of data format by using Bio::AAindex class
+  #  aax2 = Bio::AAindex.auto("DAYM780301.aaindex2")
+  #
+  #  # parse a file and get contents
+  #  aax2 = Bio::AAindex2.new("DAYM780301.aaindex2")
+  #  aax2.entry_id
+  #  aax2.matrix
+  #  aax2.matrix[2,2]
+  #  aax2.matrix('R', 'A')
+  #  aax2['R', 'A']
+  #
+  # == References
+  #
+  # * http://www.genome.jp/aaindex/
+  #
   class AAindex2 < AAindex
 
     def initialize(entry)

data/lib/bio/db/soft.rb

@@ -217,13 +217,13 @@ class SOFT
       end
       
       def [](x)
-        if x.kind_of?( Fixnum )
+        if x.kind_of?( Integer )
           super(x)
         else
           begin
             x = x.to_s.downcase.to_sym
             z = @header_object.column_index[x]
-            unless z.kind_of?( Fixnum )
+            unless z.kind_of?( Integer )
               raise IndexError, "#{x.inspect} is not a valid index.  Contents of @header_object.column_index: #{@header_object.column_index.inspect}"
             end
             self[ z ]

data/lib/bio/io/flatfile/autodetection.rb

@@ -547,6 +547,11 @@ module Bio
         #BottomRule.is_prior_to(debug_last)
         #fastaformat.is_prior_to(debug_last)
 
+        ## for suppressing warnings
+        p medline, aaindex, litdb, fantom, clustal,
+          gcg_msf, gcg_seq, blastxml, rpsblast, blat,
+          spidey, hmmer, sim4 if false
+
         a.rehash
         return a
       end

data/lib/bio/map.rb

@@ -90,7 +90,7 @@ module Bio
     #   class MyMapThing
     #     include Bio::Map::ActsLikeMap
     #     
-    #     def initialize (name)
+    #     def initialize(name)
     #       @name = name
     #       @mappings_as_maps = Array.new
     #     end
@@ -177,7 +177,7 @@ module Bio
     #   class MyMarkerThing
     #     include Bio::Map::ActsLikeMarker
     #     
-    #     def initialize (name)
+    #     def initialize(name)
     #       @name = name
     #       @mappings_as_marker = Array.new
     #     end
@@ -301,7 +301,7 @@ module Bio
       # * _map_: a Bio::Map::SimpleMap object
       # * _marker_: a Bio::Map::Marker object
       # * _location_: a Bio::Locations object
-      def initialize (map, marker, location = nil)
+      def initialize(map, marker, location = nil)
         @map, @marker, @location = map, marker, location
       end
       attr_accessor :map, :marker, :location
@@ -350,7 +350,7 @@ module Bio
       # * type: type of the map (e.g. linkage, radiation_hybrid, cytogenetic, ...)
       # * units: unit of the map (e.g. cM, cR, ...)
       # *Returns*:: new Bio::Map::SimpleMap object
-      def initialize (name = nil, type = nil, length = nil, units = nil)
+      def initialize(name = nil, type = nil, length = nil, units = nil)
         @name, @type, @length, @units = name, type, length, units
         @mappings_as_map = Array.new
       end

data/lib/bio/shell/plugin/seq.rb

@@ -82,7 +82,7 @@ module Bio::Shell
       rep << "Codon usage       :\n"
       hash = Hash.new("0.0%")
       seq.codon_usage.sort.each do |codon, num|
-        percent = format("%.1f%", 100.0 * num / (seq.length / 3))
+        percent = format("%.1f%%", 100.0 * num / (seq.length / 3))
         hash[codon] = percent
       end
       rep << codontable(1, hash).output

data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb

@@ -151,7 +151,7 @@ class CalculatedCuts
   def remove_incomplete_cuts(size=nil)
     @strands_for_display_current = false
     @size = size if size
-    raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular
+    raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Integer) and not @circular
 
     vcuts = @vc_primary + @vc_complement
     hcuts = @hc_between_strands

data/lib/bio/util/sirna.rb

@@ -278,6 +278,8 @@ module Bio
       
       # human readable report
       def report
+        # raise NomethodError for compatibility
+        raise NoMethodError if !defined?(@top_strand) || !@top_strand
         report = "### shRNA\n"
         report << "Top strand shRNA (#{@top_strand.length} nt):\n"
         report << "  5'-#{@top_strand.upcase}-3'\n"

data/lib/bio/version.rb

@@ -10,7 +10,7 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [1, 5, 1].extend(Comparable).freeze
+  BIORUBY_VERSION = [1, 5, 2].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates development version.

data/test/unit/bio/test_alignment.rb

@@ -628,9 +628,9 @@ module Bio
 
     def test_seqclass_when_seqclass_set
       alignment = Alignment.new
-      alignment.seqclass = Fixnum
+      alignment.seqclass = Integer
       alignment << "this doesn't really make sense"
-      assert_equal(Fixnum, alignment.seqclass)
+      assert_equal(Integer, alignment.seqclass)
     end
 
     # Alignment#gap_char

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio
 version: !ruby/object:Gem::Version
-  version: 1.5.1
+  version: 1.5.2
 platform: ruby
 authors:
 - BioRuby project
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-09-07 00:00:00.000000000 Z
+date: 2018-09-20 00:00:00.000000000 Z
 dependencies: []
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org
@@ -674,7 +674,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.5.2.1
 signing_key: 
 specification_version: 4
 summary: Bioinformatics library