bioroebe 0.10.80

metadata

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+--- !ruby/object:Gem::Specification
+name: bioroebe
+version: !ruby/object:Gem::Version
+  version: 0.10.80
+platform: ruby
+authors:
+- Robert A. Heiler
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2022-06-24 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: chemistry_paradise
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: cyberweb
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: colours
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: convert_global_env
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: directory_paradise
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: opn
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: "\nWelcome to the bioroebe-0.10.x release series! It is recommended to\nuse
+  ruby 3.x for this series, as it is the most tested version of \nruby in regards
+  to this project.\n\nThe bioroebe-project is a software suite focusing on bio-related\nlife
+  sciences in general - in particular molecular biology, molecular\ngenetics, bioinformatics,
+  biotechnology, system biology, synthetic\nbiology and related topics close to the
+  life sciences in general.\n\nThe primary objective for the bioroebe project is to
+  provide a\n\"practical glue\" between these different topics while also focusing\non
+  \"getting real work done\", as a toolset-project, trying to\nefficiently solve existing
+  problems.\n\nFor additional information about this project, have a look at the\nlink
+  called \"documentation\" on the rubygems webpage of this gem,\non the very bottom
+  right side (The direct URL is: \nhttps://www.rubydoc.info/gems/bioroebe/ ).\n\n"
+email: shevy@inbox.lt
+executables:
+- advanced_dotplot
+- align_open_reading_frames
+- all_positions_of_this_nucleotide
+- aminoacid_composition
+- aminoacid_frequencies
+- aminoacid_substitution
+- automatically_rename_this_fasta_file
+- base_composition
+- batch_create_windows_executables
+- biomart_console
+- bioroebe
+- bioroebe_controller
+- bioshell
+- blosum_2D_table
+- calculate_n50_value
+- chunked_display
+- codon_frequency
+- codon_to_aminoacid
+- colourize_this_fasta_sequence
+- compact_fasta_file
+- complement
+- complementary_dna_strand
+- complementary_rna_strand
+- compseq
+- consensus_sequence
+- count_AT
+- count_GC
+- create_random_aminoacids
+- decode_this_aminoacid_sequence
+- deduce_aminoacid_sequence
+- deduce_most_likely_aminoacid_sequence
+- display_aminoacid_table
+- display_open_reading_frames
+- dna_to_aminoacid_sequence
+- dna_to_rna
+- downcase_chunked_display
+- download_this_pdb
+- fasta_index
+- fetch_data_from_uniprot
+- filter_away_invalid_nucleotides
+- find_substring
+- genbank_to_fasta
+- hamming_distance
+- input_as_dna
+- is_palindrome
+- leading_five_prime
+- levensthein
+- longest_ORF
+- longest_substring
+- n_stop_codons_in_this_sequence
+- open_reading_frames
+- overwrite_fasta_header
+- palindrome_2D_structure
+- palindrome_generator
+- parse_fasta
+- partner_nucleotide
+- possible_codons_for_this_aminoacid
+- random_dna_sequence
+- random_sequence
+- raw_hamming_distance
+- return_longest_substring_via_LCS_algorithm
+- reverse_complement
+- reverse_sequence
+- ruler
+- scan_this_input_for_startcodons
+- short_aminoacid_letter_from_long_aminoacid_name
+- show_atomic_composition
+- show_codon_usage
+- show_fasta_header
+- show_nucleotide_sequence
+- show_this_codon_table
+- show_this_dna_sequence
+- showorf
+- simplify_fasta
+- sort_aminoacid_based_on_its_hydrophobicity
+- split_this_fasta_file_into_chromosomes
+- strict_filter_away_invalid_aminoacids
+- taxonomy
+- three_to_one
+- to_rna
+- trailing_three_prime
+- trypsin_digest
+- upcase_this_aminoacid_sequence_and_remove_numbers
+extensions: []
+extra_rdoc_files: []
+files:
+- LICENSE.md
+- README.md
+- bin/advanced_dotplot
+- bin/align_open_reading_frames
+- bin/all_positions_of_this_nucleotide
+- bin/aminoacid_composition
+- bin/aminoacid_frequencies
+- bin/aminoacid_substitution
+- bin/automatically_rename_this_fasta_file
+- bin/base_composition
+- bin/batch_create_windows_executables
+- bin/biomart_console
+- bin/bioroebe
+- bin/bioroebe_controller
+- bin/bioshell
+- bin/blosum_2D_table
+- bin/calculate_n50_value
+- bin/chunked_display
+- bin/codon_frequency
+- bin/codon_to_aminoacid
+- bin/colourize_this_fasta_sequence
+- bin/compact_fasta_file
+- bin/complement
+- bin/complementary_dna_strand
+- bin/complementary_rna_strand
+- bin/compseq
+- bin/consensus_sequence
+- bin/count_AT
+- bin/count_GC
+- bin/create_random_aminoacids
+- bin/decode_this_aminoacid_sequence
+- bin/deduce_aminoacid_sequence
+- bin/deduce_most_likely_aminoacid_sequence
+- bin/display_aminoacid_table
+- bin/display_open_reading_frames
+- bin/dna_to_aminoacid_sequence
+- bin/dna_to_rna
+- bin/downcase_chunked_display
+- bin/download_this_pdb
+- bin/fasta_index
+- bin/fetch_data_from_uniprot
+- bin/filter_away_invalid_nucleotides
+- bin/find_substring
+- bin/genbank_to_fasta
+- bin/hamming_distance
+- bin/input_as_dna
+- bin/is_palindrome
+- bin/leading_five_prime
+- bin/levensthein
+- bin/longest_ORF
+- bin/longest_substring
+- bin/n_stop_codons_in_this_sequence
+- bin/open_reading_frames
+- bin/overwrite_fasta_header
+- bin/palindrome_2D_structure
+- bin/palindrome_generator
+- bin/parse_fasta
+- bin/partner_nucleotide
+- bin/possible_codons_for_this_aminoacid
+- bin/random_dna_sequence
+- bin/random_sequence
+- bin/raw_hamming_distance
+- bin/return_longest_substring_via_LCS_algorithm
+- bin/reverse_complement
+- bin/reverse_sequence
+- bin/ruler
+- bin/scan_this_input_for_startcodons
+- bin/short_aminoacid_letter_from_long_aminoacid_name
+- bin/show_atomic_composition
+- bin/show_codon_usage
+- bin/show_fasta_header
+- bin/show_nucleotide_sequence
+- bin/show_this_codon_table
+- bin/show_this_dna_sequence
+- bin/showorf
+- bin/simplify_fasta
+- bin/sort_aminoacid_based_on_its_hydrophobicity
+- bin/split_this_fasta_file_into_chromosomes
+- bin/strict_filter_away_invalid_aminoacids
+- bin/taxonomy
+- bin/three_to_one
+- bin/to_rna
+- bin/trailing_three_prime
+- bin/trypsin_digest
+- bin/upcase_this_aminoacid_sequence_and_remove_numbers
+- bioroebe.gemspec
+- doc/IUPAC_aminoacids_code.md
+- doc/IUPAC_nucleotide_code.md
+- doc/README.gen
+- doc/blosum.md
+- doc/compatibility/BIO_PHP.md
+- doc/compatibility/README.md
+- doc/compatibility/emboss.md
+- doc/extensive_usage_example.md
+- doc/german_names_for_the_aminoacids.md
+- doc/instructions_for_the_taxonomy_subproject.md
+- doc/legacy_paths.md
+- doc/pdb_ATOM_entry.md
+- doc/quality_control/README.md
+- doc/quality_control/commandline_applications.md
+- doc/resources.md
+- doc/setup.rb
+- doc/statistics/statistics.md
+- doc/todo/README.md
+- doc/todo/bioroebe_GUI_todo.md
+- doc/todo/bioroebe_todo.md
+- doc/using_biomart.md
+- html/test.html
+- lib/bioroebe.rb
+- lib/bioroebe/aminoacids/aminoacid_substitution.rb
+- lib/bioroebe/aminoacids/aminoacids_mass_table.rb
+- lib/bioroebe/aminoacids/codon_percentage.rb
+- lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb
+- lib/bioroebe/aminoacids/create_random_aminoacids.rb
+- lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb
+- lib/bioroebe/aminoacids/display_aminoacid_table.rb
+- lib/bioroebe/aminoacids/show_hydrophobicity.rb
+- lib/bioroebe/annotations/README.md
+- lib/bioroebe/annotations/create_annotation_format.rb
+- lib/bioroebe/autoinclude.rb
+- lib/bioroebe/base/base.rb
+- lib/bioroebe/base/colours.rb
+- lib/bioroebe/base/colours_for_base/colours_for_base.rb
+- lib/bioroebe/base/commandline_application/README.md
+- lib/bioroebe/base/commandline_application/aminoacids.rb
+- lib/bioroebe/base/commandline_application/commandline_application.rb
+- lib/bioroebe/base/commandline_application/commandline_arguments.rb
+- lib/bioroebe/base/commandline_application/directory.rb
+- lib/bioroebe/base/commandline_application/extract.rb
+- lib/bioroebe/base/commandline_application/misc.rb
+- lib/bioroebe/base/commandline_application/opn.rb
+- lib/bioroebe/base/commandline_application/reset.rb
+- lib/bioroebe/base/commandline_application/warnings.rb
+- lib/bioroebe/base/commandline_application/write_what_into.rb
+- lib/bioroebe/base/initialize.rb
+- lib/bioroebe/base/misc.rb
+- lib/bioroebe/base/namespace.rb
+- lib/bioroebe/base/prototype/README.md
+- lib/bioroebe/base/prototype/e_and_ee.rb
+- lib/bioroebe/base/prototype/misc.rb
+- lib/bioroebe/base/prototype/mkdir.rb
+- lib/bioroebe/base/prototype/prototype.rb
+- lib/bioroebe/base/prototype/reset.rb
+- lib/bioroebe/base/reset.rb
+- lib/bioroebe/biomart/LICENSE.md
+- lib/bioroebe/biomart/attribute.rb
+- lib/bioroebe/biomart/biomart.rb
+- lib/bioroebe/biomart/database.rb
+- lib/bioroebe/biomart/dataset.rb
+- lib/bioroebe/biomart/filter.rb
+- lib/bioroebe/biomart/server.rb
+- lib/bioroebe/blosum/blosum.rb
+- lib/bioroebe/calculate/calculate_blosum_score.rb
+- lib/bioroebe/calculate/calculate_gc_content.rb
+- lib/bioroebe/calculate/calculate_levensthein_distance.rb
+- lib/bioroebe/calculate/calculate_melting_temperature.rb
+- lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb
+- lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb
+- lib/bioroebe/cell/README.md
+- lib/bioroebe/cell/cell.rb
+- lib/bioroebe/cleave_and_digest/README.md
+- lib/bioroebe/cleave_and_digest/cleave.rb
+- lib/bioroebe/cleave_and_digest/digestion.rb
+- lib/bioroebe/cleave_and_digest/trypsin.rb
+- lib/bioroebe/codon_tables/README.md
+- lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml
+- lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml
+- lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml
+- lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml
+- lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml
+- lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml
+- lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml
+- lib/bioroebe/codon_tables/frequencies/README.md
+- lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb
+- lib/bioroebe/codons/README.md
+- lib/bioroebe/codons/codon_table.rb
+- lib/bioroebe/codons/codon_tables.rb
+- lib/bioroebe/codons/codons.rb
+- lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb
+- lib/bioroebe/codons/detect_minimal_codon.rb
+- lib/bioroebe/codons/determine_optimal_codons.rb
+- lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb
+- lib/bioroebe/codons/sanitize_codon_frequency.rb
+- lib/bioroebe/codons/show_codon_tables.rb
+- lib/bioroebe/codons/show_codon_usage.rb
+- lib/bioroebe/codons/show_this_codon_table.rb
+- lib/bioroebe/codons/start_codons.rb
+- lib/bioroebe/colours/colour_schemes/README.md
+- lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb
+- lib/bioroebe/colours/colour_schemes/buried.rb
+- lib/bioroebe/colours/colour_schemes/colour_scheme.rb
+- lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb
+- lib/bioroebe/colours/colour_schemes/helix.rb
+- lib/bioroebe/colours/colour_schemes/hydropathy.rb
+- lib/bioroebe/colours/colour_schemes/nucleotide.rb
+- lib/bioroebe/colours/colour_schemes/score.rb
+- lib/bioroebe/colours/colour_schemes/simple.rb
+- lib/bioroebe/colours/colour_schemes/strand.rb
+- lib/bioroebe/colours/colour_schemes/taylor.rb
+- lib/bioroebe/colours/colour_schemes/turn.rb
+- lib/bioroebe/colours/colour_schemes/zappo.rb
+- lib/bioroebe/colours/colourize_sequence.rb
+- lib/bioroebe/colours/colours.rb
+- lib/bioroebe/colours/misc_colours.rb
+- lib/bioroebe/colours/rev.rb
+- lib/bioroebe/colours/sdir.rb
+- lib/bioroebe/colours/sfancy.rb
+- lib/bioroebe/colours/sfile.rb
+- lib/bioroebe/colours/simp.rb
+- lib/bioroebe/colours/swarn.rb
+- lib/bioroebe/colours/use_colours.rb
+- lib/bioroebe/configuration/configuration.rb
+- lib/bioroebe/configuration/constants.rb
+- lib/bioroebe/constants/GUIs.rb
+- lib/bioroebe/constants/aminoacids_and_proteins.rb
+- lib/bioroebe/constants/base_directory.rb
+- lib/bioroebe/constants/carriage_return.rb
+- lib/bioroebe/constants/codon_tables.rb
+- lib/bioroebe/constants/database_constants.rb
+- lib/bioroebe/constants/files_and_directories.rb
+- lib/bioroebe/constants/misc.rb
+- lib/bioroebe/constants/newline.rb
+- lib/bioroebe/constants/nucleotides.rb
+- lib/bioroebe/constants/regex.rb
+- lib/bioroebe/constants/roebe.rb
+- lib/bioroebe/constants/row_terminator.rb
+- lib/bioroebe/constants/tabulator.rb
+- lib/bioroebe/constants/unicode.rb
+- lib/bioroebe/constants/urls.rb
+- lib/bioroebe/conversions/README.md
+- lib/bioroebe/conversions/convert_aminoacid_to_dna.rb
+- lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb
+- lib/bioroebe/count/README.md
+- lib/bioroebe/count/count_amount_of_aminoacids.rb
+- lib/bioroebe/count/count_amount_of_nucleotides.rb
+- lib/bioroebe/count/count_at.rb
+- lib/bioroebe/count/count_gc.rb
+- lib/bioroebe/css/README.md
+- lib/bioroebe/css/project.css
+- lib/bioroebe/data/README.md
+- lib/bioroebe/data/bam/README.md
+- lib/bioroebe/data/data.txt
+- lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta
+- lib/bioroebe/data/fasta/alu_elements.fasta
+- lib/bioroebe/data/fasta/lady_slippers_orchid.fasta
+- lib/bioroebe/data/fasta/loxP.fasta
+- lib/bioroebe/data/fasta/ls_orchid.fasta
+- lib/bioroebe/data/fasta/pax6_in_mouse.fasta
+- lib/bioroebe/data/fasta/test.fasta
+- lib/bioroebe/data/fasta/test_DNA.fasta
+- lib/bioroebe/data/fastq/fastq_example_file.fastq
+- lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq
+- lib/bioroebe/data/fastq/one_random_fastq_entry.fastq
+- lib/bioroebe/data/genbank/sample_file.genbank
+- lib/bioroebe/data/genbank/standard.fasta
+- lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3
+- lib/bioroebe/data/gff/sample.gff
+- lib/bioroebe/data/gff/test_gene.gff
+- lib/bioroebe/data/gff/transcripts.gff
+- lib/bioroebe/data/gtf/README.md
+- lib/bioroebe/data/json/example_config.json
+- lib/bioroebe/data/pdb/1VII.pdb
+- lib/bioroebe/data/pdb/ala_phe_ala.pdb
+- lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta
+- lib/bioroebe/data/phylip/README.md
+- lib/bioroebe/data/phylip/example.phylip
+- lib/bioroebe/data/svg/example.svg
+- lib/bioroebe/databases/README.md
+- lib/bioroebe/databases/download_taxonomy_database.rb
+- lib/bioroebe/dotplots/README.md
+- lib/bioroebe/dotplots/advanced_dotplot.rb
+- lib/bioroebe/dotplots/dotplot.rb
+- lib/bioroebe/electron_microscopy/coordinate_analyzer.rb
+- lib/bioroebe/electron_microscopy/fix_pos_file.rb
+- lib/bioroebe/electron_microscopy/generate_em2em_file.rb
+- lib/bioroebe/electron_microscopy/parse_coordinates.rb
+- lib/bioroebe/electron_microscopy/read_file_xmd.rb
+- lib/bioroebe/electron_microscopy/simple_star_file_generator.rb
+- lib/bioroebe/encoding/README.md
+- lib/bioroebe/encoding/encoding.rb
+- lib/bioroebe/enzymes/README.md
+- lib/bioroebe/enzymes/has_this_restriction_enzyme.rb
+- lib/bioroebe/enzymes/restriction_enzyme.rb
+- lib/bioroebe/enzymes/restriction_enzymes_file.rb
+- lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb
+- lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb
+- lib/bioroebe/enzymes/show_restriction_enzymes.rb
+- lib/bioroebe/exceptions/README.md
+- lib/bioroebe/exceptions/exceptions.rb
+- lib/bioroebe/ext/LICENCE.md
+- lib/bioroebe/ext/README.md
+- lib/bioroebe/ext/main.cpp
+- lib/bioroebe/ext/nucleotide.cpp
+- lib/bioroebe/ext/nussinov_algorithm.cpp
+- lib/bioroebe/ext/sequence
+- lib/bioroebe/ext/sequence.cpp
+- lib/bioroebe/fasta_and_fastq/README.md
+- lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb
+- lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb
+- lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb
+- lib/bioroebe/fasta_and_fastq/download_fasta.rb
+- lib/bioroebe/fasta_and_fastq/fasta_defline/README.md
+- lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb
+- lib/bioroebe/fasta_and_fastq/fasta_parser.rb
+- lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb
+- lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb
+- lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb
+- lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb
+- lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb
+- lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb
+- lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb
+- lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb
+- lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb
+- lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb
+- lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb
+- lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb
+- lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb
+- lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb
+- lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb
+- lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb
+- lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/menu.rb
+- lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/misc.rb
+- lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb
+- lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb
+- lib/bioroebe/genbank/README.md
+- lib/bioroebe/genbank/genbank_flat_file_format_generator.rb
+- lib/bioroebe/genbank/genbank_parser.rb
+- lib/bioroebe/gene/gene.rb
+- lib/bioroebe/genomes/genome_pattern.rb
+- lib/bioroebe/genomes/genome_retriever.rb
+- lib/bioroebe/gui/experimental/README.md
+- lib/bioroebe/gui/experimental/snapgene/snapgene.rb
+- lib/bioroebe/gui/gtk3/README.md
+- lib/bioroebe/gui/gtk3/alignment/alignment.rb
+- lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb
+- lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb
+- lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.config
+- lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb
+- lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb
+- lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config
+- lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb
+- lib/bioroebe/gui/gtk3/controller/controller.rb
+- lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb
+- lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config
+- lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb
+- lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb
+- lib/bioroebe/gui/gtk3/format_converter/format_converter.rb
+- lib/bioroebe/gui/gtk3/gene/gene.rb
+- lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.config
+- lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb
+- lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.config
+- lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb
+- lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb
+- lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb
+- lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb
+- lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config
+- lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb
+- lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb
+- lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config
+- lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb
+- lib/bioroebe/gui/gtk3/show_codon_table/misc.rb
+- lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb
+- lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb
+- lib/bioroebe/gui/gtk3/sizeseq/sizeseq.rb
+- lib/bioroebe/gui/gtk3/three_to_one/three_to_one.rb
+- lib/bioroebe/gui/gtk3/three_to_one/title.rb
+- lib/bioroebe/gui/gtk3/www_finder/www_finder.config
+- lib/bioroebe/gui/gtk3/www_finder/www_finder.rb
+- lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb
+- lib/bioroebe/gui/libui/README.md
+- lib/bioroebe/gui/libui/alignment/alignment.rb
+- lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb
+- lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb
+- lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb
+- lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb
+- lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb
+- lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb
+- lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb
+- lib/bioroebe/gui/libui/random_sequence/random_sequence.rb
+- lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb
+- lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb
+- lib/bioroebe/gui/libui/three_to_one/three_to_one.rb
+- lib/bioroebe/gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb
+- lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb
+- lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb
+- lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb
+- lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb
+- lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb
+- lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb
+- lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb
+- lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb
+- lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb
+- lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb
+- lib/bioroebe/gui/tk/three_to_one/three_to_one.rb
+- lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb
+- lib/bioroebe/images/BIOROEBE.png
+- lib/bioroebe/images/BIOROEBE_NEW_LOGO.png
+- lib/bioroebe/images/BlosumMatrixViewer.png
+- lib/bioroebe/images/DnaToAminoacidWidget.png
+- lib/bioroebe/images/PRINTED_AMINOACID_TABLE.png
+- lib/bioroebe/images/class_ConvertAminoacidToDNA.png
+- lib/bioroebe/images/class_SimpleStringComparer.png
+- lib/bioroebe/images/example_of_FASTA_coloured_output.png
+- lib/bioroebe/images/libui_hamming_distance_widget.png
+- lib/bioroebe/images/pretty_DNA_picture.png
+- lib/bioroebe/images/primer_design_widget.png
+- lib/bioroebe/images/restriction_enzyme_commandline_result.png
+- lib/bioroebe/images/ruby-gtk_three_to_one_widget.png
+- lib/bioroebe/images/small_DNA_logo.png
+- lib/bioroebe/images/small_drosophila_image.png
+- lib/bioroebe/java/README.md
+- lib/bioroebe/java/bioroebe.jar
+- lib/bioroebe/java/bioroebe/AllInOne.class
+- lib/bioroebe/java/bioroebe/AllInOne.java
+- lib/bioroebe/java/bioroebe/Base.class
+- lib/bioroebe/java/bioroebe/Base.java
+- lib/bioroebe/java/bioroebe/BisulfiteTreatment.class
+- lib/bioroebe/java/bioroebe/BisulfiteTreatment.java
+- lib/bioroebe/java/bioroebe/Cat.class
+- lib/bioroebe/java/bioroebe/Codons.class
+- lib/bioroebe/java/bioroebe/Codons.java
+- lib/bioroebe/java/bioroebe/Esystem.class
+- lib/bioroebe/java/bioroebe/Esystem.java
+- lib/bioroebe/java/bioroebe/GUI/BaseFrame.class
+- lib/bioroebe/java/bioroebe/GUI/BaseFrame.java
+- lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.class
+- lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.java
+- lib/bioroebe/java/bioroebe/IsPalindrome.class
+- lib/bioroebe/java/bioroebe/IsPalindrome.java
+- lib/bioroebe/java/bioroebe/PartnerNucleotide.class
+- lib/bioroebe/java/bioroebe/PartnerNucleotide.java
+- lib/bioroebe/java/bioroebe/README.md
+- lib/bioroebe/java/bioroebe/RemoveFile.class
+- lib/bioroebe/java/bioroebe/RemoveFile.java
+- lib/bioroebe/java/bioroebe/RemoveNumbers.class
+- lib/bioroebe/java/bioroebe/RemoveNumbers.java
+- lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class
+- lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java
+- lib/bioroebe/java/bioroebe/SaveFile.java
+- lib/bioroebe/java/bioroebe/Sequence.java
+- lib/bioroebe/java/bioroebe/ToCamelcase.class
+- lib/bioroebe/java/bioroebe/ToCamelcase.java
+- lib/bioroebe/java/bioroebe/ToplevelMethods.class
+- lib/bioroebe/java/bioroebe/ToplevelMethods.java
+- lib/bioroebe/java/bioroebe/enums/DNA.java
+- lib/bioroebe/matplotlib/matplotlib_generator.rb
+- lib/bioroebe/misc/quiz/README.md
+- lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb
+- lib/bioroebe/misc/ruler.rb
+- lib/bioroebe/misc/useful_formulas.rb
+- lib/bioroebe/ncbi/efetch.rb
+- lib/bioroebe/ncbi/ncbi.rb
+- lib/bioroebe/ngs/README.md
+- lib/bioroebe/ngs/phred_quality_score_table.rb
+- lib/bioroebe/nucleotides/complementary_dna_strand.rb
+- lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb
+- lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb
+- lib/bioroebe/nucleotides/sanitize_nucleotide_sequence.rb
+- lib/bioroebe/nucleotides/show_nucleotide_sequence.rb
+- lib/bioroebe/palindromes/palindrome_2D_structure.rb
+- lib/bioroebe/palindromes/palindrome_finder.rb
+- lib/bioroebe/palindromes/palindrome_generator.rb
+- lib/bioroebe/parsers/biolang_parser.rb
+- lib/bioroebe/parsers/blosum_parser.rb
+- lib/bioroebe/parsers/genbank_parser.rb
+- lib/bioroebe/parsers/gff.rb
+- lib/bioroebe/parsers/parse_embl.rb
+- lib/bioroebe/parsers/stride_parser.rb
+- lib/bioroebe/patterns/README.md
+- lib/bioroebe/patterns/analyse_glycosylation_pattern.rb
+- lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb
+- lib/bioroebe/patterns/profile_pattern.rb
+- lib/bioroebe/patterns/rgg_scanner.rb
+- lib/bioroebe/patterns/scan_for_repeat.rb
+- lib/bioroebe/pdb/download_this_pdb.rb
+- lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb
+- lib/bioroebe/pdb/parse_mmCIF_file.rb
+- lib/bioroebe/pdb/parse_pdb_file.rb
+- lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb
+- lib/bioroebe/perl/README.md
+- lib/bioroebe/perl/local_to_global.pl
+- lib/bioroebe/project/project.rb
+- lib/bioroebe/protein_structure/alpha_helix.rb
+- lib/bioroebe/protein_structure/helical_wheel.rb
+- lib/bioroebe/raw_sequence/README.md
+- lib/bioroebe/raw_sequence/raw_sequence.rb
+- lib/bioroebe/readline/README.md
+- lib/bioroebe/readline/readline.rb
+- lib/bioroebe/regexes/README.md
+- lib/bioroebe/regexes/regexes.rb
+- lib/bioroebe/requires/commandline_application.rb
+- lib/bioroebe/requires/require_all_aminoacids_files.rb
+- lib/bioroebe/requires/require_all_calculate_files.rb
+- lib/bioroebe/requires/require_all_codon_files.rb
+- lib/bioroebe/requires/require_all_colour_scheme_files.rb
+- lib/bioroebe/requires/require_all_count_files.rb
+- lib/bioroebe/requires/require_all_dotplot_files.rb
+- lib/bioroebe/requires/require_all_electron_microscopy_files.rb
+- lib/bioroebe/requires/require_all_enzymes_files.rb
+- lib/bioroebe/requires/require_all_fasta_and_fastq_files.rb
+- lib/bioroebe/requires/require_all_nucleotides_files.rb
+- lib/bioroebe/requires/require_all_palindromes_files.rb
+- lib/bioroebe/requires/require_all_parser_files.rb
+- lib/bioroebe/requires/require_all_pattern_files.rb
+- lib/bioroebe/requires/require_all_pdb_files.rb
+- lib/bioroebe/requires/require_all_sequence_files.rb
+- lib/bioroebe/requires/require_all_string_matching_files.rb
+- lib/bioroebe/requires/require_all_svg_files.rb
+- lib/bioroebe/requires/require_all_taxonomy_files.rb
+- lib/bioroebe/requires/require_all_utility_scripts_files.rb
+- lib/bioroebe/requires/require_cleave_and_digest.rb
+- lib/bioroebe/requires/require_colours.rb
+- lib/bioroebe/requires/require_encoding.rb
+- lib/bioroebe/requires/require_sequence.rb
+- lib/bioroebe/requires/require_the_bioroebe_project.rb
+- lib/bioroebe/requires/require_the_bioroebe_shell.rb
+- lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb
+- lib/bioroebe/requires/require_the_constants.rb
+- lib/bioroebe/requires/require_the_toplevel_methods.rb
+- lib/bioroebe/requires/require_yaml.rb
+- lib/bioroebe/sequence/alignment.rb
+- lib/bioroebe/sequence/dna.rb
+- lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb
+- lib/bioroebe/sequence/protein.rb
+- lib/bioroebe/sequence/reverse_complement.rb
+- lib/bioroebe/sequence/sequence.rb
+- lib/bioroebe/shell/add.rb
+- lib/bioroebe/shell/assign.rb
+- lib/bioroebe/shell/chop_and_cut.rb
+- lib/bioroebe/shell/colours/colours.rb
+- lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml
+- lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml
+- lib/bioroebe/shell/configuration/upcase_nucleotides.yml
+- lib/bioroebe/shell/configuration/use_silent_startup.yml
+- lib/bioroebe/shell/constants.rb
+- lib/bioroebe/shell/download.rb
+- lib/bioroebe/shell/enable_and_disable.rb
+- lib/bioroebe/shell/enzymes.rb
+- lib/bioroebe/shell/fasta.rb
+- lib/bioroebe/shell/gtk.rb
+- lib/bioroebe/shell/help/class.rb
+- lib/bioroebe/shell/help/help.rb
+- lib/bioroebe/shell/history.rb
+- lib/bioroebe/shell/initialize.rb
+- lib/bioroebe/shell/loop.rb
+- lib/bioroebe/shell/menu.rb
+- lib/bioroebe/shell/misc.rb
+- lib/bioroebe/shell/prompt.rb
+- lib/bioroebe/shell/random.rb
+- lib/bioroebe/shell/readline/readline.rb
+- lib/bioroebe/shell/reset.rb
+- lib/bioroebe/shell/scan_and_parse.rb
+- lib/bioroebe/shell/search.rb
+- lib/bioroebe/shell/sequences.rb
+- lib/bioroebe/shell/shell.rb
+- lib/bioroebe/shell/show_report_and_display.rb
+- lib/bioroebe/shell/startup.rb
+- lib/bioroebe/shell/taxonomy.rb
+- lib/bioroebe/shell/tk.rb
+- lib/bioroebe/shell/user_input.rb
+- lib/bioroebe/shell/xorg.rb
+- lib/bioroebe/siRNA/README.md
+- lib/bioroebe/siRNA/siRNA.rb
+- lib/bioroebe/string_matching/README.md
+- lib/bioroebe/string_matching/find_longest_substring.rb
+- lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb
+- lib/bioroebe/string_matching/hamming_distance.rb
+- lib/bioroebe/string_matching/levensthein.rb
+- lib/bioroebe/string_matching/simple_string_comparer.rb
+- lib/bioroebe/string_matching/smith_waterman.rb
+- lib/bioroebe/svg/README.md
+- lib/bioroebe/svg/glyph.rb
+- lib/bioroebe/svg/mini_feature.rb
+- lib/bioroebe/svg/page.rb
+- lib/bioroebe/svg/primitive.rb
+- lib/bioroebe/svg/svgee.rb
+- lib/bioroebe/svg/track.rb
+- lib/bioroebe/taxonomy/README.md
+- lib/bioroebe/taxonomy/chart.rb
+- lib/bioroebe/taxonomy/class_methods.rb
+- lib/bioroebe/taxonomy/colours.rb
+- lib/bioroebe/taxonomy/constants.rb
+- lib/bioroebe/taxonomy/edit.rb
+- lib/bioroebe/taxonomy/help/help.rb
+- lib/bioroebe/taxonomy/help/helpline.rb
+- lib/bioroebe/taxonomy/info/check_available.rb
+- lib/bioroebe/taxonomy/info/info.rb
+- lib/bioroebe/taxonomy/info/is_dna.rb
+- lib/bioroebe/taxonomy/interactive.rb
+- lib/bioroebe/taxonomy/menu.rb
+- lib/bioroebe/taxonomy/node.rb
+- lib/bioroebe/taxonomy/parse_fasta.rb
+- lib/bioroebe/taxonomy/shared.rb
+- lib/bioroebe/taxonomy/taxonomy.rb
+- lib/bioroebe/toplevel_methods/ad_hoc_task.rb
+- lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb
+- lib/bioroebe/toplevel_methods/atomic_composition.rb
+- lib/bioroebe/toplevel_methods/base_composition.rb
+- lib/bioroebe/toplevel_methods/blast.rb
+- lib/bioroebe/toplevel_methods/calculate_n50_value.rb
+- lib/bioroebe/toplevel_methods/cat.rb
+- lib/bioroebe/toplevel_methods/chunked_display.rb
+- lib/bioroebe/toplevel_methods/cliner.rb
+- lib/bioroebe/toplevel_methods/complement.rb
+- lib/bioroebe/toplevel_methods/convert_global_env.rb
+- lib/bioroebe/toplevel_methods/databases.rb
+- lib/bioroebe/toplevel_methods/delimiter.rb
+- lib/bioroebe/toplevel_methods/digest.rb
+- lib/bioroebe/toplevel_methods/download_and_fetch_data.rb
+- lib/bioroebe/toplevel_methods/e.rb
+- lib/bioroebe/toplevel_methods/editor.rb
+- lib/bioroebe/toplevel_methods/esystem.rb
+- lib/bioroebe/toplevel_methods/exponential_growth.rb
+- lib/bioroebe/toplevel_methods/extract.rb
+- lib/bioroebe/toplevel_methods/fasta_and_fastq.rb
+- lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb
+- lib/bioroebe/toplevel_methods/frequencies.rb
+- lib/bioroebe/toplevel_methods/hamming_distance.rb
+- lib/bioroebe/toplevel_methods/infer.rb
+- lib/bioroebe/toplevel_methods/is_on_roebe.rb
+- lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb
+- lib/bioroebe/toplevel_methods/levensthein.rb
+- lib/bioroebe/toplevel_methods/log_directory.rb
+- lib/bioroebe/toplevel_methods/longest_common_substring.rb
+- lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb
+- lib/bioroebe/toplevel_methods/matches.rb
+- lib/bioroebe/toplevel_methods/misc.rb
+- lib/bioroebe/toplevel_methods/nucleotides.rb
+- lib/bioroebe/toplevel_methods/number_of_clones.rb
+- lib/bioroebe/toplevel_methods/open_in_browser.rb
+- lib/bioroebe/toplevel_methods/open_reading_frames.rb
+- lib/bioroebe/toplevel_methods/opn.rb
+- lib/bioroebe/toplevel_methods/palindromes.rb
+- lib/bioroebe/toplevel_methods/parse.rb
+- lib/bioroebe/toplevel_methods/phred_error_probability.rb
+- lib/bioroebe/toplevel_methods/rds.rb
+- lib/bioroebe/toplevel_methods/remove.rb
+- lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb
+- lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb
+- lib/bioroebe/toplevel_methods/rna_splicing.rb
+- lib/bioroebe/toplevel_methods/rnalfold.rb
+- lib/bioroebe/toplevel_methods/searching_and_finding.rb
+- lib/bioroebe/toplevel_methods/shuffleseq.rb
+- lib/bioroebe/toplevel_methods/statistics.rb
+- lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb
+- lib/bioroebe/toplevel_methods/taxonomy.rb
+- lib/bioroebe/toplevel_methods/three_delimiter.rb
+- lib/bioroebe/toplevel_methods/time_and_date.rb
+- lib/bioroebe/toplevel_methods/to_camelcase.rb
+- lib/bioroebe/toplevel_methods/truncate.rb
+- lib/bioroebe/toplevel_methods/url.rb
+- lib/bioroebe/toplevel_methods/verbose.rb
+- lib/bioroebe/utility_scripts/align_open_reading_frames.rb
+- lib/bioroebe/utility_scripts/analyse_local_dataset.rb
+- lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb
+- lib/bioroebe/utility_scripts/compacter.rb
+- lib/bioroebe/utility_scripts/compseq/compseq.rb
+- lib/bioroebe/utility_scripts/consensus_sequence.rb
+- lib/bioroebe/utility_scripts/create_batch_entrez_file.rb
+- lib/bioroebe/utility_scripts/determine_antigenic_areas.rb
+- lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb
+- lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb
+- lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb
+- lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb
+- lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb
+- lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb
+- lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb
+- lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb
+- lib/bioroebe/utility_scripts/dot_alignment.rb
+- lib/bioroebe/utility_scripts/download_files_from_rebase.rb
+- lib/bioroebe/utility_scripts/find_gene.rb
+- lib/bioroebe/utility_scripts/mirror_repeat.rb
+- lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb
+- lib/bioroebe/utility_scripts/parse_taxonomy.rb
+- lib/bioroebe/utility_scripts/pathways.rb
+- lib/bioroebe/utility_scripts/permutations.rb
+- lib/bioroebe/utility_scripts/punnet/punnet.rb
+- lib/bioroebe/utility_scripts/show_this_dna_sequence.rb
+- lib/bioroebe/utility_scripts/showorf/constants.rb
+- lib/bioroebe/utility_scripts/showorf/help.rb
+- lib/bioroebe/utility_scripts/showorf/initialize.rb
+- lib/bioroebe/utility_scripts/showorf/menu.rb
+- lib/bioroebe/utility_scripts/showorf/reset.rb
+- lib/bioroebe/utility_scripts/showorf/run.rb
+- lib/bioroebe/utility_scripts/showorf/show.rb
+- lib/bioroebe/utility_scripts/showorf/showorf.rb
+- lib/bioroebe/version/version.rb
+- lib/bioroebe/viennarna/README.md
+- lib/bioroebe/viennarna/rnafold_wrapper.rb
+- lib/bioroebe/with_gui.rb
+- lib/bioroebe/www/bioroebe.cgi
+- lib/bioroebe/www/embeddable_interface.rb
+- lib/bioroebe/www/sinatra/sinatra.rb
+- lib/bioroebe/yaml/agarose/agarose_concentrations.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_english.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml
+- lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml
+- lib/bioroebe/yaml/aminoacids/hydropathy_table.yml
+- lib/bioroebe/yaml/aminoacids/molecular_weight.yml
+- lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml
+- lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml
+- lib/bioroebe/yaml/antisense/antisense.yml
+- lib/bioroebe/yaml/base_composition_of_dna.yml
+- lib/bioroebe/yaml/blosum/blosum45.yml
+- lib/bioroebe/yaml/blosum/blosum50.yml
+- lib/bioroebe/yaml/blosum/blosum62.yml
+- lib/bioroebe/yaml/blosum/blosum80.yml
+- lib/bioroebe/yaml/blosum/blosum90.yml
+- lib/bioroebe/yaml/blosum/blosum_matrix.yml
+- lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml
+- lib/bioroebe/yaml/codon_tables/1.yml
+- lib/bioroebe/yaml/codon_tables/10.yml
+- lib/bioroebe/yaml/codon_tables/11.yml
+- lib/bioroebe/yaml/codon_tables/12.yml
+- lib/bioroebe/yaml/codon_tables/13.yml
+- lib/bioroebe/yaml/codon_tables/14.yml
+- lib/bioroebe/yaml/codon_tables/15.yml
+- lib/bioroebe/yaml/codon_tables/16.yml
+- lib/bioroebe/yaml/codon_tables/2.yml
+- lib/bioroebe/yaml/codon_tables/21.yml
+- lib/bioroebe/yaml/codon_tables/22.yml
+- lib/bioroebe/yaml/codon_tables/23.yml
+- lib/bioroebe/yaml/codon_tables/24.yml
+- lib/bioroebe/yaml/codon_tables/25.yml
+- lib/bioroebe/yaml/codon_tables/26.yml
+- lib/bioroebe/yaml/codon_tables/27.yml
+- lib/bioroebe/yaml/codon_tables/28.yml
+- lib/bioroebe/yaml/codon_tables/29.yml
+- lib/bioroebe/yaml/codon_tables/3.yml
+- lib/bioroebe/yaml/codon_tables/30.yml
+- lib/bioroebe/yaml/codon_tables/31.yml
+- lib/bioroebe/yaml/codon_tables/33.yml
+- lib/bioroebe/yaml/codon_tables/4.yml
+- lib/bioroebe/yaml/codon_tables/5.yml
+- lib/bioroebe/yaml/codon_tables/6.yml
+- lib/bioroebe/yaml/codon_tables/9.yml
+- lib/bioroebe/yaml/codon_tables/overview.yml
+- lib/bioroebe/yaml/configuration/README.md
+- lib/bioroebe/yaml/configuration/browser.yml
+- lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml
+- lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml
+- lib/bioroebe/yaml/configuration/temp_dir.yml
+- lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml
+- lib/bioroebe/yaml/configuration/use_opn.yml
+- lib/bioroebe/yaml/configuration/use_this_database.yml
+- lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml
+- lib/bioroebe/yaml/default_dna_input.yml
+- lib/bioroebe/yaml/enzymes/enzyme_classes.yml
+- lib/bioroebe/yaml/enzymes/pH-Optima.yml
+- lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml
+- lib/bioroebe/yaml/genomes/README.md
+- lib/bioroebe/yaml/humans/README.md
+- lib/bioroebe/yaml/humans/human_chromosomes.yml
+- lib/bioroebe/yaml/laboratory/README.md
+- lib/bioroebe/yaml/laboratory/pipettes.yml
+- lib/bioroebe/yaml/mRNA/mRNA.yml
+- lib/bioroebe/yaml/nuclear_localization_sequences.yml
+- lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml
+- lib/bioroebe/yaml/nucleotides/nucleotide_density.yml
+- lib/bioroebe/yaml/nucleotides/nucleotides.yml
+- lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml
+- lib/bioroebe/yaml/pathways/README.md
+- lib/bioroebe/yaml/pathways/citric_acid_cycle.yml
+- lib/bioroebe/yaml/pathways/glycolysis.yml
+- lib/bioroebe/yaml/pathways/shikimate_pathway.yml
+- lib/bioroebe/yaml/pathways/urea_cycle.yml
+- lib/bioroebe/yaml/primers/README.md
+- lib/bioroebe/yaml/primers/primers.yml
+- lib/bioroebe/yaml/promoters/35S.yml
+- lib/bioroebe/yaml/promoters/strong_promoters.yml
+- lib/bioroebe/yaml/proteases/proteases.yml
+- lib/bioroebe/yaml/proteins/ubiquitin.yml
+- lib/bioroebe/yaml/remote_urls/README.md
+- lib/bioroebe/yaml/remote_urls/remote_urls.yml
+- lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml
+- lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta
+- lib/bioroebe/yaml/sequences/README.md
+- lib/bioroebe/yaml/talens.yml
+- lib/bioroebe/yaml/viruses/ecoli_phages.yml
+- lib/bioroebe/yaml/viruses/viruses.yml
+- spec/testing_toplevel_method_editor.rb
+- spec/testing_toplevel_method_url.rb
+- spec/testing_toplevel_method_verbose.rb
+- test/advanced_svg_example.rb
+- test/testing_bioroebe.rb
+- test/testing_codons.rb
+- test/testing_dna_to_rna_conversion.rb
+- test/testing_parse_pdb_file.rb
+- test/testing_reverse_complement.rb
+- test/testing_svg_component_of_bioroebe.rb
+- test/testing_svg_component_of_bioroebe_from_json_dataset.rb
+- test/testing_taxonomy.rb
+homepage: https://rubygems.org/gems/bioroebe
+licenses:
+- LGPL-2.1
+metadata: {}
+post_install_message: |2+
+
+  This project relates to the life sciences, in particular molecular biology
+  and bioinformatics. It is primarily a toolset project, meaning that the
+  code that can be found within this project, ought to be "useful" in daily
+  work setups and routines related to the field of life sciences.
+
+  The simplest way to use this project is to start the interactive shell,
+  called BioShell.
+
+  The executable file for the BioShell is simply called:
+
+      bioshell
+
+  It resides in the bin/ subdirectory of this gem. It can also be started
+  from ruby code, such as through the following two lines of ruby code:
+
+      require 'bioroebe'
+      Bioroebe.start_shell
+
+  Ideally this should work just fine. If not, have a look at your specific
+  GEM_PATH to find out where the bioroebe-related files are kept.
+
+  "gem install bioroebe" should properly have handled all dependencies
+  for the bioroebe gem.
+
+  For more documentation, have a look at:
+
+    https://www.rubydoc.info/gems/bioroebe/0.10.80
+
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.5.8
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 3.3.16
+requirements: []
+rubygems_version: 3.3.16
+signing_key:
+specification_version: 4
+summary: 'Welcome to the bioroebe-0.10.x release series! It is recommended to use
+  ruby 3.x for this series, as it is the most tested version of  ruby in regards to
+  this project.  The bioroebe-project is a software suite focusing on bio-related
+  life sciences in general - in particular molecular biology, molecular genetics,
+  bioinformatics, biotechnology, system biology, synthetic biology and related topics
+  close to the life sciences in general.  The primary objective for the bioroebe project
+  is to provide a "practical glue" between these different topics while also focusing
+  on "getting real work done", as a toolset-project, trying to efficiently solve existing
+  problems.  For additional information about this project, have a look at the link
+  called "documentation" on the rubygems webpage of this gem, on the very bottom right
+  side (The direct URL is:  https://www.rubydoc.info/gems/bioroebe/ ).'
+test_files: []
+...