Skip to content

Instantly share code, notes, and snippets.

Toshiaki Katayama ktym

  • Database Center for Life Science
  • Japan
Block or report user

Report or block ktym

Hide content and notifications from this user.

Learn more about blocking users

Contact Support about this user’s behavior.

Learn more about reporting abuse

Report abuse
View GitHub Profile
ktym / dp.rb
Last active Jul 11, 2019
See for newer version.
View dp.rb
#!/usr/bin/env ruby
# Pairwise sequence alignment algorithms
Currently implements Needleman-Wunsch, Smith-Waterman
and Needleman-Wunsch-Gotoh algorithms based on
the Dynamic Programming (DP).
## Coordinates
View bwt.rb
#!/usr/bin/env ruby
class BWT
def initialize(str)
@str = str + '$'
View idorg-ontology-dblink.owl
View select_reads_on_uniq_path.rb
#!/usr/bin/env ruby
require 'json'
uniq ="uniq_node.txt").map {|x| x.stip.to_i}
json = JSON.parse(
json.each do |ary|
read_id = ary.shift
View select_uniq_path.rb
#!/usr/bin/env ruby
matrix = []
ARGF.each do |line|
ary = line.strip.split
matrix << ary
matrix.transpose.each do |row|
View Dockerfile
# Dockerfile for
FROM ubuntu:16.04
ARG node_version=v7.9.0
RUN apt-get -qq update && apt-get -qq install -y \
pkg-config \
sudo \
curl \
View jst-csv2nt.rb
#!/usr/bin/env ruby-2.3
# SPARQL endpoint
# SPARQL query
select *
where {
?term a skos:Concept ;
ktym /
Last active Aug 29, 2015
AJACS 55 Introduction of pathway databases




500 以上のデータベースが下記の分類でリストアップされています。

ktym / lodconvert.rb
Last active Aug 29, 2015
RDF format converter
View lodconvert.rb
#!/usr/bin/env ruby
# % gem install linkeddata
# % lodconvert.rb -h
# % lodconvert.rb [-i input_format] [-o output_format] inputfile > outputfile
require 'rubygems'
require 'linkeddata'
require 'getoptlong'
ktym / Sample_ruby_native_apps_script.rb
Created Oct 30, 2014
Ruby port of the BaseSpace Native App test python script
View Sample_ruby_native_apps_script.rb
require 'json'
def metadatajson
json = JSON.parse('
"Name": "",
"Description": "",
"HrefAppSession": "",
"Properties": [
You can’t perform that action at this time.