Toshiaki Katayama ktym

ktym / ajacs55.md

Last active August 29, 2015 14:26

AJACS 55 Introduction of pathway databases

パスウェイデータベースを使ってみる

まずは、様々なパスウェイデータベースの一覧を見てみましょう。

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 August 29, 2015 14:09

RDF format converter

	#!/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 October 30, 2014 12:23

Ruby port of the BaseSpace Native App test python script

ktym / jquery-sparql.html

Created July 5, 2014 09:31

	<!DOCTYPE html>
	<meta charset="utf-8">
	<html>
	<head>
	<!-- Twitter Bootstrap http://getbootstrap.com/2.3.2/ を取得してインストール -->
	<link rel="stylesheet" type="text/css" href="bootstrap.css"/>
	<!-- jQuery http://jquery.com/ を取得してインストール -->
	<script src="jquery.min.js"></script>
	<script>
	// SPARQL 検索を行う query() 関数を定義

ktym / rw-l5.rb

Last active August 29, 2015 14:03

Ruby Warrior Level 5 https://www.bloc.io/ruby-warrior

	class Player
	def play_turn(warrior)
	# cool code goes here
	@health \|\|= warrior.health
	if warrior.feel.captive?
	warrior.rescue!
	elsif warrior.feel.enemy?
	warrior.attack!
	else
	if warrior.health < 20 and !(warrior.health < @health)

ktym / d3-sparql-forcegraph.html

Last active August 29, 2015 14:03

	<!DOCTYPE html>
	<meta charset="utf-8">
	<html>
	<head>
	<!-- Twitter Bootstrap http://getbootstrap.com/2.3.2/ を取得してインストール -->
	<link rel="stylesheet" type="text/css" href="lib/bootstrap/css/bootstrap.css"/>
	<!-- D3.js http://d3js.org/ を取得してインストール -->
	<script src="lib/d3/d3.v3.min.js"></script>
	<script>
	function query() {

ktym / taxdump2owl.rb

Last active August 29, 2015 13:56

INSDC (NCBI) taxdump to OWL converter

	#!/usr/bin/env ruby
	#
	# Taxonomy ontology generator
	#
	# Copyright (C) 2013, 2014 Toshiaki Katayama <[email protected]>
	#
	# Version: Jan 29, 2014
	#
	# Usage:
	#

ktym / sparql2das.rb

Created January 18, 2014 10:07

Generate BioDAS XML from a SPARQL endpoint which stores genome sequences/annotations using FALDO

	#!/usr/bin/env ruby
	#
	# Usage:
	# DAS XML for http://togogenome.org/das/645657/features?segment=NC_017196.1:1,100000 can be generated by
	# % ruby sparql2das.rb 645657 features segment=NC_017196.1:1,100000
	# With ruby -d option, you'll see debug massages with pretty formatted XML (will miss <?xml> tag though)
	#
	# TODO:
	# Wrap as an Rack app and add X-DAS-* HTTP headers
	#

ktym / .emacs

Last active December 20, 2015 02:09

Configuration for multi-line editing mode in Emacs 24.

	;;; library

	(let ((default-directory "~/lib/lisp"))
	(normal-top-level-add-subdirs-to-load-path))

	;; multiple-cursors

	; % git clone https://github.com/magnars/multiple-cursors.el.git
	; % mv multiple-cursors.el lib/lisp/multiple-cursors

ktym / refseq2ttl.rb

Last active December 17, 2015 03:59

refseq2ttl.rb version 8 (migrated into https://github.com/dbcls/rdfsummit/tree/master/insdc2ttl in 2014)

	#!/usr/bin/env ruby

	require 'rubygems'
	require 'uri'
	require 'bio'
	require 'json'
	require 'securerandom'

	# [TODO] integrate this into BioRuby
	module Bio