Toshiaki Katayama ktym

## insdc.owl
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix : <http://insdc.org/owl/#> .

<http://insdc.org/owl/>
    a owl:Ontology .

## unwebarchive.rb
#!/usr/bin/env ruby
#
# Mac OS X webarchive is a binary format of a plist file. You can extract the contents manually:
#  1. convert the plist file into XML by "plutil -convert xml1 file.webarchive"
#  2. parse the resulted XML file by some XML parser
#  3. decode "WebResourceData" by Base64.decode64(data) in each key
#  4. save the decoded content into a file indicated by "WebResourceData"
# Thankfully, the plist library can take care of annoying steps 2 and 3.
#
# Preparation:

## refseq2ttl.rb
#!/usr/bin/env ruby

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

# [TODO] integrate this into BioRuby
module Bio

## .emacs
;;; 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

## sparql2das.rb
#!/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
#

## taxdump2owl.rb
#!/usr/bin/env ruby
#
# Taxonomy ontology generator
#
#  Copyright (C) 2013, 2014 Toshiaki Katayama <ktym@dbcls.jp>
#
# Version: Jan 29, 2014
#
# Usage:
#

## d3-sparql-forcegraph.html
<!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() {

## rw-l5.rb
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)

## jquery-sparql.html
<!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

## Sample_ruby_native_apps_script.rb
require 'json'

def metadatajson
  json = JSON.parse('
{
  "Name": "",
  "Description": "",
  "HrefAppSession": "",
  "Properties": [
    {
	@prefix owl: <http://www.w3.org/2002/07/owl#> .
	@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
	@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
	@prefix xml: <http://www.w3.org/XML/1998/namespace> .
	@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
	@prefix obo: <http://purl.obolibrary.org/obo/> .
	@prefix : <http://insdc.org/owl/#> .

	<http://insdc.org/owl/>
	a owl:Ontology .
	#!/usr/bin/env ruby
	#
	# Mac OS X webarchive is a binary format of a plist file. You can extract the contents manually:
	# 1. convert the plist file into XML by "plutil -convert xml1 file.webarchive"
	# 2. parse the resulted XML file by some XML parser
	# 3. decode "WebResourceData" by Base64.decode64(data) in each key
	# 4. save the decoded content into a file indicated by "WebResourceData"
	# Thankfully, the plist library can take care of annoying steps 2 and 3.
	#
	# Preparation:
	#!/usr/bin/env ruby

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

	# [TODO] integrate this into BioRuby
	module Bio
	;;; 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
	#!/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
	#
	#!/usr/bin/env ruby
	#
	# Taxonomy ontology generator
	#
	# Copyright (C) 2013, 2014 Toshiaki Katayama <ktym@dbcls.jp>
	#
	# Version: Jan 29, 2014
	#
	# Usage:
	#
	<!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() {
	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)
	require 'json'

	def metadatajson
	json = JSON.parse('
	{
	"Name": "",
	"Description": "",
	"HrefAppSession": "",
	"Properties": [
	{