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Toshiaki Katayama ktym

  • Database Center for Life Science
  • Japan
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@ktym
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": [
{
View 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
View 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)
View 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() {
@ktym
ktym / taxdump2owl.rb
Last active Aug 29, 2015
INSDC (NCBI) taxdump to OWL converter
View taxdump2owl.rb
#!/usr/bin/env ruby
#
# Taxonomy ontology generator
#
# Copyright (C) 2013, 2014 Toshiaki Katayama <ktym@dbcls.jp>
#
# Version: Jan 29, 2014
#
# Usage:
#
@ktym
ktym / sparql2das.rb
Created Jan 18, 2014
Generate BioDAS XML from a SPARQL endpoint which stores genome sequences/annotations using FALDO
View 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
#
@ktym
ktym / .emacs
Last active Dec 20, 2015
Configuration for multi-line editing mode in Emacs 24.
View .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
@ktym
ktym / refseq2ttl.rb
Last active Dec 17, 2015
refseq2ttl.rb version 8 (migrated into https://github.com/dbcls/rdfsummit/tree/master/insdc2ttl in 2014)
View refseq2ttl.rb
#!/usr/bin/env ruby
require 'rubygems'
require 'uri'
require 'bio'
require 'json'
require 'securerandom'
# [TODO] integrate this into BioRuby
module Bio
@ktym
ktym / unwebarchive.rb
Created Feb 12, 2013
Extract contents of a .webarchive file.
View 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:
@ktym
ktym / insdc.owl
Created Dec 12, 2012
Draft version of INSDC (DDBJ/EMBL/GenBank/RefSeq) ontology in RDF/Turtle format.
View 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 .
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