Julian Mazzitelli thejmazz

PHYLIFY Questions

Question 1

The R way of storing data

The first task of PHYLIFY was to take bare ontology data from an obo file, specifically ff-phase2-140729.obo.

The OBO flat file format is not terribly complicated, and is detailed in a spec. The main part is that we have (a lot of) Term stanzas as such:

three.js

UVs

Texture Mapping

Docker

docker-cheat-sheet

Make a container that normally exits keep running as daemon: docker run -d imageName tail -f /dev/null

Links

Colours

Navigation

Using CSS Cursors

tmux

tmux shortcuts & cheatsheet

sed (Stream Editor)

sed s/-/\ /g substitute globally (- to spaces in this case)

users and groups

list all users: cut -d: -f1 /etc/passwd OR compgen -u
list all groups: compgen -g

Databases

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ontologies

EFO

Tutorials

vcf

see URLs

What is a URL?

A Uniform Resource Locator is a subset of the Uiniform Resource Identifier (URI) family. In that, a URL is totally specific, contrary to a URI which can be "general", since a URI can be defined as "a string of characters used to identify a resource" Some example URLs are

http://www.rcsb.org/
http://www.ncbi.nlm.nih.gov/

Some example URIs are

The Cycle

data -> interpreation via "tool"
tool -> interpret
self -> tool
go back to 1.

Criteria

submitting code/plots to github before the presentation

	#!/bin/bash

	URL1="http://fantom.gsc.riken.jp/5/tet/search/?c=0&c=1&c=4&c=5&c=6&c="
	URL2_RAW="&filename=hg19.cage_peak_phase1and2combined_counts_ann_decoded.osc.txt.gz"
	URL2_RLE="&filename=hg19.cage_peak_phase1and2combined_tpm_ann_decoded.osc.txt.gz"

	nums="7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 105 106 107 108 109 110 111 113 114 116 117 119 120 122 123 125 126 128 129 131 132 134 135 137 138 140 141 143 144 146 147 149 150 152 153 155 156 158 159 162 164 165 167 168 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 243 244 245 24

	'use strict'

	const rp = require('request-promise')
	const htmlparser = require('htmlparser2')

	// Example params
	const baseJasparUri = 'http://fantom.gsc.riken.jp/5/sstar/JASPAR_motif:'
	const requestUri = 'http://fantom.gsc.riken.jp/5/sstar/FF:10017-101C8'
	const className = 'Jaspar-motif'