Charles Tapley Hoyt cthoyt

Charlie's PhD, The Drinking Game

How to play:

Read Charlie's PhD thesis... or just skim through it looking for fun
Drink based on the following rules:

1 Sip

Charlie uses too many references

BioGRID Identifiers Problem, Solved

The file I included here has a set of organisms in the BioGRID identifiers download (version 3.5.184), latest as of time of writing on 2020-04-17) whose ORGANISM_OFFICIAL_NAME is not correct. I went and mapped these all with a mixture of synonym search on NCBITaxon and manual intervention. Each has the taxonomy identifier, so it can be used to get the most up-to-date information.

I would highly suggest including a taxonomy ID in this dump as well as the name, so it can be programatically mapped for anyone trying to integrate this

	[544] [19:04] [cthoyt@microvac:~]
	$ rvm use 2.3.0 --install
	ruby-2.3.0 is not installed - installing.
	Searching for binary rubies, this might take some time.
	No binary rubies available for: osx/10.12/x86_64/ruby-2.3.0.
	Continuing with compilation. Please read 'rvm help mount' to get more information on binary rubies.
	Checking requirements for osx.
	Certificates in '/usr/local/etc/openssl/cert.pem' are already up to date.
	Requirements installation successful.
	Installing Ruby from source to: /Users/cthoyt/.rvm/rubies/ruby-2.3.0, this may take a while depending on your cpu(s)...

	mkdir /tmp/beltest
	cd /tmp/beltest

	curl http://resources.openbel.org/belframework/1.0/knowledge/small_corpus.bel > small.bel
	curl http://resources.openbel.org/belframework/1.0/knowledge/large_corpus.bel > large.bel

	# Test Python
	python -m pip install pybel
	time python -m pybel convert --path small.bel --pickle small.gpickle
	time python -m pybel convert --path large.bel --pickle large.gpickle

	# Pip is actually a python package!
	import pip

	# It's screwy and not really written to be used this way, but we still can
	pip_install_cmd = pip.commands.InstallCommand()

	# load up all the args you'd use after pip install and away we go!
	args = ['--upgrade', '--user', 'requests']
	pip_install_cmd.main(args)

	#!/usr/bin bash

	mkdir output

	# Download and install pybel-tools
	git clone https://github.com/pybel/pybel-tools
	cd pybel-tools
	python3 -m pip install --user .

	cd ..

	import unittest

	from contextlib import contextmanager

	# see https://stackoverflow.com/questions/12594148/skipping-execution-of-with-block

	@contextmanager
	def when_truthy(argument):
	"""
	The point of this function is to make it so you never have to write

	import pubchempy as pcp

	keys = '''MXDPZUIOZWKRAA-UZOALHFESA-K
	MJUVRTYWUMPBTR-MRXNPFEDSA-N
	HJBWBFZLDZWPHF-UHFFFAOYSA-N
	HZIYEEMJNBKMJH-UHFFFAOYSA-N
	CPZBLNMUGSZIPR-NVXWUHKLSA-N
	GKDRMWXFWHEQQT-UHFFFAOYSA-N
	KSMAGQUYOIHWFS—UHFFFAOYSA-N
	OFZJKCQENFPZBH-UHFFFAOYSA-N

	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="UTF-8">
	<title>Human Brain Pharmacome Knowledge</title>
	<script src="https://unpkg.com/ideogram@1.5.0/dist/js/ideogram.min.js"></script>
	</head>
	<body>
	<script>
	var ideogram = new Ideogram({