Charles Tapley Hoyt cthoyt

## hbp_ideogram.html
<!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({

## southan_challenge.py
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

## truthycontext.py
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

## update_resources.sh
#!/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 ..

## use_pip.py
# 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)

## compare_bel_compilers.sh
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

## process.sh
[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)...

## bertini_utils.py
def parse_bertini_main_data(fl):
    """
    Parses main_data output from Bertini 1.5.1
    :param fl: file object for main_data
    :type f1: file-like object
    :return: list of solutions
    """
    it = (line.strip() for line in fl)
    number_variables = next(it)
    solution_dimension = int(number_variables[21:])

## keybase.md

      
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                cthoyt
                / keybase.md
            
            
              Created
              September 12, 2016 19:23
            
          
    Keybase proof

I hereby claim:

I am cthoyt on github.
I am cthoyt (https://keybase.io/cthoyt) on keybase.
I have a public key whose fingerprint is 91A7 A8AA B13B E6CE 6812  DD70 8FCE 28AC BC44 3133

To claim this, I am signing this object:

  
## coalesce_zeta.py
#! /usr/bin/env python3

"""

This script coalesces the results from running Fraunhofer FIT ZETA and
merges all of the output files from the evaluation task.

From the terminal, run something like:

`python3 coalesce_zeta_results.py -d ~/Desktop/HCA\ 2016\ Data/assay/resultPath -o ~/Desktop/coalesced.csv`
	<!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({
	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
	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
	#!/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 ..
	# 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)
	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
	[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)...
	def parse_bertini_main_data(fl):
	"""
	Parses main_data output from Bertini 1.5.1
	:param fl: file object for main_data
	:type f1: file-like object
	:return: list of solutions
	"""
	it = (line.strip() for line in fl)
	number_variables = next(it)
	solution_dimension = int(number_variables[21:])
	#! /usr/bin/env python3

	"""

	This script coalesces the results from running Fraunhofer FIT ZETA and
	merges all of the output files from the evaluation task.

	From the terminal, run something like:

	`python3 coalesce_zeta_results.py -d ~/Desktop/HCA\ 2016\ Data/assay/resultPath -o ~/Desktop/coalesced.csv`