Kevin Brown thelahunginjeet

thelahunginjeet / vim-spaces-to-tabs

Created November 8, 2013 20:46

spaces to tabs in vim (useful for fixing python indentation issues)

:%s/<space><space><space><space>/<tab>/g

thelahunginjeet / latex-chem-reactions

Last active December 27, 2015 19:29

useful latex commands for chemical reactions

	\usepackage{amsmath}

	% ensures non-italicized chemical species name
	\newcommand{\ch}[1]{\mathrm{#1}}
	% adds brackets to indicate concentrations
	\newcommand{\conc}[1]{[\mathrm{#1}]}
	% single right reaction arrow, with rate argument on top
	\newcommand{\react}[1]{\stackrel{#1}{\rightarrow}}
	% double left/right reaction arrow decorated above/below with rates
	\newcommand{\doublereact}[2]{\mathrel{\substack{#1\\\rightleftharpoons\\#2}}}

thelahunginjeet / startup.m

Created November 8, 2013 21:09

MATLAB startup.m file commands to get nicer looking plots by default

thelahunginjeet / scattertext.m

Created January 31, 2014 16:42

simple example of labeling plotted points with text

	% also works with scatter
	% may need to play around with axis labels and text positioning to get it to look nice
	data = rand(10,2);
	plot(data(:,1),data(:,2),'ko','MarkerFaceColor','k');
	labels = num2str((1:size(data,1))','%d');
	text(data(:,1),data(:,2),labels,'horizontal','left','vertical','bottom');

thelahunginjeet / python_array_job.sh

Last active August 29, 2015 13:57

LSF array job with python

	#!/bin/bash
	#BSUB -L /bin/bash
	#BSUB -J paj[1-10]
	#BSUB -e paj.%I.err
	#BSUB -o paj.%I.out
	#BSUB -n 1

	python -c "import sys; print(sys.version); import pyica; from numpy.random import randn; print '%f' % randn()"

	# comments:

thelahunginjeet / python_job.sh

Last active August 29, 2015 13:57

LSF example of a serial python job, with a virtual environment

	#!/bin/bash
	#
	#BSUB -o pyjob.%J.out
	#BSUB -e pyjob.%J.err
	#BSUB -n 1

	# do stuff
	source ~/venv/bin/activate
	python -c "import pyica; import sys; print(sys.version); from numpy.random import randn; x = randn(); print '%f' %x"

thelahunginjeet / pip_alternate.sh

Created March 28, 2014 20:14

python package installation using pip, to the distutils "user" location

pip install --install-option="--user" package_name

thelahunginjeet / parse_command_line.py

Last active August 29, 2015 13:58

basic example of python parsing of command-line arguments

	#!/usr/bin/python

	import sys, getopt

	def config_file_parser(configfile):
	"""
	Very basic code for reading a simple config file and returning
	a dictionary of options.
	"""
	config = {}

thelahunginjeet / python_array_args_job.sh

Last active July 19, 2018 10:51

example LSF array job showing how to use node-specific inputs and outputs

	#!/bin/bash
	#BSUB -L /bin/bash
	#BSUB -J paj[1-4]
	#BSUB -e paj.%I.err
	#BSUB -o paj.%I.out
	#BSUB -n 1

	source ~/venv/bin/activate
	python parse_command_line.py --config=conf_${LSB_JOBINDEX}.cfg --output=results_${LSB_JOBINDEX}.out

thelahunginjeet / redirect-fish

Last active August 29, 2015 14:01

redirect of stdout/stderr in fish shell