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Erick Matsen matsen

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matsen / keybase.md
Created April 6, 2015 16:55
keybase.md

Keybase proof

I hereby claim:

  • I am matsen on github.
  • I am ematsen (https://keybase.io/ematsen) on keybase.
  • I have a public key whose fingerprint is BEE5 925E E22C 76C3 EC0D 4074 319F C81F 9510 3B94

To claim this, I am signing this object:

@matsen
matsen / response-to-exascale-hpc-rfi.md
Last active October 1, 2015 12:19
Response to "Science Drivers Requiring Capable Exascale High Performance Computing" RFI

Response to Science Drivers Requiring Capable Exascale High Performance Computing RFI

We can piggyback on the coding development community.

Many good things are happening in open source and industry, and we face many of the same issues that they do. For example, GitHub has provided enormous value to science, both through filling a need and by direct engagement. It has gotten almost unbelievably popular in the computational life sciences. However, other tools such as continuous integration, for example by Travis CI, or containers, for example by Docker, have gotten less traction despite the

@matsen
matsen / SConstruct
Created December 5, 2012 20:06
SConstruct (http://scons.org) I use for building latex documents, featuring continuous build and auto SVG -> PDF conversion via inkscape.
from SCons.Script import VariantDir, Environment, \
Builder, Depends, Flatten
import os
VariantDir('_build', src_dir='.')
env = Environment(ENV=os.environ)
inkscape = Builder(action = 'inkscape --without-gui --export-pdf=$TARGET $SOURCE')
env['BUILDERS']['Inkscape'] = inkscape
env['BUILDERS']['Latexdiff'] = Builder(action = 'latexdiff $SOURCES > $TARGET')
@matsen
matsen / from_scratch.sh
Last active December 15, 2015 12:49
Script for installing all of the software that I use.
#!/bin/sh
set -e
set -o
sudo apt-get update
sudo apt-get upgrade -y
sudo apt-get install -y \
autojump \
@matsen
matsen / sysbio.tex
Last active December 15, 2015 15:29
Framework for a latex file designed for both arXiv and Systematic Biology submission.
%%For arXiv, uncomment this block and comment the next block.
%\documentclass{amsart}
%\usepackage{amsmath,amsfonts,amssymb,amsthm}
%\usepackage[english]{babel}
%\usepackage{graphicx}
%\usepackage{url}
%\usepackage[round]{natbib}
%\newcommand{\forarxiv}[1]{#1}
%\newcommand{\notforarxiv}[1]{}
@matsen
matsen / parasite.svg
Created January 25, 2016 20:07
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@matsen
matsen / seqs2png
Last active February 9, 2016 04:11
A simple script to render a molecular sequence file as a PNG, with a specified number of pixels per symbol.
#!/usr/bin/env python
"""
Turn a sequence file into a PNG, with a specified number of pixels per symbol.
Gaps are shown in light gray.
Unknown symbols, including N and X, are shown in pink.
Requires matplotlib, seqmagick, and their dependencies.
"""
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matsen / prep-crouton.sh
Last active October 17, 2016 17:55
Preparing a crouton chroot environment for productivity.
#!/bin/sh
# sudo visudo
# matsen ALL = (root) NOPASSWD: /usr/local/bin/xiwi,/usr/bin/evince,/usr/bin/inkscape
set -e
set -o
sudo hostnamectl set-hostname flyx
@matsen
matsen / latex-skeleton.tex
Last active October 27, 2016 19:52
Framework for a latex file designed for both arXiv and journal submission.
\documentclass{amsart}
\usepackage[round]{natbib}
\usepackage{graphicx}
\usepackage[notref,notcite]{showkeys}
\usepackage{url}
% in case of supplementary material
% \usepackage{xr}
% \externaldocument{lcfit_supp}
@matsen
matsen / gallifrey-ve.zsh-theme
Last active March 28, 2019 09:16
# A modification of `gallifrey` to show virtualenv information.
# I also found the return code information to be annoying, so it's commented out.
#local return_code="%(?..%{$fg[red]%}%? ↵%{$reset_color%})"
PROMPT='%{$fg[green]%}%m%{$reset_color%} $(virtualenv_prompt_info)%2~ $(git_prompt_info)%{$reset_color%}%B»%b '
#RPS1="${return_code}"
ZSH_THEME_GIT_PROMPT_PREFIX="%{$fg[yellow]%}‹"
ZSH_THEME_GIT_PROMPT_SUFFIX="› %{$reset_color%}"