Shaun Jackman sjackman

## README.md

      
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                fnichol
                / README.md
            
            
              Created
              March 12, 2011 20:52
            
              
                Download a cacert.pem for RailsInstaller
              
          
    Why?

There is a long standing issue in Ruby where the net/http library by default does not check the validity of an SSL certificate during a TLS handshake. Rather than deal with the underlying problem (a missing certificate authority, a self-signed certificate, etc.) one tends to see bad hacks everywhere. This can lead to problems down the road.
From what I can see the OpenSSL library that Rails Installer delivers has no certificate authorities defined. So, let's go fetch some from the curl website. And since this is for ruby, why don't we download and install the file with a ruby script?
Installation

The Ruby Way! (Fun)


## gist:1155906

      
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                clintel
                / gist:1155906
            
            
              Created
              August 19, 2011 02:40
            
              
                Fenced code in bullet lists with GitHub-flavoured MarkDown??
              
          
    Fenced code blocks inside ordered and unordered lists


This is a numbered list.


I'm going to include a fenced code block as part of this bullet:
Code
More Code


## ipython-0.0.1.py
#!/usr/bin/env python
"""
Interactive execution with automatic history, tries to mimic Mathematica's
prompt system. This environment's main features are:

- Numbered prompts (In/Out) similar to Mathematica. Only actions that produce
  output (NOT assingments, for example) affect the counter and cache.

- The following GLOBAL variables always exist (so don't overwrite them!):
  _p: stores previous result which generated printable output.

## genbank_to_tbl.py
# requires biopython
# run like:
#   genbank_to_tbl.py "my organism name" "my strain ID" "ncbi project id" < my_sequence.gbk
#   writes seq.fsa, seq.tbl as output

import sys
from copy import copy
from Bio import SeqIO

def find_gene_entry(features, locus_tag):

## web-servers.md

      
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                willurd
                / web-servers.md
            
            
              Last active
              May 6, 2024 09:12
            
              
                Big list of http static server one-liners
              
          
    Each of these commands will run an ad hoc http static server in your current (or specified) directory, available at http://localhost:8000. Use this power wisely.
Discussion on reddit.
Python 2.x

$ python -m SimpleHTTPServer 8000

  
## alg1-ropebwt2.txt
This document is a partial presentation of the RopeBWT2 pre-print

http://arxiv.org/abs/1406.0426

It is the transcript of a presentation made within the Medvedev group at Penn State
in July 2014. It focuses on illustrating some notions from the methods, and
illustrating and proving Algorithm 1. While this document does not cover the main
contribution of the RopeBWT2 paper, I hope it can be helpful towards understanding
the theoretical foundations that led to Algorithms 2 and 3.

## 2014-10-12_stop-working-directory-insanity.md

      
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                jennybc
                / 2014-10-12_stop-working-directory-insanity.md
            
            
              Last active
              September 23, 2022 04:43
            
              
                Stop the working directory insanity
              
          
    There are packages for this now!

2017-08-03: Since I wrote this in 2014, the universe, specifically Kirill Müller (https://github.com/krlmlr), has provided better solutions to this problem. I now recommend that you use one of these two packages:

rprojroot: This is the main package with functions to help you express paths in a way that will "just work" when developing interactively in an RStudio Project and when you render your file.
here: A lightweight wrapper around rprojroot that anticipates the most likely scenario: you want to write paths relative to the top-level directory, defined as an RStudio project or Git repo. TRY THIS FIRST.

I love these packages so much I wrote an ode to here.
I use these packages now instead of what I describe below. I'll leave this gist up for historical interest. 😆

  
## ds-training.md

      
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                hadley
                / ds-training.md
            
            
              Created
              March 13, 2015 18:49
            
              
                My advise on what you need to do to become a data scientist...
              
          
If you were to give recommendations to your "little brother/sister" on things
that they need to do to become a data scientist, what would those things be?

I think the "Data Science Venn Diagram" (http://drewconway.com/zia/2013/3/26/the-data-science-venn-diagram) is a great place to start. You need three things to be a good data scientist:

Statistical knowledge
Programming/hacking skills
Domain expertise

Statistical knowledge


## slide.html
<!doctype html>
<html lang="en">
  <head>
    <meta charset="utf-8">

    <title>
      {% if page.title %}
        {{ page.title }} | {{ site.title }}
      {% else %}
        {{ site.title }}

## add_mrna.lua
#!/usr/bin/env gt

function usage()
  io.stderr:write(string.format("Usage: %s <GFF annotation>\n" , arg[0]))
  os.exit(1)
end

if #arg < 1 then
  usage()
end
	#!/usr/bin/env python
	"""
	Interactive execution with automatic history, tries to mimic Mathematica's
	prompt system. This environment's main features are:

	- Numbered prompts (In/Out) similar to Mathematica. Only actions that produce
	output (NOT assingments, for example) affect the counter and cache.

	- The following GLOBAL variables always exist (so don't overwrite them!):
	_p: stores previous result which generated printable output.
	# requires biopython
	# run like:
	# genbank_to_tbl.py "my organism name" "my strain ID" "ncbi project id" < my_sequence.gbk
	# writes seq.fsa, seq.tbl as output

	import sys
	from copy import copy
	from Bio import SeqIO

	def find_gene_entry(features, locus_tag):
	This document is a partial presentation of the RopeBWT2 pre-print

	http://arxiv.org/abs/1406.0426

	It is the transcript of a presentation made within the Medvedev group at Penn State
	in July 2014. It focuses on illustrating some notions from the methods, and
	illustrating and proving Algorithm 1. While this document does not cover the main
	contribution of the RopeBWT2 paper, I hope it can be helpful towards understanding
	the theoretical foundations that led to Algorithms 2 and 3.
	<!doctype html>
	<html lang="en">
	<head>
	<meta charset="utf-8">

	<title>
	{% if page.title %}
	{{ page.title }} \| {{ site.title }}
	{% else %}
	{{ site.title }}
	#!/usr/bin/env gt

	function usage()
	io.stderr:write(string.format("Usage: %s <GFF annotation>\n" , arg[0]))
	os.exit(1)
	end

	if #arg < 1 then
	usage()
	end