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@kohlmeier
kohlmeier / ka_bnet_numpy.py
Created March 26, 2012 21:59
Bayes net example in Python with Khan Academy data
#!/usr/bin/env python
from numpy import asmatrix, asarray, ones, zeros, mean, sum, arange, prod, dot, loadtxt
from numpy.random import random, randint
import pickle
MISSING_VALUE = -1 # a constant I will use to denote missing integer values
def impute_hidden_node(E, I, theta, sample_hidden):
@MohamedAlaa
MohamedAlaa / tmux-cheatsheet.markdown
Last active August 14, 2025 02:55
tmux shortcuts & cheatsheet

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname
@dan-blanchard
dan-blanchard / create_single_machine_sge.md
Last active March 20, 2022 10:40
How to setup a single-machine (Sun) Grid Engine installation for unit tests on Travis-CI

I recently needed a way to run unit tests on Travis for a project that uses Sun Grid Engine, Grid Map. Unfortunately, it seemed like no one had figured out how to set that up on Travis before (or simply create a single-machine installation without any user interaction). After hours of trial-and-error, I now know the secrets to making a single-machine installation of SGE that runs on Travis, and I'm sharing my script to prevent other people from going through the same frustrating experience.

To use the install_sge.sh script below, you just need to copy all of the files in this gist to a travis sub-directory directly under the root of your GitHub project, and add the following lines to your .travis.yml

before_install:
  - travis/install_sge.sh
  - export SGE_ROOT=/var/lib/gridengine
  - export SGE_CELL=default
  - export DRMAA_LIBRARY_PATH=/usr/lib/libdrmaa.so.1.0
curl -O -L http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-linux-x86_64.zip
@roblanf
roblanf / genome_plots.r
Last active September 4, 2016 09:23
Make plots about genome sequencing, size, and gene content
source("http://bioconductor.org/biocLite.R")
biocLite("genomes")
library(genomes)
library(ggplot2)
valid <- c("released", "created", "submitted")
data(proks)
update(proks)

This hit #rstats today:

Has anyone made a dumbbell dot plot in #rstats, or better yet exported to @plotlygraphs using the API? https://t.co/rWUSpH1rRl

— Ken Davis (@ken_mke) October 23, 2015
<script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script>

So, I figured it was worth a cpl mins to reproduce.

While the US gov did give the data behind the chart it was all the data and a pain to work with so I used WebPlotDigitizer to transcribe the points and then some data wrangling in R to clean it up and make it work well with ggplot2.

It is possible to make the top "dumbbell" legend in ggplot2 (but not by using a guide) and color the "All Metro A

@speeddragon
speeddragon / kali-linux-wl-fix.sh
Last active February 18, 2024 13:05
Kali Linux fix for "modprobe: FATAL: Module wl not found"
# Update and install necessary packages
apt-get update
apt-get install linux-image-$(uname -r|sed 's,[^-]*-[^-]*-,,') linux-headers-$(uname -r|sed 's,[^-]*-[^-]*-,,')
# Download some extra packages, that do the trick for "wl module not found"
wget http://http.kali.org/kali/pool/main/l/linux-tools/linux-kbuild-4.3_4.3.1-2kali1_amd64.deb
wget http://http.kali.org/kali/pool/main/l/linux/linux-headers-4.3.0-kali1-common_4.3.3-5kali4_amd64.deb
wget http://http.kali.org/kali/pool/main/l/linux/linux-headers-4.3.0-kali1-amd64_4.3.3-5kali4_amd64.deb
# Install with correct order
@jsonmaur
jsonmaur / setup.sh
Last active November 13, 2017 11:43
Setup Kali on Macbook
# persistence from usb stick
mkdir -p /mnt/my_usb
mount /dev/sdb3 /mnt/my_usb
echo "/ union" > /mnt/my_usb/persistence.conf
umount /dev/sdb3 && reboot
# get wifi working
apt-get update
apt-get install -y linux-headers-$(uname -r) broadcom-sta-dkms

How To Sync Your Movie to the Professional Jokes By Professional Comedy Professionals (AKA RiffTrax)

Intro

This guide started off as a sort of checklist for myself to try to refine, and speed up the process. I'm sure that there are a good number of things that can be improved upon, but in my opinion, the steps below produce pretty consistently good results. Hopefully this will help

@yashodhank
yashodhank / kali-linux-wl-fix.sh
Last active November 13, 2017 11:43 — forked from speeddragon/kali-linux-wl-fix.sh
Kali Linux fix for "modprobe: FATAL: Module wl not found"
# Update and install necessary packages
apt-get update
apt-get install linux-image-$(uname -r|sed 's,[^-]*-[^-]*-,,') linux-headers-$(uname -r|sed 's,[^-]*-[^-]*-,,')
# Download some extra packages, that do the trick for "wl module not found"
wget http://http.kali.org/kali/pool/main/l/linux-tools/linux-kbuild-4.3_4.3.1-2kali1_amd64.deb
wget http://http.kali.org/kali/pool/main/l/linux/linux-headers-4.3.0-kali1-common_4.3.3-5kali4_amd64.deb
wget http://http.kali.org/kali/pool/main/l/linux/linux-headers-4.3.0-kali1-amd64_4.3.3-5kali4_amd64.deb
# Install with correct order