IdoBar

Setting up a cloud-based multi-user teaching server using conda

Setup steps

1. Apply for an allocation at NECTAR-RDS
2. Setup 2 key-pairs (one will be for 'root-designated' login and the other for 'general-user' login), download the private keys to a secure location. If you're planning to use KiTTY or PuTTY to login to the server from Windows, you'll need to convert the .pem key file to a .ppk, as explained here. You can (and should) password-protect this key (can be done in PuTTYgen when converting the key from the default .pem format to a PuTTY-supported .ppk).
3. Setup a customised security group to allow remote access (open port 22 for ssh logins and any addi

IdoBar

Setting up a new computer for scientific and bioinformatics data analysis

Follow these instructions to setup a new computer with commonly used tools and software for scientific data analysis (with emphasis on bioinformatics)

Windows machine

Use https://ninite.com/ to install the following open source software:

1. FileZilla - FTP file transfer
2. Firefox - web browser, add cliget addon for easy curl/wget download links
3. PuTTY - remote shell access
4. Java 8
5. .NET - framework needed for Paint.net

Brainiarc7

GNU Parallel for Bioinformatics: A primer

Installation:

A quick installation does not require root access, as shown:

(wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash

For other installation options see http://git.savannah.gnu.org/cgit/parallel.git/tree/README

lelandbatey

Description

This simple script will take a picture of a whiteboard and use parts of the ImageMagick library with sane defaults to clean it up tremendously.

The script is here:

#!/bin/bash
convert "$1" -morphology Convolve DoG:15,100,0 -negate -normalize -blur 0x1 -channel RBG -level 60%,91%,0.1 "$2"

Results