Amanda Miotto amandamiotto

## setup_nectar_teaching_server.md

      
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                IdoBar
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              March 7, 2024 14:32
            
              
                Setting up a NECTAR Cloud multi-user teaching server using conda
              
          
    Setting up a cloud-based multi-user teaching server using conda


Setup steps


Apply for an allocation at NECTAR-RDS
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).
Setup a customised security group to allow remote access (open port 22 for ssh logins and any addi


## New_computer_setup.md

      
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                IdoBar
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              February 25, 2020 03:50
            
              
                Setting up a new computer for scientific and bioinformatics data analysis
              
          
    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:


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


## gnu-parallel-bioinformatics.md

      
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                Brainiarc7
                / gnu-parallel-bioinformatics.md
            
            
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              September 6, 2023 13:59
            
              
                GNU Parallel usage in Bioinformatics with examples: A primer.
              
          
    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

  
## whiteboardCleaner.md

      
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                lelandbatey
                / whiteboardCleaner.md
            
            
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              June 16, 2024 13:44
            
              
                Whiteboard Picture Cleaner - Shell one-liner/script to clean up and beautify photos of whiteboards!
              
          
    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