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Carl Leubsdorf, Jr. carlthewebmaster

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On April 23 and 24 a group of NCBI computer scientists, subject matter experts and customer service representatives conducted an in-house tool building exercise focused on building a prototype “what’s in my tube” workflow. This event was an attempt at converting the lessons learned from the January virus hackathon into a prototype tool that strings together the disparate computational steps used in the hackathon into a single, modular pipeline that sequentially analyzes the content of user provided next generation sequencing data.

The pipeline was built into a stand-alone Jupyter notebook interface that allows users to see and edit analysis parameters and view graphic displays of results.

While the April event resulted in the basic coding of the pipeline and an initial (MVP) approach to how to run the pipeline in GCP, work remains, particularly in fleshing out effective ways to host and run Jupyter Notebooks on GCP (including access to BLAST, scaling architecture, and visualizations). By the end of the two

View proxy.ps1
$Path="HKCU:\Software\Microsoft\Windows\CurrentVersion\Internet Settings"
$proxyServer = Get-ItemProperty -path $Path ProxyServer -ErrorAction SilentlyContinue
Set-ItemProperty -path $Path ProxyEnable -value 1
Set-ItemProperty -path $Path ProxyServer -Value "localhost:3128"
Write-Host "Proxy is enabled"
else {
View v21-new-only.txt
# Carl's wp updater
# assumes wp-cli is aliased to wp
wp core check-update
read -r -p "Update Core? [y/N] " response
if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
wp core update
View anno-custom-header-size.php
// Add the following function to a child theme or plugin:
function anno_custom_header_size() {
Anno_Keeper::keep( 'header_image', new Anno_Header_Image( 'header', array (1265, 110 ) ) );
// Priority 10 to come in after the annotum's initial template initialization.
add_action( 'after_setup_theme', 'anno_custom_header_size', 10 );
carlthewebmaster /
Last active Aug 29, 2015
Github markdown syntax highlighting

Github Synxax highlighting

Some Ruby:

require 'redcarpet'
markdown ="Hello World!")
puts markdown.to_html

Some C++:

carlthewebmaster /
Last active Aug 29, 2015
apt-get for new linux setup - ubuntu
sudo apt-get install vim wget curl git subversion zip ssmtp
sudo apt-get install tasksel
sudo tasksel install lamp-server
# don't forget these steps for crouton installs!
sudo apt-get install phpmyadmin ssmtp man weather-utils
# wordpress setup with a2ensite
View docker-vagrantfile
# -*- mode: ruby -*-
# vi: set ft=ruby :
# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
# All Vagrant configuration is done here. The most common configuration
# options are documented and commented below. For a complete reference,
# please see the online documentation at
carlthewebmaster /
Created Dec 14, 2013
DNS Dump from list of domains.
ls | xargs -L1 dig -t ANY > all-dns.txt
View ssmtp.conf