Scientific Computing Resource Library

Below you will find a variety of more hands on descriptions that relate to a specific topic. These tend to be more detailed examples of the use of resources described in the main articles of the Wiki.

Note: If you would like to request content for this section or are interested in writing content, please email sciwiki, file an issue in our GitHub repo here, or see our contribution instructions here.

AWS CLI for Windows Subsystem for Linux

Windows Subsystem for Linux is a useful tool for interacting with a Windows machine using Linux commands. WSL allows users and developers to run Linux within...

Checkpointing on Gizmo (beta)

Checkpointing is a technique that provides fault tolerance for computations. It basically consists of saving a snapshot of the application’s state on persist...

GDC Hints

This page will provide some hints for using GDC on our compute hosts (gizmo, rhino, etc.)

Generating Pre-Signed URLs

In AWS (Amazon Web Services), pre-signed Uniform Resource Locators ( URL URL is an acronym for “Uniform Resource Locator”. It is a unique identifier fo...

How to Rhino

Probably the more familiar method of computing once resources beyond those available on your desktop/laptop are needed is interactive computing. Here, one w...

Intro to plyranges (Bioconductor)

plyranges provides dplyr-style operations to genomic range data infrastructure in Bioconductor. Spending 15 - 20 minutes going over this demo, you may find h...

Introduction to rslurm

The rslurm library creates a mechanism for distributing R calcuations across a set of Slurm jobs. rslurm creates and manages self-contained Slurm jobs, then...

Job Local Storage

In the gizmo compute cluster you will be provisioned a directory on the allocated node’s local disk. This directory exists only for the duration of the job....

Load Management for Rhino Hosts

The Rhino hosts provide interactive login sessions to Hutch researchers. These are intended for cluster job management, development work, and NoMachine sess...

Logging in Python

Logging in Python is performed through the simple and elegant logging module which comes in the standard Python library for both Python 2 and 3. The logging ...

Managing Aspera Connect on NoMachine

Aspera can be used on the NoMachine systems (rhino). Using Aspera requires that the plugin be installed in the browser you are running in a NoMachine sessio...

Managing Module Versions

If you do not specify a default version when you load a module you will get the currently set default version of the module. This default may change as time...

Matlab

The majority of Matlab users at the Hutch have Matlab installed on their desktop system. Most users have dedicated licenses for their desktop installs Matlab...

Proteomics using Maxquant on Gizmo

MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. This demo gives instructions for running th...

Python Virtual Environments

A Python virtual environment allows you to create an isolated Python installation with its own set of libraries and packages. This can be useful when you ar...

R Tips & Tricks

Below are some general tips and tricks for working in R that don’t fit neatly into any articles.

Rslurm and Tximport Example

This is an example of Rslurm for a bioinformatics application with the tximport package for reading in transcript level RNA-seq count data. I used this examp...

SSH Host Key Management

SSH keys are used to manage access credentials to computing resources. They are similar to names and passwords, and confirm that the identity of individual...

Shiny Applications

Shiny is an R package that makes it easy to build interactive web apps straight from R. You can host standalone apps on a webpage or embed them in R Markdown...

Snapshots

How to use snapshots for self-service file recovery or undelete The file system underlying home directories and most shared folders on Linux systems has a fe...

Tips and tricks for Git and GitHub

This tutorial includes demonstrations of a few common tasks in Git and/or GitHub, and assumes you have a basic understanding of how these tools work. For a g...

Using AWS Cloud Credits

AWS credits are a simple idea, yet applying them so that they are used optimally is surprisingly complex.

Using Markdown with Visual Studio Code

Markdown is a formatting language used when the resulting document will be rendered or converted into html documents for web-viewable material. The format i...

Using Motuz to Move Large Data

This demo provides specific examples of how to use the new tool, Motuz, to transfer data between Fred Hutch data storage locations.

Using Toolbox to Get Hutch Master Data

Did you ever want to know to which PI or division a user rolls up to or check if someone is Hutch staff or affiliated or get all users in the same department...