Scientific Computing Resource Library

Additional Resources Available

There are a handful of useful resources emerging alongside this Wiki page that are sources of assistance that might be relevant to your work.

slurm-examples GitHub Repository

SciComp is reviewing emerging contributions of example starter scripts that focus on connecting your work to computing resources supported by SciComp. You can find that repository here.

wiki-code-examples GitHub Repository

Fredhutch.io is providing and reviewing example code for various data wrangling and analysis purposes. That emerging resource can be found here.

wiki-templates GitHub Repository

The Fred Hutch wiki-templates repository aims to describe the minimum file requirements for several project types. Each project folder serves as a template and guide for following best coding practices and is an evolving resource meant to help people get started. You can find that repository here.

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.

Accessing Economy Local Storage

This demo showcases different options for accessing economy storage, including command line and API options, and how to handle the migration of large dataset...

How to Beagle

Beagle clusters serve as an extension of gizmo into AWS cloud infrastructure. It is an alternative way to send your sbatch jobs to clusters other than gizmo....

How to Gizmo

Gizmo is a capability cluster maintained by Center IT’s Scientific Computing group for use in Hutch research. Presented here is some basic information about...

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...

Matlab

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

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...

Running Tensorflow (and Keras) on GPUs

Running tensorflow with GPUs has become easier in 2019. We can either use it on Gizmo as the latest GizmoJ class nodes are equipped with GPUs or on the Koshu...

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...

Synology

Synology storage appliances (cloud sync)

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 Singularity Containers

Docker can only run containers as root so we cannot use them in shared multi-user environments such as Rhino/Gizmo with shared storage such as /home, /fh/fas...

using Docker at Fred Hutch

Accessing Docker You can either install docker on your own machine or you install on the SciComp test server farm