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.

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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