software-collection

A collection of 29 posts

software-collection

How to install and use Quarto with RStudio on a RONIN Machine

Quarto is an open-source tool designed for writing dynamic documents incorporating code chunks for data analysis, visualization, and other computational tasks. This blog post shows you how to install and use Quarto with RStudio on a RONIN Machine.

software-collection

Accessing your RONIN object storage with Rclone

Rclone is a command-line program that allows you to copy, sync, and move files between your local system to various cloud storage services. This blog post will teach you how to install and configure Rclone to manage files in your object storage bucket.

jupyter

Enhancing AI Research: Seamlessly Connecting RONIN's Jupyter Notebook to Google Colab

Google Colab is a free hosted Jupyter Notebook service. This blog post will walk you through all the steps you need to connect Google Colab to your RONIN machine so that you can receive all the benefits of the Google Colab platform, without being restricted by computational power.

mlflow

Creating an MLFlow server in RONIN

MLFlow is an open source platform for managing machine learning (ML) workflows. This blog post teaches you how to set up a MLFlow server in RONIN.

s3

Mounting your object storage bucket as a local filesystem with Mountpoint

AWS has released an open source client called Mountpoint that allows you to easily mount your object storage bucket as a local filesystem. This blog post shows you the pros and cons of Mountpoint, and how to use it.

postgresql

Creating a PostgreSQL Database in RONIN

We previously blogged about installing MySQL on a RONIN machine. But databases are different, and another open source database that is popular among researchers is PostgreSQL. This blog post teaches you how to install and connect to a PostgreSQL database with RONIN.

spack

Spack is Research Computing's Best Friend

Research and cloud computing are a perfect fit, but the reality of managing software on dynamic clusters in the cloud can be a challenge. Fortunately, nifty tools like Spack can help get you up and running with optimised versions of your required software in just minutes.

software-collection

Automatically syncing scripts to your RONIN machine with Visual Studio Code

Did you know that instead of having to manually copy scripts and other files over to your RONIN machine each time you make changes, you can instead have all of your changes automatically synced as soon as you hit save!? Here we show you how with Visual Studio Code.

software-collection

Preparing a Customized Windows Environment for Sharing

Want to share your custom Windows environment with other users but require them to set their own Administrator password? Find out how in this blog post!

software-collection

Creating and managing your own Galaxy server in RONIN

Galaxy is an open-source platform which allows users to use command-line tools via a graphical web interface. This blog post will teach you how to set up your own Galaxy server with RONIN.

hpc

Modeling Air Quality With RONIN and Odycloud

In this post, we have invited Arturo Fernandez, founder of Odycloud, to describe how he scales research IT support for a variety of air quality and weather modeling problems.

igv

Visualising Genomic Data with IGV in RONIN

The Integrative Genomics Viewer (IGV) is one of the most popular free, open source software packages for the visual exploration of genomic data. In this blog post we will show you how to install and configure IGV on your machine or cluster with RONIN LINK.

software-collection

Documenting Your Workloads With Markdown

In this blog post we are going to focus on how to take your code documentation to the next level with a popular markup language known as Markdown.

application

Useful Desktop Apps For Researchers

Because many researchers work closely with the command line to run their analyses, managing and documenting scripts and workloads is key for reproducibility. In this blog post we describe three helpful classes of desktop applications that you can use to better manage your research workflows.

database

Creating a MySQL Database in RONIN

Databases are not necessarily part of a researcher's daily toolkit, although they are an important part of websites, data management systems, and popular repositories of data that researchers access.

software-collection

Version Control of Your Scripts with Git

Git is an essential version control tool for anyone who writes their own code or scripts. This blog post will give you a simple introduction to the beginner fundamentals of Git.

matlab

Creating a MATLAB Machine

MATLAB is a programming and numeric computing platform used by millions of engineers and scientists to analyse data, develop algorithms, and create models. This blog post will show you how to create a MATLAB machine with RONIN.

s3

Connect R to Object Storage

There's so much research data out there and R is a popular way to mash it up, scrape it down, run statistics on it and make it beautiful. You can access research data available in object storage buckets directly from within R....

parallel

Parallelising Jobs with GNU Parallel

In the cloud, you can easily scale the size of your computing resources to fit your needs, meaning you have the ability to run many commands or scripts in parallel. This is where GNU parallel comes in handy!

alerts

Pipeline Alerts with Slack Webhooks

Keeping an eye on any analyses that are running in the cloud is crucial, but watching a terminal window all day is no fun! What if there was a way you could also be alerted whenever a pipeline errors or completes? Well, with a nifty tool like Slack's Incoming Webhooks, you can!

Getting Started

Running Commands in the Background with GNU Screen

Being able to run commands and scripts directly from the command-line is great; however, some commands or scripts may need to run for extended periods without interruption. GNU Screen provides a simple solution to ensure your analyses are never prematurely terminated again.

netdata

Easy and Extensive Resource Monitoring with Netdata

When running analyses in the cloud, it's essential that you can monitor your resource usage. Understanding your compute usage is crucial in ensuring your analyses are running as efficiently as possible and making the most of your valuable cloud dollars.

software

Installing and Managing Bioinformatics Software with Conda

One of the first hurdles when getting started with cloud computing is understanding how to best install and manage the software you wish to use for your analyses. Fortunately, this can be a breeze thanks to the package management system known as Conda.

server

Creating a Custom BLAST Server with SequenceServer

BLAST (Basic Local Alignment Search Tool) is a popular bioinformatics tool for finding regions of similarity between sequences. With RONIN and SequenceServer, you can set up your own custom BLAST server in just a few simple steps.

conda

Adding a Conda Environment to Jupyter Notebook

We will show you how easy it is to create a conda environment and adding it to your Jupyter notebook. If you haven't launched a Jupyter notebook on RONIN, you'll want to read the Accessing a Jupyter notebook with RONIN on how to do so before