Overview

Welcome to the CLIMB-BIG-DATA documentation!

These docs are designed to help you get the best out of the CLIMB-BIG-DATA infrastructure.

Bryn is the web interface for CLIMB-BIG-DATA, and is the primary way to access the infrastructure. From Bryn, you can manage your team, its resources, the S3 buckets and your notebooks. CLIMB Notebooks, on the other hand, are Jupyter notebooks fully integrated with CLIMB and its storage, with first-class support to Nextflow pipelines.

Getting started

Registration
How to register and access CLIMB-BIG-DATA.

Authentication
How to login to Bryn, and setup two-factor authentication.

Notebook Servers

Everything you need to understand, use and get the most out of Jupyter Notebook Servers.

Read this first!
An introduction to the what and why of notebook servers.

Quick start
How to launch, access and get started using a notebook server.

Using the terminal
How to use the terminal inside a notebook server, with an explanation of caveats.

Using the interface
Explore various features of the notebook server interface.

Using Jupyter notebooks
The basics of working with Jupyter notebooks within a notebook server.

Using RStudio
How to get started with RStudio within a notebook server.

Understanding storage
An explanation of the different storage options available and when to use what.

Installing software with Conda
How to install software using Conda, in the context of a containerized environment.

Using Nextflow
How to use Nextflow with CLIMB-BIG-DATA.

Using Visual Studio Code
How to connect to your CLIMB Notebook and work from Visual Studio Code.

403 Forbidden Error
An explanation of how to resolve login error 403 when accessing notebooks.

Walkthroughs

Metagenomics walkthrough
A simple walk-through of some CLIMB-BIG-DATA functionality.

Genome assembly
Assembling a genome from short reads using SPAdes.

Custom Nextflow workflows
A guide on writing custom nextflow workflows.

QIIME 2
How to install QIIME 2 on a notebook server and basic usage.

nf-core pipelines
How to run some of the nf-core pipelines on CLIMB notebooks.