Genomics Sandbox

type access

  • Operating System:

  • Terminal:

  • Shell:

  • Editor:

  • Package Manager:

  • Programming Language:

type access

  • Operating System:

  • Terminal:

  • Shell:

  • Editor:

  • Package Manager:

  • Programming Language:

In this app you will find material for the Genomics sandbox of the Health Data Science sandbox. This contains courses you can learn from, datasets and tools you can work with for your own research/learning purposes. Each course item of this sandbox is based on JupyterLab. JupyterLab is a web-based integrated development environment for Jupyter notebooks, code, and data. Usually, each item includes a dedicated webpage with additional information, guides, and material.

Available material

Items are periodically added to this app and can be chosen from the menu. Each item can a course, a setup to work with specific software, a research example, and comes with all necessary packages already installed, notebooks with code and explanations, and a dedicated webpage with additional material (notes, slides, recordings, ...).

Courses

The available courses are:

Course Name

Description

Link

Programming Language

Introduction to NGS
Data Analysis

A one-week course to introduce NGS data, from data alignment to bioinformatics analysis

Webpage

Python, R, Bash

Introduction to
Population Genomics

A course introducing and applying bioinformatic tools to perform a whole population genomics analysis

Webpage

Python, R, Bash

Introduction to GWAS

An introductory course in Genome-Wide Association Studies

Webpage

R, Bash

Tools

The available tools are:

Tool Name

Description

Links

Programming language

Integrative Genomics Viewer

A High-performance, easy-to-use, interactive tool for the visual exploration of genomic data. It supports flexible integration of all the common types of genomic data and metadata, investigator-generated or publicly available.

Official Manual

Interactive User Interface

Choosing an Item

You can choose a course or a tool from the drop down menu accessible in the job submission page (red circle in the figure below).

drawing

Note

The App needs to download data and packages. Depending on the selected course/tool, this can take some time. See below how to reuse data and avoid long waiting times (you still need to download data the first time you run the app).

Available options

You can use data and notebooks running in a previous session of the app, otherwise, all the datasets the notebooks will be downloaded every time a new session is started.

To choose the data from previous sessions, click on Add folder (red circle in the figure below). Then, you need to select your latest session of the sandbox (inside the folder Jobs/Genomics Sandbox, as shown in the example below) and choose the folder you need. Accepted folders are Data and Notebooks (such as the two folders chosen in the figure below).

drawing

Download Course Data and Notebooks

Each course is open-source and the datasets are freely available. Here you have the link to all repositories to download the datasets.

Course Name

Data Repository

Introduction to NGS Data Analysis

Link

Introduction to Population Genomics

Link

Introduction to GWAS

Link

Download Generated Data

You can easily download the generated files by right-clicking the selected files in JupyterLab and choosing download (see figure below).

drawing