Genomics Sandbox

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 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 items

Items are periodically added to this app and can be chosen from the menu. Each item can be a course, a setup to work with specific software, a research example and comes with all necessary packages installed, eventual notebooks with computer 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

Copying folders from your session

If you want to get some of the material you have been working on using the app, you have two possibilities.

Download only your code

You can always download specific Jupyter notebooks from JupyterLab. Simply right-click on a notebook, and choose Download. Upload the notebooks again in a future session of the app to work on them again.

Important

All your outputs from the code are lost, so you must rerun your notebooks.

Download code, data and results

You can copy the whole folder containing code, results and data. The downloaded course material can be found into the folder Jobs/Genomics Sandbox/$JOB_ID under your personal user files, where $JOB_ID is the folder related to the session. To download all the material, you have to follow these steps while you are in JupyterLab:

  • Open a new terminal using File --> New --> Terminal

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  • Write the command

    $ bash $COURSE/Scripts/copyMaterial.sh

    You will be asked to confirm if you want to copy the data.

    Note

    check if that amount of data actually fits into your storage space on UCloud before accepting.

  • If you execute the copy, you receive a confirmation message with the folder where you can find the data.

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Additional options

Before submitting the app, you can choose a course and the amount of resources you need. Additionally, you can add folders so that they will be visible when using JupyterLab. Adding folders is useful if

  • you want to use a folder containing your own data and code, with which you want to perform analysis with the Genomics tools of a course/module

  • you want to continue working on the material from a previous session of the Genomics sandbox. In such a case, add the folder containing the material using the option Add folder.