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Workshop 1 - Describing and storing data in the 12 LABOURS DigitalTWINS platform

Introduction

This 2 hour workshop aims to allow researchers in the 12 LABOURS project to become familiar with the 12 LABOURS DigitalTWINS platform. This includes understanding how to connect to the platform, store their data within a standardised dataset structure, and upload/download it to/from the platform.

This workshop has been organised by the CTT group and the 12L portal development team, and the demonstrators are Chinchien Lin, Linkun Gao, Jiali Xu, and Thiranja Prasad Babarenda Gamage.

Learning outcomes

  • How to connect to the 12 LABOURS DigitalTWINS platform via the web portal and programmatically via its python API.
  • How to create datasets in the SPARC Dataset Structure (SDS) programmatically using a python tool (sparc-me)
  • How to upload and download your data to the 12 LABOURS DigitalTWINS platform via its python API

Workshop programme

  • 15 mins - Brief overview of the workshop and tutorials
  • 1 hour 45 mins - Attendees will run through tutorials themselves and then adapt code in tutorials to the data they use in their EP projects.

Prerequisites

  • Familiarity with python >=3.9

Before the workshop

  • Pre-workshop reading materials describing the SPARC Dataset structure.
  • Mount your eResearch drive (see instructions in the Workshop FAQ section at the bottom of this documentation
  • Add your data (e.g. from a few subjects) to the eResearch drive that has been created for your EP.
    • Please upload your data to a folder called sandbox/upi (replace upi with your university upi) in the root directory of your eResearch drive.

On the day of the workshop

We will be using the computers on Level 5 at ABI. These machines do not have python installed. Please come to level 5 before midday on Mon 20th Sept and login to one of the machines. We will then install python 3.9 and the Pycharm IDE on the machine so you will be ready for the workshop.

Next steps

Guided Jupyter Notebook tutorials have been developed describing how to use the DigitalTWINS platform. This workshop involves running through these tutorials.

Tutorial Description
1 Getting started with the 12 LABOURS DigitalTWINS platform.
2 Finding and downloading datasets from the DigitalTWINS platform using the digitaltwins-api.
3 Loading and exploring SDS datasets locally using sparc-me.
4 Creating SDS datasets locally using sparc-me.
5 Uploading datasets to the DigitalTWINS platform using the digitaltwins-api.


Feedback

Once you have completed this workshop, please complete this survey, which will allow us to improve this and future workshops.