2020-21 (Winter) DataSHIELD beginners' workshops (including ATHLETE GA workshop)

In this area you will find all available materials for the Beginners' workshop taking place Wednesday 9th December 10:30-12:30 CET. If you would like to come but have not yet registered, please send an email over to datashield@newcastle.ac.uk .

Administration

Structure of the session:

Time (UK)/Europe

Duration (approx.)

Subject

(13:30 GMT)/ 14:30 CET

5

Introductions, what is DataSHIELD

14:35

15

Booting the VM, getting set up ready for analysis

14:50

15

Understanding the login script

15:05

15

Basic commands & summary statistics

15:20

15

Assign-type DataSHIELD functions

15:35

15

Graphs and visualisations in DataSHIELD

1550

15

Linear, Generalized Linear Modelling

16:05

5

How to log out, shut down VM

16:10

20

Open to questions

16:30

-

Finish

You should have received the zoom link by email.

The slides presented on the day are available in pptx file format.

Anyone viewing after the workshop has taken place, a youtube link is coming soon.

Workshop contents

Firstly, before the workshop you will have been directed (in the invitation email) to download a VM from this page: https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1696825345 , and virtualbox itself from their website.

Then, we will be importing, configuring and booting the downloaded virtual machine (what is a virtual machine? Please refer to the powerpoint slides provided, or the youtube recording, for a basic explanation).

Then we will be doing some live coding during the course of the workshop. You can write in your code live, or you can copy and paste the code provided in the:

Post-workshop homework!

I’m sure you’ll all be delighted to do some homework to understand DataSHIELD even better!

We have two challenges for you:

  • Challenge 1: the “CNSIM” dataset is not the only one stored on this virtual machine “server” that you have downloaded. There is also a COVID dataset.

    • Try using the exploratory, summary statistic, graphing and modelling functions you have learnt during the workshop to explore this data.

    • If you are struggling to customise the login script, or want some hints on how to perform some analyses, we wrote this vignette which was presented to the European R Users meetup (virtually) in Milan in June of 2020. There are code snippets found in here, such as if you want to copy and paste a working login script.

      • be aware that the connection script is different in the e-RUM COVID-19 demo! It connects to an IP address ending in .100:. The VM we have created for the beginners workshop ends in .150:. Be sure to make this correction else the login stage will fail.

  • Challenge 2: coming soon, please download this RStudio Script and then import it (instructions here) to the RStudio Server session, followed by using help functions and the wiki materials to correct the errors within the code!

We’d love to see some of your results! Tweet to us any fancy graphics you create using DataSHIELD- our handle is @DatashieldNews.

Come to future workshops!

This beginners' workshop is the first in a series of 6 over the 2020/21 winter period. If you missed Patricia Ryser-Welch’s intro to R, see youtube link coming soon, and please email datashield@newcastle.ac.uk to register interest in the upcoming workshops:

  • Resources in DataSHIELD

    • Given by: Juan R González and Yannick Marcon

    • Date and time: Friday 15 January, 10:30am - 12:30pm CET

  •  Introduction to DataSHIELD (beginners’ workshop during Athlete GA)

    • Given by: Demetris Avraam and Alex Westerberg

    • Date and time: Monday 25 January, 2.30 – 4.30pm CET

  • Resources in DataSHIELD (during Athlete GA)

    • Given by: Juan R González and Yannick Marcon

    • Date and time: Tuesday 26 January, 2.30 – 4.30pm CET

    • (‘Highly recommended’ for ATHLETE project members who want to follow the omics workshop the next day)  

  • Omics analysis in DataSHIELD (during Athlete GA)

    • Given by: Juan R González

    • Date and time: Wednesday 27 January, 14:30-16:30 (CET)