Exploratory Analysis of Biological Data: Data Carpentry

EMBL

Online

Jan 31-Feb 4, 2022

9:00-17:00

Instructors: Renato Alves, Gaurav Diwan, Florian Huber, Ece Kartal, Supriya Khedkar, Fotis E. Psomopoulos, Hugo Tavares

Helpers: Lisanna Paladin, Christian Schudoma

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Jan 31-Feb 4, 2022. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email renato.alves@embl.de or lisanna.paladin@embl.de for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 0

Before the course Setup all required software

Day 1

09:00-10:00 (CET)
04:00-05:00 (EDT)
Onboarding
10:00-10:30 (CET)
05:00-05:30 (EDT)
Lightning talks (instructors)
10:30-10:45 (CET)
05:30-05:45 (EDT)
Coffee break
10:45-12:30 (CET)
05:45-07:30 (EDT)
Data Organization in Spreadsheets
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
OpenRefine for Data Cleaning
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-15:40 (CET)
10:00-10:40 (EDT)
Lightning talks (candidates)
15:40-15:50 (CET)
10:40-10:50 (EDT)
Coffee break
15:50-17:00 (CET)
10:50-12:00 (EDT)
Virtual Social Programme: Speed networking: 1-1

Day 2

10:00-11:00 (CET)
05:00-06:00 (EDT)
Introduction to R
11:00-11:10 (CET)
06:00-06:10 (EDT)
Coffee break
11:10-12:30 (CET)
06:10-07:30 (EDT)
Introduction to R (cont.)
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Introduction to R (cont.)
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-15:40 (CET)
10:00-10:40 (EDT)
Lightning talks (candidates)

Day 3

10:00-11:00 (CET)
05:00-06:00 (EDT)
Data analysis and visualization in R:
Data manipulation with dplyr
11:00-11:10 (CET)
06:00-06:10 (EDT)
Coffee break
11:10-12:30 (CET)
06:10-07:30 (EDT)
Data analysis and visualization in R (cont.):
Data manipulation with dplyr
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Data analysis and visualization in R (cont.):
Data visualisation with ggplot2
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-16:00 (CET)
10:00-11:00 (EDT)
Data analysis and visualization in R (cont.):
Data visualisation with ggplot2
16:00-16:10 (CET)
11:00-11:10 (EDT)
Coffee break
16:10-16:40 (CET)
11:10-11:40 (EDT)
Virtual Social Programme: To Be Confirmed

Day 4

10:00-11:00 (CET)
05:00-06:00 (EDT)
Data analysis and visualization in R (cont.):
Data visualisation with ggplot2
11:00-11:10 (CET)
06:00-06:10 (EDT)
Coffee break
11:10-12:30 (CET)
06:10-07:30 (EDT)
Data analysis and visualization in R (cont.):
Data visualisation with ggplot2
12:30-13:30 (CET)
07:30-08:30 (EDT)
Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Data analysis with applications to genomics
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-16:00 (CET)
10:00-11:00 (EDT)
Data analysis with applications to genomics (cont.)
16:00-16:10 (CET)
11:00-11:10 (EDT)
Coffee break
16:10-17:00 (CET)
11:10-12:00 (EDT)
Virtual Social Programme: Pub Quiz

Day 5

10:00-11:00 (CET)
05:00-06:00 (EDT)
Data analysis with applications to genomics (cont.)
11:00-11:10 (CET)
06:00-06:10 (EDT)
Coffee break
11:10-12:30 (CET)
06:10-07:30 (EDT)
Data analysis with applications to genomics (cont.)
12:30-13:30 (CET)
07:30-08:30 (EDT)
Group photo & Lunch break
13:30-14:50 (CET)
08:30-09:50 (EDT)
Data analysis with applications to genomics (cont.)
14:50-15:00 (CET)
09:50-10:00 (EDT)
Coffee break
15:00-16:00 (CET)
10:00-11:00 (EDT)
Q&A session
16:00-16:30 (CET)
11:00-11:30 (EDT)
Discussion & Wrap-Up
16:30 (CET)
11:30 (EDT)
End of course

Setup

To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

This workshop is designed to be run on your laptop. First, you will need to download the data we use in the workshop. Then, you need to install some software. After following the instructions on this page, you should have everything you need to participate fully in the workshop!

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

Data

You can download all of the data used in this workshop by clicking this download link. The file is 38.4 MB.

Clicking the download link will automatically download all of the files to your default download directory as a single compressed (.zip) file. To expand this file, double click the folder icon in your file navigator application (for Macs, this is the Finder application).

For a full description of the data used in this workshop see the data page.

Software

Software Install Manual Available for Description
Spreadsheet program Link Link Linux, MacOS, Windows Spreadsheet program for organizing tabular data.
OpenRefine Link Link Linux, MacOS, Windows Program for reproducibly cleaning data.
R See install instructions below.   Linux, MacOS, Windows Programming language for data analysis and visualisation.
RStudio Link Cheatsheet Linux, MacOS, Windows Integrated development environment for R.

Spreadsheet program

OpenRefine

R and RStudio

Windows

If you already have R and RStudio installed

If you don’t have R and RStudio installed

macOS

If you already have R and RStudio installed

If you don’t have R and RStudio installed

Linux

For everyone