Exploratory Analysis of Biological Data
Max Delbrück Center for Molecular Medicine
Online
Feb 16-19, 2021
9:00 - 13:00
Instructors: Monah Abou Alezz, Tobias Busch, Liz Ing-Simmons, Aleksander Jankowski
Helpers: Harithaa Anandakumar, Aleix Arnau Soler, Kerstin Haase
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: Feb 16-19, 2021. 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 Hanna.Singer@mdc-berlin.de or ajank@mimuw.edu.pl for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
Sponsors: This workshop is being sponsored by the HEIBRiDS and HIDA.
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.
Schedule
Day 1
| Before starting | Pre-workshop survey |
| 9:00 | Data Organization in Spreadsheets |
| 11:00 | OpenRefine for Data Cleaning |
| 13:00 | Wrap-up |
Day 2
| 9:00 | Introduction to R |
| 11:00 | Continuation of R: Starting with data |
| 13:00 | Wrap-up |
Day 3
| 9:00 | Continuation of R: Manipulating, analyzing and exporting data |
| 13:00 | Wrap-up |
Day 4
| 9:00 | Continuation of R: Data visualization |
| 13:00 | Wrap-up |
| End | Post-workshop survey |
Setup
To participate in a Data Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
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 a spreadsheet program, OpenRefine, R and RStudio
Please install a spreadsheet program (such as LibreOffice or Microsoft Excel), OpenRefine, and a recent version of R and RStudio. The setup instructions can be found at the workshop overview site. If you encounter any problems, you can get help during the troubleshooting session on the day before the workshop. Note that we will mostly follow the curriculum of the Data Carpentry Ecology workshops (with R). There is no need to install SQLite Browser.
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:
- Two monitors: If you have two monitors, plan to have the tool you are learing up on one monitor and the video conferencing software on the other.
- Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
- Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.