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.

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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


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:

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