September 2020 Genomics Workshop @TUDelft

Online

Sept 16-17 and 23-24, 2020

09:00 - 13:00

Instructors: Esther Plomp, Carlos Teijeiro Barjas, Santosh Ilamparuthi, Raul Ortiz Merino, Marcel van den Broek

Helpers: Mario Beck, Wijb Dekker

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 based at TU Delft or at the other 4TU universities in the Netherlands. 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: Sept 16-17 and 23-24, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop 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 E.Plomp@tudelft.nl , F.vanGiessen@tudelft.nl , Raul.Ortiz@tudelft.nl or marcel.vandenbroek@tudelft.nl 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 1 - September 16

Before Pre-workshop survey
09:00 Welcome and introduction
09:30 Project Organization and Management
10:30 Coffee
10:45 Introduction to Cloud Computing for Genomics
11:45 Coffee
12:00 Introduction to Cloud Computing for Genomics (Continued)
13:00 END

Day 2 - September 17

09:00 Introduction and instructions for the day
09:30 Introduction to the Command Line
10:30 Coffee
10:45 Introduction to the Command Line (Continued)
11:45 Coffee
12:00 Introduction to the Command Line (Continued)
13:00 END

Day 3 - September 23

09:00 Introduction and instructions for the day
09:30 Data Wrangling and Processing 1
10:30 Coffee
10:45 Data Wrangling and Processing 1 (Continued)
11:45 Coffee
12:00 Data Wrangling and Processing 1 (Continued)
13:00 END

Day 4 - September 24

09:00 Introduction and instructions for the day
09:30 Data Wrangling and Processing 2 (Continued)
10:30 Coffee
10:45 Data Wrangling and Processing 2 (Continued)
11:45 Coffee
12:00 Data Wrangling and Processing 2 (Continued)
12:55 Post-workshop Survey
13:00 END

Syllabus


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.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site

.