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Data Carpentry Genomics Workshop

University of Amsterdam

13 - 14 December 2017

9:00 - 16.30

Instructors: Dennis Schmitz, Sam Nooij, Marc Galland, Anita Schürch

Helpers: Zsofia Koma, Like Fokkens

General Information

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. The focus of this workshop is on working with genomics data and data management and analysis for genomics research.

We will cover project organization and management, introduction to the command line, data wrangling and processing and introduction to cloud computing for genomics. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Who: The course is aimed at graduate students and other researchers.

Where: Roeterseilandcampus, Amsterdam, room E0.15. Get directions with OpenStreetMap or Google Maps or 9292ov.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail for more information.

Preliminary Schedule


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

Pre-workshop Survey

Post-workshop Survey

13 December

09:00 Introduction to Data CarpentryAS
09:30 Introduction to the Data SetAS
09:45 Data managementAS
10:00 Coffee break
10:15 Data management continuedAS
11:00 Introducting the shellSN
11:45 Navigating Files and DirectoriesSN
12:30 Lunch break
13:00 Working with Files and DirectoriesSN
13:45 RedirectionSN
15:00 Coffee break
15:15 Writing scriptsSN
15:45 Project OrganizationSN
16:30 Wrap up day 1AS

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


To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Please follow these Setup Instructions.

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.