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University of Oslo

Mar 15-16, 2016

9:00 am - 4:30 pm

Instructors: Tracy Teal, Carrie Andrew, Lex Nederbragt

Helpers: Hanna Helgeland, Halfdan Rydbeck, Karin Lagesen, William Brynildsen

General Information

Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.

The focus of this workshop will be on working with genomics data and data management and analysis for genomics research. We will cover metadata organization in spreadsheets, data organization, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows, and R for data analysis and visualization. We will not be teaching any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline.

This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.

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 workshop is for any researcher who has data they want to analyze, and no prior computational experience is required.

Where: Niels Henrik Abels hus, Moltke Moes vei 35, Oslo. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (see below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail for more information.


(NOTE subject to change)

Day 1

09:00 Introduction
 Workshop overview, Introduction to the dataset, Examining data on SRA
10:30 Coffee
10:45Data organization and tidiness
11:15Using cloud computing for genomics
12:00 Lunch break
13:00 Introduction to the command line
14:30 Coffee
16:00 Wrap-up

Day 2

09:00 Data wrangling and processing
 Project setup, Quality control of NGS data, Automating a workflow
10:30 Coffee
12:00 Lunch break
13:00 R for data analysis and visualization
14:30 Coffee
16:00 Wrap-up

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


To participate in this Data Carpentry workshop, you will need access to some software. 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.

Please follow these Setup Instructions