Data Carpentry, Genomics

University of Oslo

March 23-24, 2020

9:00 am - 4:00 pm

Instructors: Lex Nederbragt, Tina Visnovska

Helpers: Sabry Razick, Mohamed Abdelhalim

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: Seminar room 3508 (day 1), 3627 (day 2), Kristine Bonnevies Hus, Blindernveien 31, 0851 Oslo. Get directions with OpenStreetMap or Google Maps.

When: March 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 committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email contact-us@swcarpentry.uio.no for more information.

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

Before starting Pre-workshop survey
Morning Project Organization and Management
Why and How to Log on Cloud
Introduction to the Command Line
AfternoonData Wrangling and Processing
Evening END

Day 2

MorningContinuation: Data Wrangling and Processing
AfternoonMore of Cloud Computing for Genomics
Post-workshop survey
Evening END

Syllabus

Project Organization and Management

Introduction to the Command Line

Data Wrangling and Processing for Genomics

Introduction to Cloud Computing for Genomics

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.

This lesson requires a working spreadsheet program. If you don’t have a spreadsheet program already, you can use LibreOffice. It’s a free, open source spreadsheet program. We also kindly ask Windows users to either install Git for Windows or PuTTY, look into Windows Install Instructions for more details.

Windows Install Instructions

Mac OS X Install Instructions

Linux Install Instructions