University of Zurich
July 1-2, 2019
9:00 - 17:00
Instructors: Helen Lindsay, Gosia Nowicka, Stephan Schmeing
Helpers:
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ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 |
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".
This workshop is hosted by the SIB Swiss Institute of Bioinformatics and the Institute of Molecular Life Sciences at the University of Zurich (UZH). It is sponsored by ELIXIR-EXCELERATE.
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: room Y55 L-06/08, Winterthurerstrasse 190, Irchel Campus, Univ. Zurich. Get directions with OpenStreetMap or Google Maps. Use the following map to locate the building and room Univ. Zurich - Irchel Campus Map
When: July 1-2, 2019. 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).
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.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
- The room is wheelchair / scooter accessible.
- Accessible restrooms are available.
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 mark.robinson@imls.uzh.ch or patricia.palagi@sib.swiss for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
Post-workshop Survey of ELIXIR
Schedule
Day 1
| Before starting 08:30-09:00 | Helpdesk |
| Morning | Project Organization and Management |
| Introduction to the Command Line | |
| Afternoon | Introduction to the Command Line cont. |
| Data Wrangling and Processing |
Day 2
| Morning | Data Analysis and Visualization in R |
| Afternoon | Data Analysis and Visualization in R cont. |
| Post-workshop survey |
Helpdesk
Helping in final setup and making sure participants have all the necessary software installed.
Break times
Start: 9:00
Morning break: 10:30 - 11:00
Lunch break: 12:30 - 13:30
Afternoon break: 15:00 - 15:30
Finish: 17:00
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Syllabus
Project Organization and Management
Introduction to the Command Line
Data Wrangling and Processing 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.
This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. With the exception of a spreadsheet program all of the software and data used in the workshop are hosted on an Amazon Machine Image (AMI).
Instances will be set up for you and your instructor will supply the ip_address and password that you need to login. You will need an SSH client to connect to the instances.
Please, make sure that you have the following:
- Spreadsheet program such as Excel, or free LibreOffice.
- SSH client. On a Mac or Linux machine, you can access it through a program called Terminal, which is already available on your computer. If you’re using Windows, you’ll need to download a separate program to access the cloud instance, such as PuTTY.
For details on how to install them, please, see section Required additional software.
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.