General Information

This workshop is hosted by the SIB Swiss Institute of Bioinformatics and the Institute of Molecular Life Sciences at the University of Zurich (UZH).

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.

We will cover Introduction to R; Data organization in spreadsheets, Introduction to R; Data analysis in R, Data visualization in R and Introduction to command line; additional topics. 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 with little to no R experience.

Where: Winterthurerstrasse 190 (Irchel campus), Room Y34-J-01. Get directions with OpenStreetMap or Google Maps.

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 mark.robinson@imls.uzh.ch for more information.

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Preliminary Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

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

Etherpad: https://public.etherpad-mozilla.org/p/2016-07-18-zurich.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code. Please keep the discussion and chat professional, and abide by Data Carpentry's Code of Conduct.

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Lesson content

Course materials will be based on the Data Carpentry Ecology Workshop and Genomics Workshop lessons, available on the Data Carpentry website.

• Introduction to R; Data analysis in R: These lessons will be based on the R-ecology: Data Analysis and Visualization in R and R-genomics: Data analysis in R lessons. You will need to download the following data files: combined.csv (for the R-ecology lesson) and Ecoli_metadata.csv (for the R-genomics lesson). Links to these files are also available in the lesson materials.

• Data organization in spreadsheets: This session will show you best practices for organizing experiment meta-data in spreadsheets. The materials will be based on the Data Carpentry Spreadsheets for Ecology lesson. Please download the following spreadsheet file for this lesson: survey_data_spreadsheet_messy.xls.

• Data visualization in R: This session will introduce plotting in R using the ggplot2 framework. Lesson materials are available here: https://github.com/jennybc/ggplot2-tutorial.

• Introduction to the command line: This session will be based on the Software Carpentry "Unix Shell" lesson (all Software Carpentry lessons are also available here). You will need a working Terminal application for the exercises. On Mac and Linux systems, this is installed by default (for Mac users: search for "Terminal" in Spotlight Search, or look for Terminal.app under Utilities in Applications). Windows users should install Git Bash. If you are using a Windows laptop, please download, install, and try to open the application before Tuesday afternoon. Please also download the following data file: shell-novice-data.zip.

Setup

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.