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A Software/Data Carpentry Workshop

McMaster University, Hamilton Hall room 104

June 7 - 8, 2018

9:00 am - 5:00 pm

Instructors: Jake Szamosi, Shahrokh Shekarriz, Laura Rossi

Helpers: Patrick Schenck, Daphnée Lamarche, Hiba Shareefdeen

Registration

Registration for this workshop must be done in advance and costs $20. You can sign up on Eventbrite. We encourage PIs to cover the cost of the workshop for their trainees out of grants wherever possible. If payment by credit card or p-card is not possible, please email us to arrange to pay with a grant number.

General Information

Software 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 Unix shell and Data organization in spreadsheets, Introduction to R, Data management in R and Git and GitHub. 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, post-docs, and PIs who want to improve their data management and analysis skills. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room TBD, McMaster University, Hamilton Hall room 104, 1280 Main St. W, Hamiton, ON. 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 The Carpentries' Code of Conduct.

We expect all participants to come with all needed software installed. If you have trouble, or would like help with, installing any of the software, please attend our software installation party, Monday, June 4, 3:30 - 5:00 in LSB 216.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.

Materials will be provided in advance of the workshop; please notify the organizers in advance if you need large-print handouts.

Contact: Please mail Jake at szamosjc@mcmaster.ca for more information.


Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Thursday, June 7

Morning Unix shell and Data organization in spreadsheets
Afternoon Introduction to R

Friday, June 8

Morning Data management in R
Afternoon Git and GitHub

Etherpad: http://pad.software-carpentry.org/2018-06-17-McMaster.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference

Data Organization and Spreadsheets

  • Formatting data and tables
  • Common formatting problems
  • Clean directory structure and organization
  • Reference

Programming in R

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Reference

Setup

To participate in a Data Carpentry workshop, you will need working copies of the described software and data. Please make sure to install everything before the start of the 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 download the data files here and unzip them on your computer. The directory that creates is a good place to work during the workshop. To install all required software, 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.