Software Carpentry

• Registration
• Useful links
• General Information
• Schedule
• Syllabus
• Setup
• Acknowledgments

Registration

Registration is required and is limited to those affiliated with the Biological Sciences Division. Please register at 2017-09-23-chicago.eventbrite.com.

Useful links

• Please complete both of the post-workshop surveys. Your responses are critical for us to improve our teaching and to request funding for future workshops.
  • UChicago post-workshop survey
  • Software Carpentry post-workshop survey
• The UChicago pre-workshop survey is closed.
• The Software Carpentry pre-workshop survey is closed.
• Click here to sign up for the Github Student Developer Pack
• Github repo for the workshop

General Information

This interactive workshop will cover the basics of R, the Unix shell, and version control. R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis.

Coffee and lunch will be provided.

When: 8:00 am - 4:30 pm, Saturday-Sunday, Sep 23-34, 2017

Who: The course is limited to graduate students and other researchers in the Biological Sciences Division at the University of Chicago.

Prerequisites: There are no prerequisites. Attendees are expected to have no (or little) previous programming experience.

Where: Stuart 105, 5835 South Greenwood Avenue Chicago, IL 60637. 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).

Instructors: Arjun Biddanda, Nicholas Knoblauch

Helpers: Peter Carbonetto, Gao Wang, John Blischak, Sahar Mozaffari, Briana Mittleman, Yeonwoo Park, Maryn Carlson

Faculty advisor: Allan Drummond

Administrator: Candice Lewis

Funding: This workshop was made possible through the generous sponsorship of the Office of Graduate and Postdoctoral Affairs, the Department of Human Genetics, and the Department of Biochemistry and Molecular Biology.

Contact: Please mail abiddanda@uchicago.edu or nwknoblauch@uchicago.edu for more information.

Schedule

Sep 23

Sep 24

Syllabus

Introduction to RStudio

We will introduce the basic functionalities of RStudio, a useful integrated development environment (IDE) for writing R code.

Analyze data with R

We will demonstrate how to import a data set, calculate descriptive statistics, and create some basic plots.

Organize your code with R functions

We can extend R by converting common routines into functions. This allows us to execute the same commands on many different input arguments. Best of all, writing functions makes it easier to read and maintain your code. In this lesson, we convert the analysis we performed in the previous lesson into a function that can then be applied to any similar input data set.

Automate tasks with loops

One of the main advantages of writing code over using spreadsheet software is that it is easier to repeat the analysis on new data sets. In this lesson, we use loops to automatically apply the function we wrote in the previous lesson to process multiple data sets.

Make choices with if/else statements

Automated data analysis pipelines can be made even more powerful by allowing the code to make decisions based on the input parameters and data. In this lesson, we modify our code from the previous lessons so that it will save the analysis plots to a specific file only if we provide a filename as input. This allows us to choose whether to immediately view the results in the RStudio window or save the results to a file.

Introduction to the Unix shell

We will introduce the Unix shell and motivate it's usefulness. Specifically, we will quickly introduce how to manage files with the Unix shell and how to navigate the file system.

Tracking code development

We will cover how to track code development using the version control software Git. This facilitates both experimenting with new ideas and the ability to reproduce past results with a specific version of the code. Furthermore, we will teach how to share their code online and collaborate using the website GitHub.

Setup

To participate in a Software 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.

Acknowledgments

This workshop was made possible by the instructor training and lesson development created by the Software Carpentry team and of course our generous sponsors (OGPA, HG, BMB).

This page was generated by GitHub Pages using the Architect theme by Jason Long.