Table of Contents

General Information

A SESYNC Computational Synthesis Institute provides science teams from the socio-environmental synthesis community with hands-on training in open source tools for collaborative coding and data management, analysis, visualization, and product dissemination. The goals of the workshop are to learn new concepts, skills and approaches for data-driven research, advance work on team projects, and become familiar with a variety of open-source tools. The agenda provides an overview of topics we will address through classroom-style instruction that integrates live-coding and trainee challenge exercises. In addition, the agenda allots time for science teams to work on a mini-project with a designated SESYNC coach.

SESYNC Instructors:
Ian Carroll, Data Scientist
Mary Shelley, Associate Director of Synthesis
Philippe Marchand, Data Scientist
Kelly Hondula, Quantitative Researcher
Kate Weiss, Computational Research Assistant

Sep 14-16, 2016

1 Park Place Suite 300, Annapolis, MD 21401

Get directions with OpenStreetMap or Google Maps.

Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). The software noted below must be installed prior to starting the workshop. Contact with installation questions at least two business days before the event.

Please email with any questions or for information not covered here.


Wednesday 9:00 am Welcome to SESYNC
  9:15 Collaborative & Reproducible Workflows
  10:30 Break
  10:45 Team Practice #1
  12:00 Team Introductions
  12:30 pm Lunch
  1:30 Bas(e)ic R
  3:30 Break
  3:45 Database Principles and Use
Thursday 9:00 am Manipulating Tabular Data
  10:30 Break
  10:45 Visualizations the ggplot Way
  12:30 pm Lunch
  1:30 Introduction to Shiny Apps
  3:30 Break
  3:45 Team Practice #2
Friday 9:00 am Visualizations with Maps
  10:30 Break
  10:45 pm Qualitative Data
  12:00 Lunch … followed by
  1:30 Leaflet cont’d
    Team Practice #3
  2:30 pm Scrimmage (a.k.a. Team Presentations)

Pre-Arrival Instructions

To participate, you will need working copies of the software described below. Please make sure to install and/or download everything before the start of the short course. Contact the instructor before the course begins if you run into any trouble.


If you do not already have a GitHub account, please create one at Note that students and educators with a .edu e-mail address are eligible for some free stuff through GitHub’s Student Developer Pack.


The table below lists software we will use in this short course. Please use the default installation options, and install in order moving down the table. If you have previously installed this software, please upgrade to the latest version available in your operating system.

For Windows users, an installer for each item is available at the given download site. Mac users may also find an installer at the download site, but are encouraged to use the Homebrew software manager via the Terminal application. Most packages in the list below can be installed on a Mac with Homebrew by typing brew install %package% in the Terminal and pressing return, but packages with an * require brew cask install %package%. Ubuntu users may install from the shell with sudo apt-get install %package%, and other Linux users are on their own.

Software Download Site Homebrew Package(s) Aptitude Package(s)
git git git
R Base r r-base
RStudio rstudio* use download site

R Packages

The following R packages (i.e. add-on pieces of software) need to be installed. Open RStudio and, for each package listed below, type install.packages("%package%") in the Console (where you see a >) and press return. To install the tidyr package, for example, you type install.packages("tidyr"), and then follow the instructions given. If the Console prints a “Warning” that the installation “had non-zero exit status”, then the installation has failed.

  • tidyr
  • ggplot2
  • RSQLite
  • rgdal
  • rgeos
  • shiny
  • leaflet

Additional Software for Mac Users Only

The steps here may not be necessary, depending on your system. Only follow these steps if the R Package installations above failed for rgdal or rgeos. First, attempt to install those two packages with install.packages("%package%", type = "mac.binary.mavericks"). If that also fails, install the software below, then re-attempt the package installations with install.packages("%package%", type = "source").

Software Download Site Homebrew Package(s) Aptitude Package(s)
Homebrew for Mac users only:    
GDAL separate install not required on Windows gdal geos gdal-bin

Acknowledgments & Support

Portions of the instructional materials are adopted from Data Carpentry and Software Carpentry. The structure of the curriculum as well as the teaching style are informed by Software Carpentry.