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A Data Carpentry Workshop

Florida State University

June 29-30, 2017

9:00 am - 4:30 pm

Instructors: Deborah Paul (FSU), Matthew Collins (UF), Sergio Marconi (UF), Henry Senyondo (UF)

Helpers: Plato Smith, Micah Vandegrift, Renaine Julian, Emily Darrow

General Information

This Data Carpentry workshop is the first ever to be offered at Florida State University. We hope to bring Data Carpentry and Software Carpentry to FSU on a regular basis in the near future. The workshop is targeted to researchers and graduate students in the Biology, Psychology, and iSchool communities who want to learn skills and tools to analyze and manage their data more effectively. No prior computational experience is required.

Space is limited to 20 attendees. So, once the link is live, don't wait!

Lunch is included in the fee.

We will cover Data organization in spreadsheets and OpenRefine, SQL for data management, Introduction to R and Data analysis and visualization in R. 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 current researchers.

Where: Will be held in the R & D Commons in Strozier Library, accessible via Scholars Commons. There will be signage. 116 Honors Way Tallahassee, FL 32306. 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 rsmart@fsu.edu for more information.

Background for Data Carpentry:

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Our mission is to provide researchers high-quality, domain-specific training covering the full lifecycle of data-driven research. Data Carpentry is a sibling organization of Software Carpentry. Where Software Carpentry teaches best practices in software development, our focus is on the introductory computational skills needed for data management and analysis in all domains of research. Our lessons are domain specific, rom life and physical sciences to social science and build on the existing knowledge of learners to enable them to quickly apply skills learned to their own research. Our initial target audience is learners who have little to no prior computational experience. We create a friendly environment for learning to empower researchers and enable data driven discovery.


Preliminary Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Day 1

08:15 check-in, setup
08:45 Welcome and introductions
09:00 Data Organization in Spreadsheets
10:30 Break
11:00 Open Refine
12:00 Lunch
13:30 Introduction to R
14:30 Break
15:00 Introduction to dplyr
16:30 End

Day 2

09:00 Data management with SQL
10:30 Break
11:00 Data management with SQL (cont'd)
12:00 Lunch
13:30 Data visualization and Databases in R
14:30 Break
15:00 Data visualization and Databases in R
16:30 End

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) and try opening software to make sure it works before the start of your workshop. If you run into any problems, please feel free to email the instructor or arrive early to your workshop on the first day. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Requirements: Data Carpentry's teaching is hands-on, so participants are encouraged to bring in and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. (We provide these instructions and help on setting up the required software well in advance for this purpose). There are no pre-requisites, and we will assume no prior knowledge about the tools.

Contact: Please email rsmart@fsu.edu for questions and information not covered here.

This workshop will be using the software outlined in the install instructions below. Please see the section for your operating system for those directions.

Windows

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program
    For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Windows should automatically be selected. Click on the button below "Main Installer" Download Version x.y.z. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.

  2. OpenRefine
    OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download OpenRefine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.
    • Go to the OpenRefine download page
    • Click on Windows kit to download the install file
    • To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead)
    • OpenRefine will then open in your web browser.
    • If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.

  3. R
    In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
    • Download R from here
    • Run the .exe file that was just downloaded
    • Go to the RStudio Download page
    • Under Installers select RStudio 0.98.1103 - Windows XP/Vista/7/8
    • Double click the file to install it
    • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

  4. SQLite
    For this workshop we're going to use the Firefox SQLite Plugin. It works through the web browser Firefox.
    • If you don't already have Firefox installed install Firefox
    • Start Firefox
    • Go to the plugin homepage.
    • Click the "Add Now" button.
    • Click "Install Now" on the dialog that appears after the download completes.
    • Restart Firefox when prompted.
    • Select "SQLite Manager" from the "Tools" menu and it will open within Firefox

Mac

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program
    For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Mac should automatically be selected. Click on the button below "Main Installer" Download Version x.y.z. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.

  2. OpenRefine
    OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download OpenRefine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.
    • Go to the OpenRefine download page
    • Click on Mac kit to download the install file
    • Open the downloaded .dmg file
    • Drag the icon in to the Applications folder
    • Double click on the icon and OpenRefine will then open in your web browser.
    • If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.

  3. R
    In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
    • Go to CRAN and click on Download R for (Mac) OS X
    • Select the .pkg file for the version of OS X that you have and the file will download.
    • Double click on the file that was downloaded and R will install
    • Go to the RStudio Download page
    • Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) to download it.
    • Once it's downloaded, double click the file to install it
    • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

  4. SQLite
    For this workshop we're going to use the Firefox SQLite Plugin. It works through the web browser Firefox.
    • If you don't already have Firefox installed install Firefox
    • Start Firefox
    • Go to the plugin homepage.
    • Click the "Add to Firefox" button.
    • Click "Install Now" on the dialog that appears after the download completes.
    • Restart Firefox when prompted.
    • Select "SQLite Manager" from the "Tools" menu and it will open within Firefox

Linux

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program
    For this workshop you will need a spreadsheet program. LibreOffice comes preinstalled with several Linux distributions. If you don't already have it, use your package manager to install it: (e.g., sudo apt-get install libreoffice for Ubuntu and other Debian-based distributions).

  2. OpenRefine
    OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download Google Refine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.
    • Go to the OpenRefine download page
    • Click on Linux kit to download the install file
    • Download and extract
    • Type ./refine in your terminal and Google Refine will then open in your web browser.
    • If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.

  3. R
    In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
    • Follow the instructions for your distribution from CRAN. For most distributions, you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora run sudo yum install R) but make sure that you have at least R 3.2.2 (as pre-packaged versions might be out of date).
    • To install RStudio, go to the RStudio Download page
    • Under Installers select the version for your distribution.
    • Once it's downloaded, double click the file to install it (or sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
    • Once it's installed, open RStudio to make sure it works and you don't get any error messages.

  4. SQLite
    For this workshop we're going to use the Firefox SQLite Plugin. It works through the web browser Firefox.
    • If you don't already have Firefox installed install Firefox
    • Start Firefox
    • Go to the plugin homepage.
    • Click the "Add Now" button.
    • Click "Install Now" on the dialog that appears after the download completes.
    • Restart Firefox when prompted.
    • Select "SQLite Manager" from the "Tools" menu and it will open within Firefox

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.