Getting started with Reproducible and Open Research

Feb 11-12, 2020

9:30 am - 5:00 pm

Instructors: Barbara Vreede, Johan Hidding

Helpers: Pablo Rodríguez-Sánchez, Mateusz Kuzak

General Information

Getting Started with Reproducible and Open Research workshop introduces the challenges in reproducibility and transparent, reproducible and open research principles. Transparency, open sharing, and reproducibility are core values of science, but not always part of daily practice. This workshop provides an overview of current status in reproducible analysis in order to provide transparency in research. The workshop covers the use of version controll, collboration, literate programming with Jupyter Notebooks and publishing the code in citable way. Going beyond simple listing and presentations, the workshop focuses on hands-on skill building.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Hoog Overborch Office Building (Hoog Catharijne) 3511 EP Utrecht Moreelsepark 48. Get directions with OpenStreetMap or Google Maps.

When: Feb 11-12, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. Please let us know if you have any accessibility requirements.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email training@esciencecenter.nl for more information.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Surveys

Please be sure to complete this surveys after the workshop.

Post-workshop Survey


Schedule

Day 1

09:30 Introductions
10:00 Introduction to Reproducibility Crisis
10:30 Transparent and Open Research Practice
11:00 Starting a reproducible software project
12:00 Lunch break
13:00 Opening up your project
15:00 Introduction to Jupyter Notebook
16:45 Wrap-up
17:00 END of day one.

Day 2

09:30 Exploring Data with Notebooks
11:45 Using Notebooks with version control
12:00 Lunch break
13:00 Collaboration on GitHub
14:30 Open research software in practice with Zenodo and MyBinder
16:15 Wrap-up
16:30 Borrel

Syllabus

Reproducible and Open Reasearch

  1. Introduction to reproducibility crisis.
  2. transparent and Open Research Practice
  3. Starting a Project.
    • Start Git Repository
    • Create Repository on Github
    • Publish Repository on GitHub
    • How to Choose a License and Why it Matters?
  4. Intorudction to Jupyter Notebooks
    • Create Narrative with Markdown
    • Exploring Data with Notebooks
    • Adding interactive elements to Notebooks
  5. Working Effectively with Notebooks & Git
    • NbDime
    • Review Nb
  6. Collaborating on GitHub
    • Why you Need a Code of Conduct and How to Implement One?
    • Collaboration Models
    • Issues & Pull Requests
  7. Publish your Analysis on Zenodo
    • Connect GitHub Repository with Zenodo
    • Get a Digital Object Identifier
    • Tell Others How to Cite Your Work
      • Add a DOI button
      • Add a BibTeX Snippet to your README
  8. Make your Analysis Reusable with MyBider
    • Add MyBinder Button
    • Describe your Dependencies
    • How to Get Data Into MyBinder?
  9. Evaluate How Reproducible is Your Analysis

Setup

To participate in a Reproducible and Open Research workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

Software Carpentry maintains 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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu select "Use the nano editor by default" and click on "Next".
    3. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
    5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure that "Use Windows' default console window" is selected and click on "Next".
    7. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Video Tutorial
  1. Open https://www.anaconda.com/distribution/#download-section with your web browser.
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
  1. Open https://www.anaconda.com/distribution/#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter. You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter to approve the default location for the files. Type yes and press Enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.