University Milano-Bicocca

Feb 14-15, 2019

9:00 - 16:30

Instructors: Monah Abou Alezz, Ana Costa Conrado

Helpers: Gianluca Della Vedova, Murray Patterson, Simone Ciccolella

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

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: U7 building, Via Bicocca degli Arcimboldi, 8, Milano. Get directions with OpenStreetMap or Google Maps.

When: Feb 14-15, 2019. 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). They are also required to abide by Data Carpentry's Code of Conduct.

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

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 gianluca.dellavedova@unimib.it for more information.


Surveys

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

Pre-workshop Survey

Post-workshop Survey

Elixir questionnaire


Schedule

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


Syllabus

Data Organization in Spreadsheets for Ecologists

  • Introduction
  • Formatting data tables in Spreadsheets
  • Formatting problems
  • Dates as data
  • Quality control
  • Exporting data
  • Reference...

Data Cleaning with OpenRefine for Ecologists

  • Introduction
  • Working with OpenRefine
  • Filtering and Sorting with OpenRefine
  • Examining Numbers in OpenRefine
  • Scripts from OpenRefine
  • Exporting and Saving Data from OpenRefine
  • Other Resources in OpenRefine
  • Reference...

Data Analysis and Visualization in Python for Ecologists

  • Short Introduction to Programming in Python
  • Starting With Data
  • Indexing, Slicing and Subsetting DataFrames in Python
  • Data Types and Formats
  • Combining DataFrames with Pandas
  • Data Workflows and Automation
  • Making Plots with plotnine
  • Data Ingest and Visualization - Matplotlib and Pandas
  • Assessing SQLite Databases Using Python and Pandas
  • Reference...

Data Management with SQL for Ecologists

  • Databases using SQL
  • Basic Queries
  • SQL Aggregation and aliases
  • Joins
  • Reference...

Setup

To participate in a Data 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.

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.

Windows

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.

macOS

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.

Linux

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. 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).

Windows

Video Tutorial
  1. Open https://www.anaconda.com/download/#windows with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.

macOS

Video Tutorial
  1. Open https://www.anaconda.com/download/#macos with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. Download the Python 3 installer 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.
  4. Type
    bash Anaconda3-
    and then press Tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
    cd Downloads
    Then, try again.
  5. Press Return. 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.

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons. We will use the DB Browser for SQLite program, which is available for all major platforms.

Windows

Windows releases can be downloaded from Data Carpentry Windows Installer . Note - If for some reason the standard Windows release doesn't work for you (eg it gives an error), try a nightly build. Nightly builds for Windows and OSX can be downloaded from Nightly builds. They often fix bugs reported after the last release.

macOS

OSX releases can be downloaded from Data Carpentry MacOS Installer. Or install via Homebrew Cask:

brew cask install db-browser-for-sqlite

Linux

For Arch Linux users, a package is provided through pacman. For Fedora users, run

sudo dnf install sqlitebrowser
. For Debian users, run
sudo apt-get update
, then install the package using
sudo apt-get install sqlitebrowser
. For Ubuntu users, run first
sudo add-apt-repository -y ppa:linuxgndu/sqlitebrowser
, then
sudo apt-get update
, then run
sudo apt-get install sqlitebrowser
.

OpenRefine

For this lesson you will need OpenRefine and a web browser. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.

Windows

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It will not run correctly in Internet Explorer.

Download software from http://openrefine.org/

Create a new directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".

Go to your newly created OpenRefine directory.

Launch OpenRefine by clicking openrefine.exe (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

Mac

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari.

Download software from http://openrefine.org/.

Create a new directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory by double-clicking it.

Go to your newly created OpenRefine directory.

Launch OpenRefine by dragging the icon into the Applications folder.

Use Ctrl-click/Open ... to launch it.

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

Linux

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.

Download software from http://openrefine.org/.

Make a directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory.

Go to your newly created OpenRefine directory.

Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

Spreadsheet

To interact with spreadsheets, we can use LibreOffice, Microsoft Excel, Gnumeric, OpenOffice.org, or other program. Commands may differ a bit between programs, but the general ideas for thinking about spreadsheets are the same. If you don’t have a spreadsheet program already, you can use LibreOffice. It’s a free, open source spreadsheet program.

Windows

Download the Installer:

Install LibreOffice by going to the installation page. The version for Windows should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.

Once the installer is downloaded, double click on it and LibreOffice should install.

Mac

Download the Installer:

Install LibreOffice by going to the installation page. The version for Mac should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.

Once the installer is downloaded, double click on it and LibreOffice should install.

Linux

Download the Installer:

Install LibreOffice by going to the installation page. The version for Linux should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.

Once the installer is downloaded, double click on it and LibreOffice should install.