Introduction to the Workshop

Overview

Teaching: 15 min
Exercises: 0 min

Questions

• What is The Carpentries?

• What will the workshop cover?

• What else do I need to know about the workshop?

Objectives

• Introduce The Carpentries.

• Go over logistics.

• Introduce the workshop goals.

What is The Carpentries?

The Carpentries is a global organization whose mission is to teach researchers, and others, the basics of coding so that you can use it in your own work. We believe everyone can learn to code, and that a lot of you will find it very useful for things such as data analysis and plotting.

Our workshops are targeted to absolute beginners, and we expect that you have zero coding experience coming in. That being said, you’re welcome to attend a workshop if you already have a coding background but want to learn more!

To provide an inclusive learning environment, we follow The Carpentries Code of Conduct. We expect that instructors, helpers, and learners abide by this code of conduct, including practicing the following behaviors:

• Use welcoming and inclusive language.
• Be respectful of different viewpoints and experiences.
• Gracefully accept constructive criticism.
• Focus on what is best for the community.
• Show courtesy and respect towards other community members.

You can report any violations to the Code of Conduct by filling out this form.

Introducing the instructors and helpers

Now that you know a little about The Carpentries as an organization, the instructors and helpers will introduce themselves and what they’ll be teaching/helping with.

The etherpad & introducing participants

Now it’s time for the participants to introduce themselves. Instead of verbally, the participants will use the etherpad to write out their introduction. We use the etherpad to take communal notes during the workshop. Feel free to add your own notes on there whenever you’d like. Go to the etherpad and write down your name, role, affiliation, and work/research area.

The “goal” of the workshop

Now that we all know each other, let’s learn a bit more about why we’re here. Our goal is to write a report to the United Nations on the relationship between GDP, life expectancy, and CO2 emissions. In other words, we are going to analyze how countries’ economic strength or weakness may be related to public health status and climate pollution, respectively.

To get to that point, we’ll need to learn how to manage data, make plots, and generate reports. The next section discusses in more detail exactly what we will cover.

What will the workshop cover?

This workshop will introduce you to some of the programs used everyday in computational workflows in diverse fields: microbiology, statistics, neuroscience, genetics, the social and behavioral sciences, such as psychology, economics, public health, and many others.

A workflow is a set of steps to read data, analyze it, and produce numerical and graphical results to support an assertion or hypothesis encapsulated into a set of computer files that can be run from scratch on the same data to obtain the same results. This is highly desirable in situations where the same work is done repeatedly – think of processing data from an annual survey, or results from a high-throughput sequencer on a new sample. It is also desirable for reproducibility, which enables you and other people to look at what you did and produce the same results later on. It is increasingly common for people to publish scientific articles along with the data and computer code that generated the results discussed within them.

The programs to be introduced are:

1. Python, JupyterLab: a general purpose program and a interface to it. We’ll use these tools to manage data and make pretty plots!
2. Git: a program to help you keep track of changes to your programs over time.
3. GitHub: a web application that makes sharing your programs and working on them with others much easier. It can also be used to generate a citable reference to your computer code.
4. The Unix shell (command line): A tool that is extremely useful for managing both data and program files and chaining together discrete steps in your workflow (automation).

We will not try to make you an expert or even proficient with any of them, but we hope to demonstrate the basics of controlling your code, automating your work, and creating reproducible programs. We also hope to provide you with some fundamentals that you can incorporate in your own work.

At the end, we provide links to resources you can use to learn about these topics in more depth than this workshop can provide.

Asking questions and getting help

One last note before we get into the workshop.

If you have general questions about a topic, please raise your hand (in person or virtually) to ask it. Virtually, you can also ask the question in the chat. The instructor will definitely be willing to answer!

For more specific nitty-gritty questions about issues you’re having individually, we use sticky notes (in person) or Zoom buttons (red x/green check) to indicate whether you are on track or need help. We’ll use these throughout the workshop to help us determine when you need help with a specific issue (a helper will come help), whether our pace is too fast, and whether you are finished with exercises. If you indicate that you need help because, for instance, you get an error in your code (e.g. red sticky/Zoom button), a helper will message you and (if you’re virtual) possibly go to a breakout room with you to help you figure things out. Feel free to also call helpers over through a hand wave or a message if we don’t see your sticky!

Other miscellaneous things

If you’re in person, we’ll tell you where the bathrooms are! If you’re virtual we hope you know. :) Let us know if there are any accommodations we can provide to help make your learning experience better!

Key Points

• We follow The Carpentries Code of Conduct.

• Our goal is to generate a shareable and reproducible report by the end of the workshop.

• This lesson content is targeted to absolute beginners with no coding experience.