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Arcadia Users' Group

Arcadia Users’ Group (AUG) is a forum for Arcadians to bring their biological data and discuss high level conceptual problems (what is genome assembly?), low level coding problems (what does this error message even mean?!), and everything in between. Like the start codon, AUG aims to get Arcadians started on projects and help them get re-started after they run into problems. AUG is a weekly hybrid meetup. On training weeks, we offer 20 minute - 1 hour training or code review sessions. See the tables below for upcoming and past lesson materials. On non-training weeks, we host a 2 hour hybrid remote/in-person office-hours style working group to ask and answer questions and to co-work on data-relevant problems.

What is a Users’ group? A users’ group is a club focused on a computer-related technology. Unlike python users’ groups (PUGs) and R users’ groups (RUGs), AUG is language- and technology-agnostic. We focus on anything Arcadians need to be successful with their data-related biology.

This is the landing page for tutorials delivered during AUG sessions.

Upcoming trainings

The schedule is subject to change.

Date Tutorial Description
Mar 5, 2024 GitHub Templates: new repos with set structures This lesson provides an overview of how to create a new repository from a GitHub template. Using a Python analysis repository as an example, it walks through the function of each file in the template and the benefits that come from using templates.
Mar 19, 2024 Office hours
Apr 16, 2024 Intro to Machine Learning 1
Apr 30, 2024 Intro to Machine Learning 2
May 14, 2024 Office hours
May 28, 2024 Code Organization (when do you make a class? when do you split something up?)
Jun 11, 2024 Office hours
Jun 25, 2024 Principles of Data Visualization
Jul 9, 2024 Data Visualization for Pubs
Jul 23, 2024 Interactive Data Visualization
Aug 6, 2024 Office hours
Aug 20, 2024 Numpy: matrices, arrays, and math
Sep 3, 2024 Pandas: data frames in python
Sep 17, 2024 Applied Machine Learning 1: scikit learn or similar
Oct 1, 2024 Applied Machine Learning 2: pytorch or similar
Oct 15, 2024 Office hours
Oct 29, 2024 Chat GPT to empower biologists to code
Nov 12, 2024 TBD
Dec 10, 2024 TBD

Previous trainings

Note recordings are only available to people with email addresses.

Date Tutorial Description Link to recording
Feb 6, 2024 Code formatting, linting, and style guides This lesson dives into the essentials of Python code formatting, linting, and style guides. It emphasizes why consistent code style is crucial for readability and maintenance and introduces tools like black for auto-formatting and ruff for linting. The session also explains Python-specific conventions, such as PEP8 and the Google Python Style Guide, with practical examples to illustrate how these practices improve code quality. recording
Nov 28, 2023 Building test data sets Tests should run quickly, ensure that code produces the correct output, and ensure that the output makes sense. Designing test data sets that fulfill all of these criteria is an art. This lesson will cover some guiding principles and strategies for making new test data sets. recording
Nov 14, 2023 Testing concepts & terminology Unit tests & assertions & continuous integration, oh my! This introduction to testing will cover the concepts and goals of unit testing and provide a hands-on primer for writing & running tests. recording 1 recording 2
Oct 31, 2023 Intro to R & tidyverse This lesson will provide a quick introduction to R and its objects and then cover how to manipulate, analyze, and export data using tidyverse packages. This lesson is derived from the Data Carpentry Data Analysis and Visualisation in R for Ecologists lessons. recording
Oct 17, 2023 Intro to R & data visualization with ggplot2 This lesson will cover how to visualize data using the ggplot2 package while building a mental model for how R works. This lesson is derived from the Data Carpentry Data Analysis and Visualisation in R for Ecologists lessons. recording
Jul 11, 2023 Intro to 3D Printing Introduces learners to the basics of 3D printing, specifically focusing on designing stamps to create microchambers for cells using Autodesk Fusion 360 software and utilizing the Form2 SLA printer from Formlabs for actual 3D printing. recording
Apr 11, 2023 Automation and programming Opentrons This lesson provides an introduction to Opentrons liquid handling robot via the Python API and other programs. recording
Mar 28, 2023 Introduction to Python part 3 This is the third and final lesson in the intro to Python series. It covers how to interact with packages, how to read and write files,plotting with matplotlib, and dataframe operations with pandas. recording
Mar 14, 2023 Introduction to Python part 2 This is the second lesson in an intro to Python series. It covers data structures (lists, dictionaries), loops, conditionals, and methods. Scroll to the bottom of the lesson for another practice problem set. recording 1 recording 2
Feb 28, 2023 Introduction to Python part 1 This is the first lesson in an intro to Python series. It covers variables, data types, functions, and running scripts from the command line. Scroll to the bottom of the lesson for a practice problem set. recording
Feb 14, 2023 Code review during the pub process We'll provide an overview of what to expect from the code review component of the pub process, including common mistakes and a refresher to help the process go more smoothly.
Dec 5, 2022 Keyboard shortcuts for Terminal This lesson covers keyboard shortcuts that can be used in Terminal to quickly navigate around commands that you write. recording
Oct 31, 2022 Turning a GitHub repo into a collection of interactive notebooks with Binder This week we’ll introduce Binder, an executable environment that makes your code immediately reproducible by anyone, anywhere. recording
Oct 24, 2022 Introduction to Jupyter notebooks Jupyter notebooks are web-based interactive computing environments that combine code, equations, narrative text, and visualizations in a single document. This lesson introduces jupyter notebooks and how to install and run them locally. recording
Oct 17, 2022 Conda for software installation & environment management In bioinformatics, we often use mulitiple software tools to answer a research question. In this lesson, we will learn how to use conda to install software. Conda is a software installation and management system that helps us conduct reproducible analyses while avoiding software conflicts. Then, we'll learn how to organize our software installations into environments, and how to use environments to ensure our analyses are repeatable. recording
Oct 11, 2022 Increasing developer productivity In the last couple of weeks, we learned many shell and git commands. This week, we'll take a step back to learn about using an integrated development environment (IDE) to develop our scripts/pipelines and customizing our terminals with shortcuts and git visualizations. recording
Oct 3, 2022 Code review using GitHub As the last piece of our Git and GitHub workshop we'll go over the key element of code review and how to execute a review on GitHub.
Sept 26, 2022 Undoing changes in a Git repository This lesson is a continuation of our Git and GitHub workshop. We will cover how to undo changes in a Git repository using git restore, git revert, or git checkout. recording
Sept 19, 2022 How to use S3 with the command line interface (CLI) Arcadia uses Amazon Web Services S3 to store some files remotely. This lesson introduces 2 tools (the official AWS CLI and s5cmd) that enable command line access to S3 recording
Sept 12, 2022 Introduction to the command line part 2 This next lesson on the command line covers how to create and (re)move directories and files (mkdir, rmdir, cp, mv, rm) and how to investigate the contents of a file thoroughly (less, wc, grep) recording
Sept 6, 2022 Introduction to the command line part 1 The command line is an essential interface to control remote computers or to execute automated analysis. This lesson introduces the concept of the command line, shows how to look at files (ls, head, tail), and how to navigate around a computer (cd, pwd) recording
Aug 29, 2022 Project organization and file & resource management It’s not uncommon to generate thousands of files during a bioinformatics analysis. In this lesson, we will cover project organization strategies for keeping track of the files we generate and how we generate them. Be kind to future you: a little organization effort now can save hours of headache later! recording
Aug 22, 2022 Introduction to markdown syntax Markdown is a lightweight markup language (think HTML or LaTeX but…lighter) that’s used by lots of websites and software (Slack and Notion and GitHub, oh my!). This quick introduction will show you how to easily format plain text that is readable and that renders into beautifully formatted documents. recording