Onboarding

Welcome to the lab! I’m looking forward to working with you. As we approach your official start, there’s some onboarding that would be useful to get out of the way. Read through the info below - there’s a checklist of the various to-do tasks at the end of the page.

Administrative stuff

First, please fill out the Lab Member Info form. Second, the lab uses Slack for day-to-day communications. Matt will send you links to both the form and the lab Slack workspace when you join.

Accounts, Software, Programs, etc.

To make it easier to work with others in the lab, there’s a couple things you’ll have to set up. Please consider these to be required for any work you’re doing in the lab.

  1. Set up a GitHub account. This is a key element in the lab’s workflow, where we share code, keep track of protocols, and back up our lab notebooks. Once you’ve set this up, send me your username and I’ll add you to the lab’s GitHub spaces (one for projects and one for lab notebooks).

  2. Download R / RStudio - The lab will primarily use R for data analysis. Make sure you have an up-to-date version of both. Once installed, you’ll need to link RStudio and GitHub. There’s a nice tutorial on how to do this here.

  • Note: If you use a linux machine (e.g. a Chromebook), let me know. There’s some modifications to this process you’ll need to make.
  1. Download Obsidian - I require lab members to maintain a digital lab notebook. Obsidian is the best tool I’ve found for this purpose. We’ve set up a template lab notebook you can use to get started (available here). When you’re added to the GitHub organizations, I’ll create a lab notebook repo for you based on this template. This tutorial will walk you through how to link Obsidian and your lab notebook GitHub repo. Note: when cloning in the existing repo, the link will look something like this: https://ghp_XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX@github.com/ZEAL-Notebooks/YOUR_NAME_Notebook.git

There’s a README file in the lab notebook that walks through some additional set up steps, and provides a basic overview of how the lab notebook could be used.

  1. Download / make a Zotero account - This is what the lab uses to store / share papers. It’s also used as our reference manager when writing up manuscripts. You’re welcome to use other software for reading, annotating, etc., but you will have to maintain a Zotero library for accessing lab readings and when we work together on writing manuscripts. Once you’ve set this up, send me the email you linked to your account so I can add you to the group library.

  2. Optional, but I recommend using a program other than Microsoft Excel to deal with CSV files. I’m currently using Modern CSV. UMass Lowell does provide access to the Microsoft Office Suite - programs like Microsoft Word and Powerpoint are largely unavoidable, but Excel can make working with certain data types (especially dates) difficult.

Reading

As you get closer to actually starting in the lab, there’s some reading that might be useful. These papers / excerpts can be found in the lab Zotero library, in the ‘Onboarding’ collection. It would also be useful for you to skim my past work. Don’t feel the need to read any of my papers in depth, unless something seems interesting. This initial reading list is meant to cover only the most general background (more about the ‘vibe’ I want the lab to curate than anything else) - specific reading lists based on your project will be assembled later. 

Note, I’m not going to quiz you on any of this reading, but I will ask you about how you keep track of what you’ve read, notes you’ve taken, questions you have, etc. If you don’t have a system already (which is totally fine!), we can talk about what that could look like early in the semester.

Please also find time to read the rest of the Lab Handbook. This (work in progress) document is a summary of the lab’s principles, my expectations of you, and what you can expect from me.

If there’s any questions that come up, technical issues, or something is unclear, let me know! 

Checklist

To summarize, here are the things that you should aim to do before you start in the lab: