Month: January 2021

Summer medical student research project series Part 1: Getting set up

Summer goals and expectations

Hi there! Thanks for expressing interest in working on an epidemiology project with me this summer. This project will entail:

  • Using cohort study or clinical trial data trying to extend knowledge of cardiovascular disease (CVD).
  • You getting your hands dirty with statistical coding via R. If we don’t have our expert biostatistician available to help, I’ll be teaching you Stata instead, since that’s what I use.

My expectations for all LCOM summer students are:

  • You have a computer that works and internet that is dependable enough to allow Zoom conferences. You don’t have to be in VT.
  • In advance of the summer, you will submit a manuscript proposal to the cohort that will be used, and apply for funding through the CVRI or LCOM (typically due in February). If we need an IRB proposal (which we likely don’t since there’s probably an existing IRB), then you’ll lead the completion of that.
  • We’ll meet weekly via Zoom for an hour or so during the summer to review the project’s progress. I’ll be available in between meetings via email, Zoom, or whatnot.
  • You’ll also meet with our biostatistician to learn R pointers
  • You’ll complete the analysis, with help from me in learning the ins and outs of coding.
  • If doing a REGARDS/LCBR-related project, you’ll attend lab meetings.
  • At the end of the summer you will have: (1) A complete first draft of a manuscript and (2) a completed abstract that can be submitted to a conference.

Things to set up now.

Zotero

I use Zotero as a reference manager. It’s the bomb diggity. We will share references in a private group library that we can both edit. Only the people who have this library shared with them can see its contents.

To install Zotero, do the following:

  1. A free Zotero account. Sign up here. Please tell me your username so I can start a group library with you.
  2. Zotero’s desktop app. Make sure to log into your account in the desktop app. It’s under edit –> preferences.
  3. The Zotero web browser plugin for your web browser of choice. You need to have the Zotero desktop app open for this to work.
  4. The Zotero MS Word plugin (in Zotero desktop app, click Edit –> Preferences –> Cite –> Word Processors). This has been finicky with the specific MS Office install on the LCOM laptops so it might take some working to get it to work. But! It’ll work.

I’ll send you a shared library invitation. To accept the group library invite, do the following:

  • Go to zotero.org, log in.
  • In the top right, click on your username. A menu should drop down, click “inbox”.
  • Accept the group library invitation.
  • Open up the Zotero desktop app and let it sync (again, you need to be signed in on the desktop app, seen #2 above). The group library folder should appear in the left column all the way on the bottom.

Group libraries are awesome because we can compile references that either of us can insert into a document. Please keep the group library organized. If you add a new reference, please make a subfolder to stick it in so you don’t have to search for references one by one.

How to use Zotero

This is covered in a separate post, here.

Microsoft OneDrive

This is through LCOM. Not UVM, not your personal account.

  1. Open the OneDrive on your computer and sign in with your LCOM credentials if you aren’t already.
  2. I’ll share a research folder with you. You’ll need to sync it with your computer. To do that, go to onedrive.com, log in with your LCOM credentials (firstname dot lastname at med dot uvm dot edu).
    • After you log in, you’ll be on the landing page for OneDrive. Click “Shared” on the left column.
    • If you see a mix of files and folders, limit the view to just folders by clicking the icon of a folder to the right of “With You”.
    • Find the research folder and select it. On the top bar click “Add shortcut to My Files” (you might need to make the window full screen to see this option).
    • Allow the OneDrive desktop app to sync. Now all of the files should be available offline in the Onedrive folder on your computer.

Microsoft Word

Unfortunately, writing papers in Google Drive is a bit too onerous. Please download this manuscript file, which you will be using to draft your manuscript.

Your statistical software, option 1: Stata – note: we aren’t using this in 2023’s summer session. See R below.

At this point you should know if you are using Stata or R. I use Stata. UVM has an institutional subscription. You can download and install it from the UVM Software page, here. For this you will log in with your UVM (not LCOM) credentials. To download it, hit the down arrow (1) then download. After it’s installed, you’ll need the serial number, code, and authorization to activate it. That’s under “more info” (2).

<– Two steps to install Stata from UVM

Your statistical software, option 2: R – we are using this in 2023’s summer session.

R is a free and open source computer language intended for use in statistics. RStudio is a commercial software that makes using R much more user-friendly. I have only used R a few times and don’t have expertise in the language.

Research credentialing things

CITI training and directory modification

You need to complete the CITI training (both “human subjects training/IRB” and “GCP” trainings) in advance of starting the summer so you can be added to our human subjects IRB, see details at these links:

And please modify your directory listing so you can be added to the IRB as described here: https://www.uvm.edu/sites/default/files/media/Students_-_How_To_Sign_Up_to_Do_Research_at_UVM_2.pdf

Once you have finished these steps, let me know so we can add you to the IRB. There is a delay between when we request you to be added to the IRB and when you are added to the IRB, fyi.

Cornerstone research training

Historically, students have been required to do an online research training session in Cornerstone by the end of the first week. Details from this come from the Student Services office. I don’t have details about how to complete this. IIRC this is specifically for students doing projects that involve interacting with patients or patient data at UVMMC, which isn’t what we are doing. But, look for those details coming your way.