Table of contents

Workshop Location

The Bulk RNA-Sequencing and Reproducible Research Practices Workshop will be held at the University of Minnesota in the building located at 717 Delaware Street SE, Minneapolis, MN 55414. We will meet in Room 105. Enter through the front main entrance.

If you have trouble finding the building or the room on the first day of training, please use Slack to direct message Jen O'Malley.

Pre-workshop Information

Please review and sign the training waiver.

Here is the link to join the Slack group that we will use for communication purposes and to stay in touch after the workshop! You will be added to our #2024-august-training channel. 

This is a hands on workshop!

  • Be sure to review the Setup Instructions (on the homepage) for instructions on preparing your computer.
  • We will hold pre-workshop office hours on Friday, August 16 from 2-3pm CDT (3-4pm EDT) on Slack. Join us on the #2024-august-training channel for help getting set up and to ask any questions.

We will provide breakfast, lunch, snacks, and beverages each day. Please submit the meal form to make us aware of any dietary restrictions and to RSVP for an (optional) group dinner at nearby Surly Brewing Co. on August 20! 

Nearby Accommodations

If you are traveling to the workshop, the following hotels are located within 1 mile.

Health and Safety

Alex’s Lemonade Stand Foundation’s Childhood Cancer Data Lab will comply with any governmental requirements related to health and safety. We encourage workshop participants to adhere to US governmental guidance. You may wish to review the CDC COVID-19 data tracker when planning for workshop attendance.

If you are feeling sick, please do not attend the workshop. We will not withhold your deposit if you cannot attend because you are sick.

Workshop Structure

Our goals for the workshop include the following:

  • You will be introduced to the R programming language and the fundamentals of bulk RNA-seq analysis through a series of hands-on, interactive lessons.
  • You are able to ask questions and receive 1:1 assistance as needed during instruction. Because our instruction is almost entirely through hands-on lessons, we want to make sure we can help you through any difficulties or errors you may encounter.
  • You have the opportunity to practice the skills you learn during instruction in consultation sessions with the support of your instructors, and/or using exercise notebooks we have provided.
  • You receive consultation about the data you are working with to answer your research questions.
  • You have opportunities to interact with other participants working on similar problems.

The next sections are designed to give you an idea of what your participation in the workshop will be like and outline the communication processes we have developed in service of these goals.

Instruction sessions

During instruction sessions, an instructor may present some slides to introduce the material, and then they will instruct you to navigate to the RStudio Server (https://rstudio.ccdatalab.org), enter your RStudio login credentials, and guide you through the interactive lesson. Typically instructors will prompt you to navigate to a specific R Notebook file, and you will execute steps at the same time as your instructor. You will have access to a private training-specific Slack channel in Cancer Data Science Slack that you can use as a forum to post questions. This channel will be monitored by instructors.

Consultation sessions

During consultation sessions, you can work through exercise notebooks included as part of the course, with your own data, or with publicly available data related to your research.

The main method we use for communication during consultation sessions is Slack. You can use the training-specific private channel to post errors, get help with debugging, and interact with other participants as they work through exercises. We strongly recommend you follow these guidelines for posting errors so you can maximize others’ abilities to help you resolve your error.

Using communication platforms during consultation sessions

Our goal during consultation days is to make sure you get the support you need from instructors, to facilitate peer-to-peer learning, and to maximize the information that is available to everyone in a form that is discoverable in the future. For these reasons, the main process for communication on consultation days is the training-specific Slack channel. Again, we recommend following these guidelines for posting errors when requesting help for errors you encounter in your code.

Remember – if you have a question, another person in the course almost certainly has the same question!

Participant presentations

On the last afternoon of the workshop, we will reconvene after the consultation session for participant presentations. You will be invited to give a short (5 minutes or less) presentation on what you worked on during the week to the rest of the group. This is meant to be a low-pressure opportunity to reflect on what you’ve learned! The content and format of the presentation is entirely up to you. Here are some examples of what people have presented in the past at our workshops:

  • Talked through part of an exercise notebook, highlighting where they ran into issues and how they figured it out
  • Shown a visualization they made with their own data
  • Walked through a set of slides that included tools they’ve used in the past and how they compare to what they learned during the workshop
  • Identified some publicly available data sets relevant to their scientific questions and talked about next steps