Workshop Structure
Our goals in constructing the virtual workshop structure are the following:
- You will be introduced to R programming, the Tidyverse, and processing and analysis of bulk RNA-seq through a series of hands-on exercises.
- You are able to ask questions and receive 1:1 assistance as needed during instruction. Because our instruction is almost entirely through hands-on exercises, 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.
This document is designed to give you an idea of what your participation in the workshop will be like and outlines the communication processes we have developed in service of these goals.
Instruction sessions
During instruction sessions, you will call into a Zoom meeting and log into our RStudio Server. An instructor may present some slides to introduce the material and then they will instruct you to navigate to rstudio.ccdatalab.org, enter your RStudio login credentials, and guide you through the course material. Typically you will be asked 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. Instruction will be recorded and distributed to course participants (not posted publicly).
During periods of instruction where everyone in the course will work on the same set of exercises, you will be placed in a Zoom breakout room with an instructor and other course participants.
We will use the last half hour of instruction sessions each day (Monday-Thursday) to break into groups to answer any questions and to introduce the set of exercise notebooks related to the material covered during instruction. We use Zoom breakout room functionality for these groups.
Your instructors’ roles during instruction
During instruction, your instructors function in one of three roles:
- One person leads the hands-on exercise.
- One person is the host of the Zoom meeting and is responsible for administering that platform. The host makes sure any time-sensitive questions or problems are addressed during instruction and is responsible for pairing anyone that needs 1:1 assistance with an available instructor. The host may also group you into breakout rooms for exercises as needed.
- All other instructors are on-hand to monitor the training specific Slack channel, answer questions, provide 1:1 assistance, or help with technology or login issues.
We will clearly identify the role of each instructor at the beginning of instruction.
Using communication platforms during instruction
To make sure all your needs are addressed, we’ve put together a plan for how the communication platforms we use during instruction are intended to work together.
You can read more about how we use Zoom and Slack in the Zoom procedures and Slack procedures documentation, but we’ve put together the table below to serve as a guide at a glance.
| If this happens | Use this platform |
|---|---|
| I need something clarified before we move on with instruction | Use Zoom chat to message the meeting host with your question or use the Raise Hand button on Zoom |
| I am stuck with an error message and am no longer able to follow the hands-on instruction | Use Zoom chat to message the meeting host and let them know you need 1:1 assistance - they will pair you with an available instruction in a Zoom breakout room |
| I have a general or conceptual question that can be addressed later in the lecture or asynchronously | Post in the training-specific Slack channel |
| I am in a breakout room and want to ask my instructor a question | Use the Raise Hand button on Zoom, your instructor will ask you to unmute yourself and ask your question. You can use the chat window to message the instructor, who will be designated as a Host or Co-host of the meeting, if you prefer. You may be asked to share your screen if you encounter errors. |
| I am having trouble with my login credentials | Use Slack to direct message a an instructor that is not leading instruction or the host of the Zoom meeting |
| I am having technical difficulties that preclude me from using Zoom and Slack | Email dataCoLAB@andrew.cmu.edu |
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.
Zoom is the platform that we use to facilitate sharing your screen with an instructor, which may come in handy during consultation. If you need assistance and would like to share your screen, an instructor will initiate a Zoom call in Slack.
Your instructors’ roles during consultation
Your instructors will be available via Slack during the consultation sessions listed in the workshop schedule. You may also remain in the Zoom meeting used for the day’s instruction session, which will be used for breakout room functionality for grouping participants that want to work together. If you need to share your screen with an instructor during the a consultation day, the instructor will start a Zoom meeting and you will be able to join from Slack.
Using communication platforms during consultation sessions
Our goal during consultation sessions 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 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.
Remember – if you have a question, another person in the course almost certainly has the same question!
In addition, because the instructors is also currently all-remote, keeping most communication to the training-specific Slack channel allows us to better coordinate our efforts and make sure you get the support you need.
You can read more about how we use Zoom and Slack in the Zoom procedures and Slack procedures documentation. We’ve put together the table below to serve as a guide at a glance.
| If this happens | Use this platform |
|---|---|
| I have a question about yesterday’s instruction | Post in the training-specific Slack channel |
| I have a question about an exercise notebook | Post in the training-specific Slack channel - if you’re seeing an error, please include the file name and line number |
| I am having an issue that requires me to share my screen | Post in the training-specific Slack channel - an instructor will initiate a Zoom meeting that you can join from Slack |
| I would like to be paired up with other participants | Post in the training-specific Slack channel |
| I have a question that is highly specific to my data | Use Slack to direct message an instructor |
| I am having trouble with my login credentials | Use Slack to direct message an instructor |
| I am having technical difficulties that preclude me from using Zoom and Slack | Email dataCoLAB@andrew.cmu.edu |
Presentations
We will reconvene in a Zoom meeting on Friday at 1:30pm Eastern for presentations. You will 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 (Note that we will have limited capacity to help with your own data)
- Explain the research problem you plan to solve using what you learned this week
- 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
When it is your turn to present, you will share your screen on Zoom and unmute yourself.