Introduction to Single-Cell Analysis: Setup instructions
UM Bioinformatics Core Workshop Team
This document guides you through the installation of software necessary to participate in the workshop. To complete this setup, you will need:
- A Macintosh or Windows workstation connected to the internet.
- An email invitation to the workshop Slack workspace.
- An email titled “UM BioinfCore Workshop Login” containing your individual login and password for the shared workshop server
- About 10 minutes.
Introduction
- The virtual workshop will be conducted using Zoom and Slack for all days.
- Attendees will use their own workstation/laptop to participate; the workstation/laptop should have a microphone, camera, and reliable internet access. While not required, for laptop users we recommend using a larger monitor for the optimal workshop experience.
- The workshop will use Slack for group messaging. Messages posted to the general channel will be visible to all participants in the workshop.
- For simplicity, participants will log in to a pre-built server which has the necessary data, software, and configuration already installed.
- While not required or recommended, advanced users may elect to install some software locally; see advanced setup instructions.
How to get help
While we have endeavored to make this setup process work robust and comprehensive, installing bioinformatics software is tricky and we would be happy to lend a hand to get things working.
If you have problems/questions, please don’t hesitate to email us at: bioinformatics-workshops@umich.edu
When emailing it will speed things along if you could include:
- Whether you are using Windows or Mac (and optionally which version of the OS you are using).
- Whether you have Administrative privileges on your workstation.
- The specific text of any error messages, if applicable.
Setup steps
Zoom
If you have not used Zoom before, please use the following link to
install “Zoom client for Meetings”
https://zoom.us/download
Additional Zoom settings for Macintosh:
1.1 To enable screen sharing (useful for breakout rooms and tech support)
- System Preferences >> Security & Privacy: click on the Privacy tab
- Select Screen Recording on left tab
- Scroll to the bottom of the right tab and verify Zoom is checked.
1.2. To enable remote control (useful for breakout rooms and tech support)
- System Preferences >> Security & Privacy: click on the Privacy tab
- Select Accessibility on left tab
- Scroll to the bottom on the right tab and verify Zoom is checked.
- If it’s not checked, click the lower left lock icon and enter user password when prompted. You can now check Zoom in the right tab.
- Click the lock again.
1.3. Close and relaunch Zoom client.
Slack
2.1. In the Slack email invitation from the hosts, click the link to join the Slack workspace.
2.2. Follow the Slack instructions to login or create an account. You may edit your profile to add a photo if you choose.
2.3. Note that once your Slack account is established and you have accepted the Slack invite you can access the Slack channel by pointing your web browser here: https://umbioinfcoreworkshops.slack.com
Launch R/RStudio (from the web)
3.1 Open the following web address: https://bfx-workshop02.med.umich.edu
3.2 When prompted, enter the username and password supplied by your hosts and click Sign In.
3.3 The login page will immediately go blank - it may take several seconds for the next page to appear (sometimes up to 60 seconds, but usually faster). After this delay, you should see a new webpage that looks something like this:
If you see a screen like that above, you have successfully logged into RStudio.
Congratulations
Your workstation and logins are ready for the workshop; thank you for taking time to set this up in advance.
- You can close your RStudio session by clicking the small orange “power” button in the top-right corner (highlighted in the picture above by a red arrow). The webpage will announce R Session Ended; you may now close the web page.