Skip to content

Latest commit

 

History

History
65 lines (39 loc) · 5.15 KB

Setup.md

File metadata and controls

65 lines (39 loc) · 5.15 KB

Setup

Slack

You should have received an email inviting you to a Slack called UD CBCB Core Workshops. The Slack platform is the preferred method for communicating during the workshop. You can use Slack in a web browser or download the desktop app. If you haven't used Slack before, check out this guide for getting started.

Once you have joined the Slack channel, please complete the icebreaker so we know you're there!

Icebreaker

We want to get to know you! The icebreaker for this workshop is a game called 2 Truths and a Lie. Once you have joined the Slack, navigate to the fair-data-2022-04 channel. There, you should post 3 things about yourself. These can be anything you want: hobbies, travel, work-related, celebrity encounter, etc. The catch is, only two of those things should be true, and one should be false (2 truths and a lie). On Monday, we will incorporate these into the in-person introductions by asking people to guess which item is the lie. That means that if you don't post to the Slack, you'll have to come up with 3 things on the spot!

If you're unsure of how to play the game, check out this article.

Obsidian

We will be using Obsidian for documentation purposes in this workshop. Obsidian is available for Windows, Linux, and MacOS. Downloads can be found here.

Biomix

To connect to Biomix, UD's high performance compute cluster, you will need an ssh client. Additional Biomix documentation can be found here. Remember that your username is the first part of your udel.edu email address.

MacOS and Linux users

MacOS and most Linux distributions come with ssh clients already installed. To connect to Biomix on these systems, open your terminal and use the ssh command with your username and the name of the server:

ssh [username]@biomix.dbi.udel.edu

Hit enter and type your password when prompted. For security reasons, your password will not appear as you type. But, your password is being entered and the backspace key will work if you make any errors. Hit enter.

You should now be on Biomix! A successful login will result in a few messages, including “Welcome to BIOMIX.” Type logout and hit enter to logout of Biomix.

Windows users

Windows machines often require installation or activation of an ssh client.

If using Windows Terminal, follow these steps to activate and configure the ssh client. If using Windows PowerShell, follow these instructions instead. Once you have activated the ssh client, follow the instructions in the "MacOS and Linux users" section to connect to Biomix.

Alternatively, you can use PuTTY, which is a free ssh client for Windows. It's old-school, but easy to install and use.

  • To use PuTTY, first download the 64-bit version.
  • Open the installer file and follow the instructions. It is convenient to create a shortcut on your desktop during installation.
  • Start PuTTY by double-clicking on the icon for the desktop shortcut. In the “Host Name” box, enter biomix.dbi.udel.edu. Make sure the port box contains the number 22.
  • Hit “open.” A new window should appear. Enter your Biomix username. Hit enter.
  • Enter your password when prompted. Your username will appear as you type it but you will not be able to see your password as you type. This is normal and you should enter your password as if you could see it. The backspace key works as well, in case you make a mistake. Hit enter.
  • You should now be on Biomix! A successful login will result in a few messages, including “Welcome to BIOMIX.” Type logout and hit enter to logout of Biomix.

FileZilla

FileZilla is a Graphical User Interface (GUI) that allows you to transfer files from your local computer to a remote server, and vice versa. Visit this link to download FileZilla (note that you want the FileZilla client, NOT the server). There are additional instructions for installation here should you need them.

To check if FileZilla is working after installation, you can attempt to connect FileZilla to Biomix. To do this, open the app, fill in the four boxes along the top, and hit Quickconnect. Make sure to enter biomix.dbi.udel.edu as the host, your Biomix username and password, and 22 as the port number.

Git

Git is not strictly required for this workshop, as you can download materials directly from the GitHub. However, if you would like to interact with the workshop repository from the command line, you will need to install git on your computer.

You can find instructions for installing git here.