Local OS X Environment
For the most part, the Zamanian lab requires use of macOS on personal computers. The following is a guide for setting up one's local machine for in order to unify machines across the lab.
Update your macOS version to Ventura (v13.0)
If the Mac is UW-owned, follow these instructions to install WorkSpace One Intelligent Hub. This will allow you to directly install/update UW-licensed software, including Adobe products, the UW VPN (Cisco Global Protect), Microsoft Office products, and Zoom.
Install core software (some of which can be installed/updated via Intelligent Hub; instructions for manually installing on a personal computer are linked):
- Adobe products
- Box Drive (cloud-based shared file storage)
- Cyberduck (SFTP client)
- iTerm (feature-rich terminal replacement)
- Paperpile (reference management)
- RStudio (IDE for R scripting and plotting)
- Slack (primary lab communication tool)
- Sublime Text (lightweight text editor)
- UW VPN (VPN for off-campus resource access)
- Visual Studio Code (Versatile IDE for general programming)
- XQuartz (open-source window system on which some apps rely)
- XCode (command line tools for macOS, can also be isntalled by running
- Zoom (video meeting software)
Install additional bioinformatics and imaging software:
Change the default Shell to
bash(default on new Mac machines is
- Open System Preferences
- Click Users & Groups
- Click bottom-left lock icon and enter password
- Right-click (or hold Control and click) on your username in the left pane and select Advanced Options...
/bin/bashas the Login shell
Add contents of the lab
.bash_profileto your current
~/.bash_profile(direct link: .bash_profile). Edit aliases as needed to include your net-id.
Create your R environment:
- Use CRAN to install or update R to version 4.2.2
NOTE: We will upgrade to new versions of R as a group.
Use Homebrew to install other command-line tools (you can use Homebrew to install many bioinformatics packages as well).
Manage your Python environment using Miniconda.