#linux

Git Resources

Git is a powerful versioning control system that allows you to keep track of changes for your files. Additionally, it allows for collaboration with other people on the same project. It is recommended to develop your work using a versioning tool such as git.

• Quick Git Intro

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• Peder Larson Group:
  • Git Tutorial
  • Software Development for Scientists

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Linux Resources The radiology servers are running a Linux distribution and therefore it is highly recommended to get familiar with Linux. Note: Keep in mind that the servers run tcsh by default, which is very similar to bash with some slight differences. You can type bash into any terminal to start using bash. Beginner’s Guide to the Bash Terminal Linux cheatsheet A collection of useful Linux commands MIT Missing Semester For a more advanced dive into these concepts, the MIT Missing Semester is another great resource to learn about linux. [Read More]

Radiology SCS Server Access

All of the imaging and medical patient data is located within UCSF Radiology encrypted Linux servers. This is run by Scientific Computing Services (SCS). Information for access is at

https://wiki.radiology.ucsf.edu/bin/view/SCS/ (requires UCSF VPN login)

https://git.ucsf.edu/pages/intelligent-imaging-computational-core/i2-hpc-doc/index.html (requires UCSF VPN and UCSF GitHub account)

Please contact your PI or lab members to see which hosts to use for logging in.

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SSH The SSH (Secure Shell) protocol is an encrypted communication protocol for networking. It is a highly versatile and powerful tool that serves as the main way to access the servers. Setup Depending on the operating system you are using, follow these options: Mac and Linux users Open a terminal and type the following: ssh username@servername.radiology.ucsf.edu -L 9XXX:localhost:9XXX For the above command make sure to replace the username with your own, the servername with any of the listed server names (requires UCSF login) and the 9XXX with a number above 9020 There will be a prompt for your UCSF password PC users Use WSL, PuTTY, Cygwin or any other SSH tool: Use servername. [Read More]

VNC Unlike SSH, VNC allows you to access a virtual display of the servers. This lets you browse through the file system and open visual applications such as Matlab and a web browser in a virtual operating system. Follow these steps to start a VNC session: Download and install VNC Viewer. Once installed you will need to SSH to the server to which you will VNC into and type the following command into a terminal: myvncserver Towards the bottom of the output, take note of the last number as that will be the display number you will need to access the VNC server. [Read More]