Welcome group members

Welcome to the lab! This page organizes topics of interest to group members, our collaborators and anyone else who wishes to access our cluster via ssh. If you are not a member of the lab, please see Welcome web user. If you have ssh access, Category:Internal articles may be of interest to you.

New Lab Members

Please read this first to get started using the cluster!

Info

• Group Meeting
• Reimbursement Instructions
• Lab Security Policy
• Disk space policy
• Backups
• Tutorials

Best Practices

• Best:SGE Usage
• Best:Disk Usage
• Best:Desktop Usage
• Best:More

Computers

Please see our cluster page. You might be interested to know about the types of disk we currently support.

In Cluster 2, you log in to sgehead.ucsf.bkslab.org aka gimel.compbio.ucsf.edu. If you need fortran, ssh to fortran. If you need ppilot, ssh to ppilot. You should not need to log in to any other machine.

In Cluster 0, you log in to sgehead.bkslab.org. You should be able to do everything from there.

Access from home

• How to generate ssh keys securely
• How_to_create_a_vpn/ssh_tunnel
• ssh tunnel (Trent's way)

Good habits

Set aside a quiet hour once a month to review your disk usage, and compress, delete or move excessive usage. There are disk quotas and we do monitor them. We will make additional space available for needed lab work, but we need your cooperation to keep the signal to noise ratio high. Ask us for a Personal backup disk.

Synchrotron trips

We can help arrange to store your data in a safe place. Ask before you leave.

Third party software and databases

See the main article on third party software that we maintain on our cluster.

Updates

Some software must be updated or at least attended to annually due to license expiry. Otherwise, we generally update software on an as-needed basis. If you want something updated, ask us and give us some time. Even better, if you can take the lead, it will get done faster almost for sure.

When you leave the lab

Please discuss with John one month before you leave the lab to agree on which of your files will remain, and where they will live. We can provide you with portable disks so you can take software and data with you, if you like. If you want to take the lab software with you, we can help with that too.

FOTL: Friends of the lab

• Travel Depth, QNIFFT and related software for structural analysis from the Sharp lab
• PLOP - protein modeling program from the Jacobson group.
• Modeller - comparative modeling program from the Sali Group.
• Software vendors: OpenEye, ChemAxon, Molinspiration
• Software providers: RDKit, Knime
• Compound vendors and Annotated catalog providers
• Contract Research Organizations
• Transformative databases: DrugBank, HMDB, ChEMBL.

Special pages for certain people

• Category:Internal - ssh-level access for group members, lab visitors, collaborators
• Category:Sysadmin - cluster creator / software installer / system administrator
• Category:Developer - github user / software developer
• Category:Curator - database curator