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Welcome to the lab | 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 = | ||
If you have just joined the lab, here's what you need to know: | |||
# Ask the [[sysadmin]]s for an account on the cluster, and a workstation. Tell us what account name you prefer. | |||
# Set up a [[How_to_generate_ssh_keys_securely|public key]] so you can login from off campus. | |||
# Make sure you are on the mailing list yall, ask a [[sysadmin]] if you are not. | |||
# Get set up with github / lab tools. | |||
= 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]] | |||
* 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]]. | |||
= Computers = | |||
Please see our [[:Category:Cluster | cluster]] page. | |||
You might be interested to know about the [[Disk types | types of disk]] we currently support. | |||
If you | 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 | First, generate an ssh key securely]] | |||
* [[How_to_create_a_vpn/ssh_tunnel | Second, create a vpn/ssh tunnel]] | |||
* [[ssh tunnel (Trent's way)]] | |||
= | = 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 [[:Category:Third party software | 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 = | = When you leave the lab = | ||
Please discuss with | 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 | 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 DOCK 3.6 conversion| QNIFFT]] and [http://crystal.med.upenn.edu/software.html related software] for structural analysis from the [http://crystal.med.upenn.edu/ Sharp lab] | |||
* [[PLOP]] - protein modeling program from the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group]. | |||
* [[Modeller]] - comparative modeling program from the [http://salilab.org Sali Group]. | |||
* Software vendors: [[OpenEye]], [[ChemAxon]], [[Molinspiration]] | |||
* Software providers: [[RDKit]], [[Knime]] | |||
* [http://zinc.docking.org/browse/catalogs/purchasable.php Compound vendors] and [http://zinc.docking.org/browse/catalogs/annotated.php 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 | |||
[[Category:Internal]] | |||
[[Category:FAQ]] | |||
Latest revision as of 21:06, 30 December 2020
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
If you have just joined the lab, here's what you need to know:
- Ask the sysadmins for an account on the cluster, and a workstation. Tell us what account name you prefer.
- Set up a public key so you can login from off campus.
- Make sure you are on the mailing list yall, ask a sysadmin if you are not.
- Get set up with github / lab tools.
Info
Best Practices
- Best:SGE Usage
- Best:Disk Usage
- Best:Desktop Usage
- Best:More
- 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.
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
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