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Welcome to the lab. This page is designed for new group members, our collaborators and anyone else who wishes to access our cluster via ssh.
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.


= Guides =
= 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]]
* [[Group Meeting]]
* [[Reimbursement Instructions]]
* [[Lab Security Policy]]
* [[Disk space policy]]
* [[Backups]]
* [[Tutorials]]
* [[Tutorials]]
* [[Reimbursement Instructions]]


= Cluster access =  
= Best Practices =  
Group members have access to several cluster. Each one is separate.
* [[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.


{{TOCright}}
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.


* [[Cluster 0]] - Legacy UCSF cluster - Therese can set you up.  
In Cluster 0, you log in to sgehead.bkslab.org.  You should be able to do everything from there.
* [[Cluster 1]] - Toronto Cluster - Therese can set you up.
* [[Apply for SciNet Account]] - if you need it
* [[Cluster 2]] - new UCSF cluster - not ready yet.
* [https://salilab.org/qb3cluster UCSF Shared Cluster]] - if you need it.  Teague can help you get set up.


= Access from home =  
= Access from home =  
* [[How to generate ssh keys securely]]
* [[How to generate ssh keys securely | First, generate an ssh key securely]]
* [[How_to_create_a_vpn/ssh_tunnel]]
* [[How_to_create_a_vpn/ssh_tunnel | Second, 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.


= Synchrotron trips =  
= Synchrotron trips =  
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= Third party software and databases =  
= Third party software and databases =  
Some of the third party software that we maintain includes:
See the main article on [[:Category:Third party software | third party software]] that we maintain on our cluster.
* CSD
* ppilot
* openeye
* cactvs
* chemaxon
* molinspiration
* AMSOL


= Updates =  
= Updates =  
Line 44: Line 50:
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.
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.


== Miscellaneous ==
= FOTL: Friends of the lab =  
  Brenda is at /raid5/backonce/joha/DB3/5_BRENDA2SDF/ORG_BRENDA_MOL_FILES_PREP/brenda_031306.ism
* [[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]
mysql is at mysql -u joha -p*secret* -h (brenda-machine-name-ask-jji) brenda
* [[PLOP]] - protein modeling program from the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group].
wombat is at ~jerome/sets/wombat/wombat_20062/wombat.20062.sdf.gz
* [[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]].


* [[Dock Users' Meeting Minutes (DUMM)|Dock Users' Meeting Minutes]]
= 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:Internal]]
[[Category:Tutorials]]
[[Category:FAQ]]
[[Category:UCSF]]
[[Category:YYZ]]

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:

  1. Ask the sysadmins for an account on the cluster, and a workstation. Tell us what account name you prefer.
  2. Set up a public key so you can login from off campus.
  3. Make sure you are on the mailing list yall, ask a sysadmin if you are not.
  4. Get set up with github / lab tools.

Info

Best Practices

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

Special pages for certain people

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