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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.


= Obtaining credentials =  
= New Lab Members =
For command line access to our cluster, please contact Teague, Therese or John for credentials.
If you have just joined the lab, here's what you need to know:


For your main email address, you may well use your gmail account or other public account for most purposes.  However, if you need personal access to the SciNet cluster, you will need a U of T email address. If you do not need access to SciNet, then you may well not need a U of T email address.
# 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.


* Step 1 is to contact Lilita, who can get you one.
= Info =
* Step 2. Is to get a Compute Canada Role Identifier (CCRI) from me (ask me).
* [[Group Meeting]]
* Step 3. is to register on SciNet (page here).
* [[Reimbursement Instructions]]
* [[Lab Security Policy]]
* [[Disk space policy]]
* [[Backups]]
* [[Tutorials]]


= Disk usage conventions =
= Best Practices =
We differential dockers from everyone else. If you are a full time member of the group, your disk space allocation will be like this:
* [[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]].


Your home directory is for important or small files. 500 GB default. Backed up.
= Computers =
/nfs/home/<userid>/
Please see our  [[:Category:Cluster | cluster]] page.
You might be interested to know about the [[Disk types | types of disk]] we currently support.


We expect you to run docking calculations in /project/. 1TB default. Not backed up.
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.
  /nfs/project/<userid>/


If you have large amounts of data you want kept, e.g. from the synchrotron, you may request repository space to keep it. Backed up. Size by agreement.
In Cluster 0, you log in to sgehead.bkslab.org.  You should be able to do everything from there.
  /nfs/repos/<userid>/


If you generate private databases, you may request /db/ space. Backup by arrangement. Size by agreement.
= Access from home =
/nfs/db/<userid>/
* [[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)]]


If you have software you want to share, you may request /software/ space. backed up. 500 GB.
= Synchrotron trips =
/nfs/software/<userid>/
We can help arrange to store your data in a safe place. Ask before you leave.


= Getting set up with lab software =  
= Third party software and databases =  
svn co dockenv
See the main article on [[:Category:Third party software | third party software]] that we maintain on our cluster.
cp $SOFT/labenv.csh ~/.csh
OR
cp $SOFT/labenv.sh ~/.bashrc
for bash users.


= Good habits =  
= Updates =  
Set aside a quiet time every month to review your disk usage, and compress, delete or move excessive usage.
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.


= Synchrotron trips =  
= When you leave the lab =  
We can help arrange to store your data. Ask before you leave.
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 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]].


= When you leave the lab =  
= Special pages for certain people =  
Please discuss with Teague or Therese or John one month before you leave the lab to agree on which of your files will remain.
* [[:Category:Internal]] - ssh-level access for group members, lab visitors, collaborators
We can also help you take some software and data with you, if you like.
* [[:Category:Sysadmin]] - cluster creator / software installer / system administrator
* [[:Category:Developer]] - github user / software developer
* [[:Category:Curator]] - database curator


[[Category:Tutorials]]
[[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:

  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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