This is an old revision of the document!
Onboarding for affiliates
Onboarding steps
Get SUNETID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff.
Get access to our
servers (ncbolabs-dev4, ncbolabs-db1). Contact Alex Skrenchuk.
VPN is needed for off-campus access and probably on-campus access as well.
Identify the
databases you need. Get authorization from database owner and work with your assigned mentor and Alex to arrange for access. Read and agree to DUA.
Complete training (HIPAA awareness on Axess, Protection of Human Subjects on CITI) and
upload your certificates
-
You are encouraged to set up a wiki page to document your project.
See example.
For details regarding specific steps, schedule a one-on-one session with the relevant person
Data sharing and Use Agreement
No copies of the data will leave Stanford BMIR servers; and no data will be shared with anyone other than those approved and certified in advance. Temporary caching during computation is allowed, and will be properly secured, accounted, and discarded in a timely fashion per the DUA.
How to connect to DB1
If you are off-campus, you will need VPN.
To connect to ncbolabs-db1.stanford.edu, a MySQL database (port 3306), tunnel via ncbolabs-dev4.stanford.edu.
ssh -L 3306:ncbolabs-db1.stanford.edu:3306 <yourusername>@ncbolabs-dev4.stanford.edu -Nf
Then connect to the database of interest
mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename>
You may also set up a MySQL GUI
-
(PC) MySQL Workbench, DB Visualizer
(Linux) MySQL Workbench
Example: setting up MySQL workbench with tunneling