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Onboarding for affiliates

Onboarding steps

  1. Get SUNET ID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff.
  2. Get access to our servers. Contact Jason Fries. VPN is needed for off-campus access and probably on-campus access as well.
  3. Identify the databases you need. Get authorization from database owner and work with your assigned mentor and Jason Fries to arrange for access. Read and agree to DUA.
  4. Complete the necessary training
    1. IF you will access data containing PHI (e.g. clinical notes), you need to complete the following training:
      1. Protecting Patient Privacy - sign up via STARS
      2. Protection of Human Subjects - GROUP 7: IRB BioMed/GCP Research - done via CITI
    2. IF you will access ONLY de-identified patient data, you need to complete the following training:
      1. Protecting Patient Privacy - sign up via STARS
    3. Provide your certificates to Jason to get access
  5. Join the lab slack
  6. Find the person in the lab who can explain the data you will use - talk to them!
  7. Set up a wiki page to document your project. See example.
  8. For details regarding specific resources, schedule a one-on-one session with the relevant person
    • Server access: Jason Fries
    • Data use agreement: Nigam Shah
    • Text processing: Jason Fries
    • Data/terminologies: Alison Callahan, Vladimir Polony

Data sharing and Use Agreement

  • Use of the data will be restricted to research questions outlined and agreed upon in advance.
  • All participants and users of data have completed CITI training, and attended an on-site tutorial at Stanford regarding the organization of the data and best practices for safeguarding the data.
  • No copies of the data will leave Stanford BMIR servers. If it does, collaboration is over.
  • All publications or presentations relating to the data will be cleared in advance through Shah lab.

How to connect to shahlab-compute (formerly dev2)

If you are off-campus (or on the wireless network), you will need VPN.
SSH command to connect (open a terminal):

ssh <yourusername> 

The first time you do this it will ask you to store the RSA key, just type yes. After the first time, this should not appear anymore.

How to connect to shahlab-database (formerly db1)

There are multiple different ways of connecting to the database server. If you are off-campus, you will need VPN.

NOTE: Your DB1 password is NOT the same as your shahlab-compute password. It is found on the .my.cnf file file on your home/your_name directories.

1) (The easiest way) Set up a MySQL GUI:
There are plenty of options to use, but we recommend:

  1. (MAC) Sequel Pro has built-in SSH tunneling:
  2. (PC) MySQL Workbench, DB Visualizer
  3. (Linux) MySQL Workbench

Example: setting up MySQL workbench with tunneling

2) (Second easiest way) From the command line :

- SSH to dev2
- Use Mysql:

mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename>

3) (hard and confusing) Create a tunnel from the database server to your computer:

- To connect to, a MySQL database (port 3306), tunnel via

ssh -L <yourusername> -Nf

- Use your local copy of MySQL (you need to instal the MySQL client on your computer)
- Then connect to the database of interest

mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename>
onboarding_affiliates.txt · Last modified: 2021/07/07 13:40 by acallaha