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onboarding_affiliates

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 (shahlab-dev2, shahlab-db1). Contact Alex Skrenchuk. 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 Alex to arrange for access. Read and agree to DUA.
  4. Complete the necessary training
    1. IF you will access db1 AND dev1, 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 db1, you need to complete the following training:
      1. Protecting Patient Privacy - sign up via STARS
    3. Upload your certificates at: http://shahlab.stanford.edu/lab_members
  5. You are encouraged to set up a wiki page to document your project. See example.
  6. For details regarding specific steps, schedule a one-on-one session with the relevant person
    • Server access: Alex Skrenchuk
    • Data use agreement: Nigam Shah
    • Text processing: Juan Banda
    • Cohort building:
    • Data analysis:

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 Dev2

If you are off-campus (or on the wireless network), you will need VPN.
Not to be confused with DB1, this only needs a simple SSH command to connect (open a terminal):

ssh <yourusername>@shahlab-dev2.stanford.edu 

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 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 dev2 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: http://www.sequelpro.com/
  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 shahlab-db1.stanford.edu, a MySQL database (port 3306), tunnel via shahlab-dev2.stanford.edu.

ssh -L 3306:shahlab-db1.stanford.edu:3306 <yourusername>@shahlab-dev2.stanford.edu -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: 2017/06/15 12:28 by acallaha