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onboarding_affiliates [2018/01/26 13:00] acallaha [Onboarding steps] |
onboarding_affiliates [2021/11/23 17:25] acallaha |
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====== Onboarding for affiliates ====== | ====== Onboarding for affiliates ====== | ||
- | ===== Onboarding steps ===== | ||
- | - Get SUNET ID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff. | ||
- | - Get access to our servers. Contact Jason Fries. [[https:// | ||
- | - Identify the [[int: | ||
- | - Complete the necessary training | ||
- | - IF you will access data containing PHI (e.g. clinical notes), you need to complete the following training: | ||
- | - Protecting Patient Privacy - sign up via [[https:// | ||
- | - Protection of Human Subjects - GROUP 7: IRB BioMed/GCP Research - done via [[https:// | ||
- | - IF you will access ONLY de-identified patient data, you need to complete the following training: | ||
- | - Protecting Patient Privacy - sign up via [[https:// | ||
- | - Upload your certificates at: http:// | ||
- | - Get on the right mailing list | ||
- | - Find the person in the lab who can explain the data you will use - talk to them! | ||
- | - Set up a wiki page to document your project. [[int: | ||
- | - 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/ | ||
- | + | See the sections on ' | |
- | ===== Data sharing and Use Agreement ===== | + | |
- | + | ||
- | * Use of the data will be restricted | + | |
- | + | ||
- | * All participants and users of data have completed CITI training, | + | |
- | + | ||
- | * __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 | + | |
- | + | ||
- | ===== How to connect to Dev2 ====== | + | |
- | If you are off-campus (or on the wireless network), you will need [[https://itservices.stanford.edu/ | + | |
- | Not to be confused with DB1, this only needs a simple SSH command to connect (open a terminal): | + | |
- | + | ||
- | < | + | |
- | + | ||
- | 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 [[https:// | + | |
- | + | ||
- | **NOTE: Your DB1 password is NOT the same as your dev2 password. It is found on the .my.cnf file file on your home/ | + | |
- | + | ||
- | 1) (The easiest way) Set up a MySQL GUI:\\ | + | |
- | There are plenty of options to use, but we recommend: | + | |
- | - (MAC) Sequel Pro has built-in SSH tunneling: http:// | + | |
- | - (PC) MySQL Workbench, DB Visualizer | + | |
- | - (Linux) MySQL Workbench | + | |
- | Example: setting up MySQL workbench with tunneling\\ | + | |
- | {{: | + | |
- | + | ||
- | 2) (Second easiest way) From the command line :\\ | + | |
- | + | ||
- | - SSH to [[http://shahlab.stanford.edu/onboarding_affiliates?& | + | |
- | - Use Mysql: < | + | |
- | + | ||
- | 3) (hard and confusing) Create a tunnel from the database server to your computer: | + | |
- | + | ||
- | - To connect to // | + | |
- | < | + | |
- | - Use your local copy of MySQL (you need to instal the MySQL client on your computer) \\ | + | |
- | - Then connect to the database of interest | + | |
- | < | + |