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====== Onboarding for affiliates ====== | ====== Onboarding for affiliates ====== | ||
- | ===== Onboarding steps ===== | ||
- | - Get SUNET ID to access | + | See the sections |
- | - Get access to our servers. Contact Jason Fries. [[https:// | + | |
- | - Identify the [[: | + | |
- | - 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 | + | |
- | - IF you will access ONLY de-identified patient data, you need to complete | + | |
- | - Protecting Patient Privacy - sign up via [[https:// | + | |
- | - Provide your certificates to Jason to get access | + | |
- | - Join the lab slack | + | |
- | - Find the person | + | |
- | - Set up a wiki page to document your project. [[: | + | |
- | - 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/ | + | |
- | + | ||
- | + | ||
- | ===== 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 [[https://itservices.stanford.edu/ | + | |
- | 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 shahlab-database (formerly 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 shahlab-compute 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 | + | |
- | < | + |