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onboarding_affiliates [2015/07/13 15:51] jmbanda [How to connect to DB1] |
onboarding_affiliates [2021/11/23 17:25] acallaha |
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- | ====== Onboarding for affiliates ===== | + | ====== 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 [[int: | + | |
- | - Identify the [[int: | + | |
- | - Complete training (HIPAA awareness on Axess, Protection of Human Subjects on CITI) and [[lab_members|upload]] your certificates | + | |
- | - Understand our [[int: | + | |
- | - You are encouraged to set up a wiki page to document your project. [[int: | + | |
- | - For details regarding specific steps, schedule a one-on-one session with the relevant person | + | |
- | * Server access: Alex Skrenchuk | + | |
- | * Data use agreement: Nigam Shah | + | |
- | * Annotation: Juan Banda | + | |
- | * Cohort building: | + | |
- | * [[int: | + | |
- | * Patient matching | + | |
- | * 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; 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. | + | |
- | + | ||
- | * 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, you will need [[https:// | + | |
- | 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:// | + | |
- | + | ||
- | 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\\ | + | |
- | {{db1connect.png? | + | |
- | + | ||
- | 2) (Second easiest way) From the command line :\\ | + | |
- | + | ||
- | - SSH to [[http:// | + | |
- | - 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 | + | |
- | < | + | |
+ | See the sections on ' |