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onboarding_affiliates [2016/02/13 18:17] acallaha [Data sharing and Use Agreement] |
onboarding_affiliates [2021/11/23 17:25] (current) 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 | + | |
- | * Text processing: 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. 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 [[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 ' |