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onboarding_affiliates [2014/06/08 18:54] nigam [How to connect to DB1] |
onboarding_affiliates [2018/06/01 09:53] cmiko [Onboarding steps] |
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- | ====== Onboarding for affiliates ===== | + | ====== Onboarding for affiliates |
===== Onboarding steps ===== | ===== Onboarding steps ===== | ||
- | | + | |
- | - Get access to our [[int: | + | |
- | - Identify the [[int: | + | - Get access to our servers. Contact |
- | - Complete training (HIPAA awareness on Axess, Protection of Human Subjects | + | - Identify the [[:int: |
- | - Understand our [[int:clinical_study|clinical study workflow]] and [[int:annotation| annotation workflow]] | + | - Complete |
- | - You are encouraged | + | - IF you will access data containing PHI (e.g. clinical notes), you need to complete the following training: |
- | - For details regarding specific | + | - Protecting Patient Privacy - sign up via [[https:// |
- | * Server access: | + | - Protection of Human Subjects |
- | * Data use agreement: | + | - IF you will access ONLY de-identified patient data, you need to complete the following training: |
- | * Annotation: | + | - Protecting Patient Privacy - sign up via [[https:// |
- | * Cohort building: | + | - Upload your certificates at: [[http:// |
- | * [[int: | + | - 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:callahan: |
+ | - For details regarding specific | ||
+ | * Server access: | ||
+ | * Data use agreement: | ||
+ | * Text processing: Jason Fries | ||
+ | * Data/ | ||
===== Data sharing and Use Agreement ===== | ===== Data sharing and Use Agreement ===== | ||
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* 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. | * 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 | + | * __No copies of the data__ will leave Stanford BMIR servers. |
- | * All __publications or presentations__ relating to the data will be cleared in advance through Shah lab | + | * 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:// | ||
+ | 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 ====== | ===== How to connect to DB1 ====== | ||
- | If you are off-campus, you will need [[https:// | + | There are multiple different ways of connecting to the database server. |
- | To connect to // | + | |
- | < | + | **NOTE: Your DB1 password is NOT the same as your dev2 password. It is found on the .my.cnf file file on your home/ |
- | Then connect to the database of interest | + | |
- | < | + | 1) (The easiest way) Set up a MySQL GUI:\\ |
- | You may also set up a MySQL GUI | + | There are plenty of options to use, but we recommend: |
- (MAC) Sequel Pro has built-in SSH tunneling: http:// | - (MAC) Sequel Pro has built-in SSH tunneling: http:// | ||
- (PC) MySQL Workbench, DB Visualizer | - (PC) MySQL Workbench, DB Visualizer | ||
- (Linux) MySQL Workbench | - (Linux) MySQL Workbench | ||
Example: setting up MySQL workbench with tunneling\\ | Example: setting up MySQL workbench with tunneling\\ | ||
- | {{db1connect.png?600}} | + | {{: |
+ | 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 | ||
+ | < |