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onboarding_affiliates [2015/07/29 15:58] nigam [Onboarding steps] |
onboarding_affiliates [2018/01/26 13:00] acallaha [Onboarding steps] |
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- | ====== Onboarding for affiliates ===== | + | ====== Onboarding for affiliates |
===== Onboarding steps ===== | ===== Onboarding steps ===== | ||
- | - Get SUNETID | + | - Get SUNET ID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff. |
- | - Get access to our [[int: | + | - Get access to our servers. Contact |
- | - Identify the [[int: | + | - Identify the [[int: |
- | - Complete training (HIPAA awareness on Axess, Protection of Human Subjects on CITI) and [[lab_members|upload]] your certificates | + | - Complete |
- | - Understand our [[int:clinical_study|clinical study workflow]] and [[int:annotation| annotation workflow]] | + | - IF you will access data containing PHI (e.g. clinical notes), you need to complete the following training: |
- | - You are encouraged | + | - Protecting Patient Privacy - sign up via [[https:// |
- | - For details regarding specific | + | - Protection of Human Subjects - GROUP 7: IRB BioMed/GCP Research - done via [[https:// |
- | * Server access: | + | - 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:callahan: | ||
+ | - For details regarding specific | ||
+ | * Server access: | ||
* Data use agreement: Nigam Shah | * Data use agreement: Nigam Shah | ||
- | * Text processing: | + | * Text processing: |
- | * Cohort building: | + | * Data/ |
- | * [[int: | + | |
- | * Patient matching | + | |
- | * Data analysis: | + | |
===== 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 ====== | ===== How to connect to Dev2 ====== | ||
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===== How to connect to DB1 ====== | ===== 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:// | 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:\\ | 1) (The easiest way) Set up a MySQL GUI:\\ | ||
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- (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 :\\ | 2) (Second easiest way) From the command line :\\ | ||
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- Then connect to the database of interest | - Then connect to the database of interest | ||
< | < | ||
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