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onboarding_affiliates [2016/11/02 17:50] jmbanda [How to connect to DB1] |
onboarding_affiliates [2021/01/20 11:54] jfries |
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====== Onboarding for affiliates ====== | ====== Onboarding for affiliates ====== | ||
===== Onboarding steps ===== | ===== Onboarding steps ===== | ||
+ | |||
- Get SUNET ID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff. | - 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 the necessary training | - Complete the necessary training | ||
- | - IF you will access | + | - IF you will access |
- | - Protecting Patient Privacy - contact Shauna Cruz (shaunalc@stanford.edu) to get signed up via LawRoom | + | - Protecting Patient Privacy - sign up via [[https:// |
- | - Protection of Human Subjects - GROUP 1: IRB REQUIRED FOR MEDICAL RESEARCH INVESTIGATORS AND STAFF - done via {{https://humansubjects.stanford.edu/ | + | - Protection of Human Subjects - GROUP 7: IRB BioMed/GCP Research |
- | - IF you will access ONLY db1, you need to complete the following training: | + | - IF you will access ONLY de-identified patient data, you need to complete the following training: |
- | - HIPAA Certification for Workforce Members who Do Not Work with PHI - contact Shauna Cruz (shaunalc@stanford.edu) to get signed | + | - Protecting Patient Privacy |
- | - Upload your certificates at: http://shahlab.stanford.edu/ | + | - Provide your certificates to Jason to get access |
- | | + | - Get on the right mailing list |
- | - You are encouraged | + | - Find the person in the lab who can explain the data you will use - talk to them! |
- | - For details regarding specific | + | - Set up a wiki page to document your project. [[:int:callahan: |
- | * Server access: | + | - For details regarding specific |
- | * Data use agreement: Nigam Shah | + | * Server access: |
- | * Text processing: | + | * Data use agreement: Nigam Shah |
- | * Cohort building: | + | * Text processing: |
- | * [[int: | + | * Data/ |
- | * Patient matching | + | |
- | * Data analysis: | + | |
===== Data sharing and Use Agreement ===== | ===== Data sharing and Use Agreement ===== | ||
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* 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 shahlab-compute (formerly dev2) ====== |
If you are off-campus (or on the wireless network), you will need [[https:// | 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. | 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 shahlab-database (formerly 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/ | + | **NOTE: Your DB1 password is NOT the same as your shahlab-compute |
1) (The easiest way) Set up a MySQL GUI:\\ | 1) (The easiest way) Set up a MySQL GUI:\\ | ||
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3) (hard and confusing) Create a tunnel from the database server to your computer: | 3) (hard and confusing) Create a tunnel from the database server to your computer: | ||
- | - To connect to //shahlab-db1.stanford.edu//, | + | - To connect to //shahlab-database.stanford.edu//, |
- | < | + | < |
- Use your local copy of MySQL (you need to instal the MySQL client on your computer) \\ | - Use your local copy of MySQL (you need to instal the MySQL client on your computer) \\ | ||
- Then connect to the database of interest | - Then connect to the database of interest | ||
< | < |