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onboarding_affiliates [2016/04/20 11:33]
jmbanda [How to connect to DB1] 		onboarding_affiliates [2019/01/14 20:45]
acallaha
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 ====== Onboarding for affiliates ====== ====== Onboarding for affiliates ======
 ===== Onboarding steps ===== ===== Onboarding steps =====
-  - Get SUNETID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff. + 
-  - Get access to our [[int:lab_information#computing_resources |servers]] (shahlab-dev2, shahlab-db1). Contact Alex Skrenchuk. [[https://itservices.stanford.edu/service/vpn| VPN]] is needed for off-campus access and probably on-campus access as well. +  - Get SUNET ID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff. 
-  - Identify the [[int:database | databases]] you need. Get authorization from database owner and work with your assigned mentor and Alex to arrange for access. Read and agree to DUA. +  - Get access to our servers. Contact Jason Fries. [[https://itservices.stanford.edu/service/vpn|VPN]] is needed for off-campus access and probably on-campus access as well. 
-  - Complete training (HIPAA awareness on Axess, Protection of Human Subjects on CITI) and [[lab_members|upload]] your certificates +  - Identify the [[:int:database|databases]] you need. Get authorization from database owner and work with your assigned mentor and Jason Fries to arrange for access. Read and agree to [[https://shahlab.stanford.edu/_media/dua_for_collaborators_shah_lab.docx|DUA]]. 
-  - Understand our [[int:clinical_study|clinical study workflow]] and [[int:annotation| annotation workflow]] +  - Complete the necessary training 
-  - You are encouraged to set up a wiki page to document your project. [[int:dou_jin| See example.]] +      - IF you will access data containing PHI (e.g. clinical notes), you need to complete the following training: 
-  - For details regarding specific steps, schedule a one-on-one session with the relevant person +        - Protecting Patient Privacy - sign up via [[https://axess.sahr.stanford.edu/group/guest/stars?psft_src=/EMPLOYEE/ELM/c/LM_SS_LEARNING.LM_BROWSE_LEARNER.GBL?type=COURSE&code=PRIV-2019|STARS]] 
-    * Server access: Alex Skrenchuk +        - Protection of Human Subjects - GROUP 7: IRB BioMed/GCP Research - done via [[https://researchcompliance.stanford.edu/hs/new/resources/training/citi.html|CITI]] 
-    * Data use agreement: Nigam Shah +      - IF you will access ONLY de-identified patient data, you need to complete the following training: 
-    * Text processing: Juan Banda +        - Protecting Patient Privacy - sign up via [[https://axess.sahr.stanford.edu/group/guest/stars?psft_src=/EMPLOYEE/ELM/c/LM_SS_LEARNING.LM_BROWSE_LEARNER.GBL?type=COURSE&code=PRIV-2018|STARS]] 
-    * Cohort building: +      - Provide your certificates to Jason to get access 
-      * [[int:clinical_study|Quick guide on querying EMR]]: +  - Get on the right mailing list 
-      * Patient matching +  - Find the person in the lab who can explain the data you will use - talk to them! 
-    * Data analysis:+  - Set up a wiki page to document your project. [[:int:callahan:medical_device_surveillance|See example.]] 
 +  - For details regarding specific resources, schedule a one-on-one session with the relevant person 
 +      * Server access: Jason Fries 
 +      * Data use agreement: Nigam Shah 
 +      * Text processing: Jason Fries 
 +      * Data/terminologies: Ken Jung, Alison Callahan, Vladimir Polony 
  
 ===== Data sharing and Use Agreement ===== ===== Data sharing and Use Agreement =====
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 ===== How to connect to Dev2 ====== ===== How to connect to Dev2 ======
 If you are off-campus (or on the wireless network), you will need [[https://itservices.stanford.edu/service/vpn| VPN]].\\ If you are off-campus (or on the wireless network), you will need [[https://itservices.stanford.edu/service/vpn| VPN]].\\
-Not to be confused with DB1, this only needs a simple SSH command to connect (open a terminal):+SSH command to connect (open a terminal):
  
 <code>ssh <yourusername>@shahlab-dev2.stanford.edu </code> <code>ssh <yourusername>@shahlab-dev2.stanford.edu </code>
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 There are multiple different ways of connecting to the database server. If you are off-campus, you will need [[https://itservices.stanford.edu/service/vpn| VPN]].\\ There are multiple different ways of connecting to the database server. If you are off-campus, you will need [[https://itservices.stanford.edu/service/vpn| VPN]].\\
  
-NOTE: Your DB1 password is NOT the same as your dev2 password. It is found on the .my.cnf file on your home/your_name directories. +**NOTE: Your DB1 password is NOT the same as your dev2 password. It is found on the .my.cnf file file on your home/your_name directories.** 
  
 1) (The easiest way) Set up a MySQL GUI:\\ 1) (The easiest way) Set up a MySQL GUI:\\
onboarding_affiliates.txt · Last modified: 2021/11/23 17:25 by acallaha

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