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onboarding_affiliates [2016/04/20 15:07]
acallaha 		onboarding_affiliates [2021/07/07 13:40]
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 HIPAA awareness training on Axess and [[https://humansubjects.stanford.edu/new/resources/training/citi.html|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]]: +  - Join the lab slack 
-      * 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: Alison Callahan, Vladimir Polony 
  
 ===== 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://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-compute.stanford.edu </code>
  
 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://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 file on your home/your_name directories. +**NOTE: Your DB1 password is NOT the same as your shahlab-compute 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:\\
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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//, a MySQL database (port 3306), tunnel via //shahlab-dev2.stanford.edu//. +- To connect to //shahlab-database.stanford.edu//, a MySQL database (port 3306), tunnel via //shahlab-dev2.stanford.edu//. 
-<code>ssh -L 3306:shahlab-db1.stanford.edu:3306 <yourusername>@shahlab-dev2.stanford.edu -Nf</code>+<code>ssh -L 3306:shahlab-database.stanford.edu:3306 <yourusername>@shahlab-compute.stanford.edu -Nf</code>
 - 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
 <code>mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename></code> <code>mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename></code>
onboarding_affiliates.txt · Last modified: 2021/11/23 17:25 by acallaha

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