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onboarding_affiliates [2015/07/01 16:56]
jmbanda [How to connect to Dev2]
onboarding_affiliates [2021/11/23 17:25] (current)
acallaha
Line 1: Line 1:
-====== Onboarding for affiliates ===== +====== Onboarding for affiliates ======
-===== 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. +
-  - 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. +
-  - Complete training (HIPAA awareness on Axess, Protection of Human Subjects on CITI) and [[lab_members|upload]] your certificates +
-  - Understand our [[int:clinical_study|clinical study workflow]] and [[int:annotation| annotation workflow]] +
-  - You are encouraged to set up a wiki page to document your project. [[int:dou_jin| See example.]] +
-  - For details regarding specific steps, schedule a one-on-one session with the relevant person +
-    * Server access: Alex Skrenchuk +
-    * Data use agreement: Nigam Shah +
-    * Annotation: Juan Banda +
-    * Cohort building: +
-      * [[int:clinical_study|Quick guide on querying EMR]]: +
-      * Patient matching +
-    * Data analysis: +
- +
-===== Data sharing and Use Agreement ===== +
- +
-  * Use of the data will be restricted to research questions outlined and agreed upon in advance. +
- +
-  * 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 is allowed, and will be properly secured, accounted, and discarded in a timely fashion per the DUA. +
- +
-  * 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, 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): +
- +
-<code>ssh <yourusername>@shahlab-dev2.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.  +
- +
-===== How to connect to DB1 ====== +
-If you are off-campus, you will need [[https://itservices.stanford.edu/service/vpn| VPN]].\\ +
-To connect to //shahlab-db1.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> +
-Then connect to the database of interest +
-<code>mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename></code> +
-You may also set up a MySQL GUI +
-      - (MAC) Sequel Pro has built-in SSH tunneling: http://www.sequelpro.com/ +
-      - (PC) MySQL Workbench, DB Visualizer +
-      - (Linux) MySQL Workbench +
-Example: setting up MySQL workbench with tunneling\\ +
-{{db1connect.png?600}}+
  
 +See the sections on 'Getting access to data' and 'Being part of the group' in the [[https://docs.google.com/document/d/1OyBTevN75HcuiA4hvfqaKuXxE3V7FLjAM8_wbELNxks/edit#|Onboarding Google Doc]].
onboarding_affiliates.1435795007.txt.gz · Last modified: 2015/07/01 16:56 by jmbanda