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onboarding_affiliates [2016/02/13 18:17]
acallaha [Data sharing and Use Agreement]
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 +
-    * Text processing: 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. If it does, collaboration is over. +
- +
-  * 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 (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): +
- +
-<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 ====== +
-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]].\\ +
- +
-1) (The easiest way) Set up a MySQL GUI:\\ +
-There are plenty of options to use, but we recommend:\\ +
-      - (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}} +
- +
-2) (Second easiest way) From the command line :\\ +
- +
-- SSH to [[http://shahlab.stanford.edu/onboarding_affiliates?&#how_to_connect_to_dev2|dev2]]\\ +
-- Use Mysql: <code>mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename></code> +
- +
-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//+
-<code>ssh -L 3306:shahlab-db1.stanford.edu:3306 <yourusername>@shahlab-dev2.stanford.edu -Nf</code> +
-- Use your local copy of MySQL (you need to instal the MySQL client on your computer) \\ +
-- Then connect to the database of interest +
-<code>mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename></code>+
  
 +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.1455416252.txt.gz · Last modified: 2016/02/13 18:17 by acallaha