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--- onboarding_affiliates [2018/01/26 15:02]
nigam [How to connect to Dev2]
+++ onboarding_affiliates [2021/11/23 17:25] (current)
acallaha
@@ Line 1: / Line 1: @@
 ====== Onboarding for affiliates ======
-===== Onboarding steps =====
-  - Get SUNET ID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff.
-  - 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.
-  - 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]].
-  - Complete the necessary training
-      - IF you will access data containing PHI (e.g. clinical notes), you need to complete the following training:
-          - Protecting Patient Privacy - sign up via [[https://starsexpress.stanford.edu/index.html?ref=LM_SS_LEARNING.LM_BROWSE_LEARNER.GBL&type=COURSE&code=PRIV-0010|STARS]]
-          - Protection of Human Subjects - GROUP 7: IRB BioMed/GCP Research - done via [[https://researchcompliance.stanford.edu/hs/new/resources/training/citi.html|CITI]]
-      - IF you will access ONLY de-identified patient data, you need to complete the following training:
-          - Protecting Patient Privacy - sign up via [[https://starsexpress.stanford.edu/index.html?ref=LM_SS_LEARNING.LM_BROWSE_LEARNER.GBL&type=COURSE&code=PRIV-0010|STARS]]
-      - Upload your certificates at: http://shahlab.stanford.edu/lab_members
-  - Get on the right mailing list
-  - Find the person in the lab who can explain the data you will use - talk to them!
-  - 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
+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]].
-===== 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]].\\
-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]].\\
-**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.**
-) (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\\
-{{:int:shahlab_db_ssh_tunnel1.png?600|}}
-) (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>
-) (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>

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