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--- onboarding_affiliates [2015/07/29 15:58]
nigam [Onboarding steps]
+++ onboarding_affiliates [2018/01/26 15:02]
nigam [How to connect to Dev2]
@@ 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 SUNET ID 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 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 Alex to arrange for access. Read and agree to DUA.
+  - 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 training (HIPAA awareness on Axess, Protection of Human Subjects on CITI) and [[lab_members|upload]] your certificates
+  - Complete the necessary training
-  - Understand our [[int:clinical_study|clinical study workflow]] and [[int:annotation| annotation workflow]]
+      - IF you will access data containing PHI (e.g. clinical notes), you need to complete the following training:
-  - You are encouraged to set up a wiki page to document your project. [[int:dou_jin| See example.]]
+          - 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]]
-  - For details regarding specific steps, schedule a one-on-one session with the relevant person
+          - Protection of Human Subjects - GROUP 7: IRB BioMed/GCP Research - done via [[https://researchcompliance.stanford.edu/hs/new/resources/training/citi.html|CITI]]
-    * Server access: Alex Skrenchuk
+      - 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: Juan Banda
+    * Text processing: Jason Fries
-    * Cohort building:
+    * Data/terminologies: Ken Jung, Alison Callahan, Vladimir Polony
-      * [[int:clinical_study|Quick guide on querying EMR]]:
-      * Patient matching
-    * Data analysis:
 ===== Data sharing and Use Agreement =====
@@ Line 22: / Line 27: @@
   * 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.
+  * __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
+  * 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):
+SSH command to connect (open a terminal):
 <code>ssh <yourusername>@shahlab-dev2.stanford.edu </code>
@@ Line 36: / Line 41: @@
 ===== 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:\\
@@ Line 43: / Line 50: @@
       - (Linux) MySQL Workbench
 Example: setting up MySQL workbench with tunneling\\
-{{db1connect.png?600}}
+{{:int:shahlab_db_ssh_tunnel1.png?600|}}
 ) (Second easiest way) From the command line :\\
@@ Line 57: / Line 64: @@
 - Then connect to the database of interest
 <code>mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename></code>

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