Differences

This shows you the differences between two versions of the page.

--- onboarding_affiliates [2015/07/01 16:56]
jmbanda [How to connect to Dev2]
+++ onboarding_affiliates [2021/07/07 13:40]
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.
+  - 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 training (HIPAA awareness on Axess, 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:
-    * Annotation: 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 =====
@@ Line 22: / Line 28: @@
   * 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 ======
+===== How to connect to shahlab-compute (formerly dev2) ======
-If you are off-campus, 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.
-===== How to connect to DB1 ======
+===== How to connect to shahlab-database (formerly db1) ======
-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]].\\
-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>
+**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.**
-Then connect to the database of interest
-<code>mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename></code>
+) (The easiest way) Set up a MySQL GUI:\\
-You may also 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}}
+{{: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-database.stanford.edu//, a MySQL database (port 3306), tunnel via //shahlab-dev2.stanford.edu//.
+<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) \\
+- Then connect to the database of interest
+<code>mysql -h localhost -P 3306 -u<yourusername> -p<yourpassword> <databasename></code>

Shah Lab

User Tools

Site Tools

Differences

Page Tools