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onboarding_affiliates [2021/07/07 13:40]
acallaha
onboarding_affiliates [2021/11/23 17:25]
acallaha
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 ====== Onboarding for affiliates ====== ====== Onboarding for affiliates ======
-===== Onboarding steps ===== 
  
-  - Get SUNET ID to access the Stanford network. External collaborators will require sponsorship from a Stanford staff. +See the sections on 'Getting access to data' and 'Being part of the groupin the [[https://docs.google.com/document/d/1OyBTevN75HcuiA4hvfqaKuXxE3V7FLjAM8_wbELNxks/edit#|Onboarding Google Doc]].
-  - 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://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]] +
-        - 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://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]] +
-      - Provide your certificates to Jason to get access +
-  - Join the lab slack +
-  - 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: Alison Callahan, Vladimir Polony +
- +
- +
-===== 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 shahlab-compute (formerly 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-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 shahlab-database (formerly 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 shahlab-compute password. It is found on the .my.cnf file file on your home/your_name directories.**  +
- +
-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\\ +
-{{:int:shahlab_db_ssh_tunnel1.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-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>+
onboarding_affiliates.txt · Last modified: 2021/11/23 17:25 by acallaha