Onboarding updates

docs/LabHome/Onboarding/Onboarding.md

@@ -1,11 +1,14 @@
 ---
 layout: default
-title: Onboarding
-parent: Lab Basics
+title: Welcome to PennLINC!
+parent: Onboarding
+grand_parent: Lab Basics
 has_children: true
+has_toc: true
 nav_order: 1
 ---
 
+
 # Welcome to PennLINC!
 
 This page is geared for new lab members soon after they arrive. Below is a checklist of tasks required to get access to relevant systems.  Beyond this, the information on ths site (especially the pages in this "Lab Basics" section) is a good place to start for information on lab meetings, resources for new members, software and environments, and tutorials.
@@ -34,7 +37,7 @@ Once general section-level onboarding is complete (especially  CITI/HIPPA traini
 
 [Github](https://github.com/PennLINC/): all code belongs in our github code repository; our [github pages webpage](https://pennlinc.github.io/) associated with this organization also houses growing knowledge base of tutorials.
 
-[Website](https://www.pennlinc.io/): Our front-facing website. Go to the "team form" under "more" to create your profile so you can appear on the "team" page. Ask Tinashe for this password on Slack.
+[Website](https://www.pennlinc.io/): Our front-facing website. Go to the "team form" under "more" to create your profile so you can appear on the "team" page. The password/instructions for doing so are on the #pennlinc_website slack channel.
 
 Additionally, we use two compute platforms that you will need access to.
 

docs/LabHome/Onboarding/accounts_systems_set-up.md

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+---
+layout: default
+title: Accounts and systems set-up
+parent: Onboarding
+grand_parent: Lab Basics
+nav_order: 4
+---
+
+# Accounts and systems set-up
+
+## Accessing different accounts:
+
+UPHS System Accounts Overview:
+
+- PennKey = University accounts
+    - Use this for anything Penn related/not through health system
+    - Stace should set up your Penn Key account. Once he does, you should get an automated email with a 7-character Penn Key setup code and instructions on how to set up your Penn Key and enroll in two-step verification.
+- UPHS = University of Pennsylvania Health Systems, i.e., hospital accounts
+    - need to enroll in Duo Two-Factor Authentication as well
+    - Stace should email you with your UPHS login information. This should include your Penn ID # and also a temporary password.
+    - Reset your password from the temporary password according to the instructions in the email from Stace.
+    - Access issues and password reset: Call the IS Service Desk at 215-662-7474
+    - Use this for anything Penn Medicine related
+
+- PMACS = IT accounts that services both University & UPHS sides
+    - PMACS hosts “static” datasets – e.g., curated datasets as well as processed derivatives.
+    - Stace will create your PMACS account.
+    - Before attempting to log into any system you must complete the following 7 steps:
+
+        1. Go to [this link](https://reset.pmacs.upenn.edu)
+
+        2. On the right side of the page where it says "Sign In" for your username type in your PennKey username
+
+        3. Use temporary password sent in email from Stace.
+
+        4. Change/Reset your Password, "Old Password" is the temporary one you logged in with. Please make note of the Password Requirements Policies for new Passwords.
+
+        5. To receive Email for when your Password will expire (important!) Click the *Enrollment* Tab.
+
+        6. Complete the setup questions. Choose obvious answers that you will remember.
+
+        7. You can continue to use this service in the future to Reset your Password if you forget it or to Unlock the account if you type in your password wrong too many times.
+
+        If you are having any issues with the reset page, please close out of your browser and hit the refresh page button while on the reset website.
+
+- VPN: Many websites as well as CUBIC and PMACS systems can only be accessed when on the PennMedicine network. When working from home, you will need to connect to VPN to access these resources.
+When using VPN and / or when on PennMedicine network, some websites cannot be accessed. To enable access, download and install the [following certificates](https://cert-install.uphs.upenn.edu/) using your UPHS credentials (instructions provided with certificate download).
+    - Big IP VPN client [Big IP VPN](http://www.uphs.upenn.edu/network/files/BIGIPMacEdgeClient2023.zip) will allow you to connect to all PMACS and UPHS systems. Use your UPHS credentials to connect.
+    - Ivanti VPN client will allow you to connect to all PMACS systems. Use your PMACS credentials to connect.
+
+Setting up email account:
+
+- Stace will set up your Penn Medicine email account, with a temporary password. You will need to login and change your password.
+- If you require help installing or configuring Outlook, please open a support ticket at [help desk](https://helpdesk.pmacs.upenn.edu/)
+
+## Additional Systems to Set Up:
+
+- [Slack](https://pennlinc.github.io/docs/LabHome/Onboarding/Onboarding/pennbbl.slack.com):
+    - Ted can add you onto the slack channel(s) before you start.
+    - *If you have a slack account tied to a different email, and want to change it so it is tied to your Penn email when you get it, Andrew can do this, or follow the instructions [here](https://slack.com/help/articles/207262907-Change-your-email-address).
+- [Google Calendars](https://calendar.google.com/calendar/r):
+    - Slack Ted with your gmail account to have him add you to the google calendar.
+    - Ted posts meeting times each week on slack. In order to schedule an individual meeting, you can create an event on the google calendar on one of the times that says ‘open for meetings’.
+- [Github](https://github.com/PennLINC/): all code belongs in our github code repository; our [github pages webpage](https://pennlinc.github.io/) associated with this organization also houses growing knowledge base of tutorials.
+    - If you do not already have a Github account, follow the instructions to create one [here](https://docs.github.com/en/get-started/start-your-journey/creating-an-account-on-github).
+    - Ask Taylor to be added to the PennLINC Github.
+    - In order to make a new project repository on Github under PennLINC, when you click ‘Create a new repository,’ under ‘Owner’ select PennLINC. There is also the option to use the PennLINC/paper-template.
+- CUBIC:
+    - used for large volumes of parallelizable subject-specific processing jobs
+    - see [CUBIC](https://www.notion.so/Accounts-Systems-Set-up-13c2e9b4cd1980c794e9fd7eaf002b8d?pvs=21) documentation for specific cubic help
+    - create a new project in CUBIC:
+        - *Note: If you would be added to a specific project/not creating a new project, no need to fill out the project form, just submit the online ticket and screenshot.
+
+        - Access the Project_data_use_template.doc document on CBICA Wiki: Main Page > Research projects > 3 Access/New Project Creation > Project Creation Request
+
+        - Fill out the information in the Project_data_use_template.doc & save as a .txt file
+        - Send an email to Ted (”Do you approve of this project folder request?”), and screenshot the conversation with data in frame of approval. Save that as an image.
+        - Save the screenshot & **text file** of Project_data_use_template.doc
+        - Submit ticket:
+            - Go [here](https://pennmedaccess.uphs.upenn.edu/my.policy) —> CBICA Request Tracker —> Home —> Create ticket
+            - ‘Cluster - New Project’ or ‘Cluster - Project Access’
+            - Fill out request with EXACT SAME INFO as just filled in the Project_data_use_template.doc & attaching supporting docs (screenshot).
+            - You should receive an email from CBICA confirming request, can return to Request Tracker to see the status of your ticket

docs/LabHome/Onboarding/coding-guide.md

@@ -1,7 +1,8 @@
 ---
 layout: default
 title: Best practices for coding for scientific computing
-parent: Lab Basics
+parent: Onboarding
+grand_parent: Lab Basics
 nav_order: 3
 has_toc: true
 ---

docs/LabHome/Onboarding/coordinator_specific.md

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+---
+layout: default
+title: Coordinator Specific
+parent: Onboarding
+grand_parent: Lab Basics
+nav_order: 5
+---
+
+# Coordinator Specific
+
+## Overview:
+
+- Admin (Log In and Access)
+- Workday Trainings
+    - CITI and HIPAA
+    - Misc. (MRI and other)
+- Databases/Servers Introduction
+    - Oracle
+    - REDCap
+- Study/Visit-Related Training
+    - Recruitment
+    - Consenting
+    - Payment
+    - MRI
+    - CNB & Adaptive CNB
+    - Adaptive GOA & other clinical interviews (e.g. GOA)
+
+    ---
+
+
+## Log In/Access:
+
+- PennKey
+- UPHS
+- Penn Email/Login (uses HUP log in)
+- Slack (Penn Neuropsych and UPenn MRI)
+- PMACS
+- REDCap (Axis and PMACS)
+- Oracle
+- Saturn
+- ClinCard/Greenphire
+- DaySmart
+- Penn+ Box
+
+---
+
+## Trainings:
+[this link](https://reset.pmacs.upenn.edu)
+
+***HIPAA:***
+
+- HIPAA (UPHS)
+[HIPAA UPHS](https://www.myworkday.com/upenn/learning/course/f5f4bac0e62010016a0082c0acd00000?record=526d324936d99000b7f0a26dc60d0000&type=9882927d138b100019b928e75843018d)
+- HIPAA (General)
+[HIPAA General](https://www.myworkday.com/upenn/learning/course/9b2946e933d91001b7d62c27b9010000?record=8859733ea2fe1000b74cc0920f7e0000&type=9882927d138b100019b928e75843018d)
+
+***CITI:***
+
+- CITI Responsible Conduct of Research Training - UNIV (+ UNIV Program)
+[CITI UNIV](https://www.myworkday.com/upenn/d/inst/15$413382/17816$533.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- CITI Good Clinical Practice (GCP)
+[CITI GCP](https://www.myworkday.com/upenn/d/inst/15$413382/17816$536.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Good Clinical Practice (GCP) Simulation
+[GCP Simulation](https://www.myworkday.com/upenn/d/inst/15$413382/23455$48.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- CITI Protection of Human Subjects Research Training - ORA (+ ORA Program)
+[CITI ORA](https://www.myworkday.com/upenn/d/inst/15$413382/17816$532.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+
+***MRI:***
+
+- MRI Basic Safety Clinical Staff (+ Program)
+[MRI Safety](https://www.myworkday.com/upenn/learning/course/9b2946e933d91001b7dde63474bc0000?record=cd3388946bc41001a09d97970dfe0000&type=9882927d138b100019b928e75843018d)
+- PennCRMS Fundamentals Training: Instructor-led *(register for a live, virtual class)*
+
+Once Above Completed:
+
+- Schedule MRI Safety with Mark Elliot
+
+***Misc.:***
+
+- REDCap: Best Practices for Maintaining HIPAA Compliance and Protecting Personal Health Information (PHI)
+[REDCap](https://www.myworkday.com/upenn/d/inst/15$413382/17816$476.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- IRB 101 - OCR
+[IRB](https://www.myworkday.com/upenn/d/inst/15$413382/17816$772.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Clinical Trial Finance Basics Online Module - OCR 
+[Clinical Trial](https://www.myworkday.com/upenn/d/inst/15$413382/17816$606.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Ethics and Human Subject Protection: A Comprehensive Introduction
+[Ethics](https://www.myworkday.com/upenn/d/inst/15$413382/17816$134.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Penn CR: Full Onboarding Program - Recruitment
+[Penn CR Recruitment](https://www.myworkday.com/upenn/d/inst/15$413382/17816$140.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Penn CR: Full Onboarding - Study Start Up and Management
+[Penn CR Study Start Up](https://www.myworkday.com/upenn/d/inst/15$413382/17816$141.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Study Close Out Overview - OCR
+[Study Close Out](https://www.myworkday.com/upenn/d/inst/15$413382/17816$612.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Penn CR: Full Onboarding Exam
+[Onboarding Exam](https://www.myworkday.com/upenn/d/inst/15$413382/17816$357.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Mandated Reporter Training
+[Mandated Reporter](https://www.reportabusepa.pitt.edu/)
+
+- CNB Training
+[CNB Training](https://redcap.med.upenn.edu/surveys/?s=FZt2ymXi3Lv5yCf3&new.)
+
+- Introduction to Slicer Dicer
+[Slicer Dicer](https://www.myworkday.com/upenn/d/inst/15$413382/17816$9.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+- Training for PennChart SlicerDicer - OCR
+[PennChart Slicer Dicer](https://www.myworkday.com/upenn/d/inst/15$413382/23455$851.htmld?metadataEntryPoint=/upenn/learning/mylearning)
+
+---
+
+## General Study Running Tasks:
+
+- Oracle Training
+    - Each Tab Walk-through
+    - Practical Application - Start to Finish of a Study
+    - Backend Usefulness (data retrievals, etc.)
+- REDCap Training
+    - Walk-through
+- Consent Training
+    - General Format
+    - Practice
+- Study Visit
+    - Start to Finish (to get bearings)
+    - Breakdown
+    - Shadow
+    - Practice/Mock Run
+- CNB Training - Outsourced to CNB team (Anu & Tarlan)
+- GOA Training - Organized by Sage
+- General Things to Go Over:
+    - ClinCard Reports
+    - How to submit IRB modifications
+    - C2/W9 Forms
+    - Tableau
+    - Study Tracker Spreadsheet
+
+
+## Resources:
+
+CRC Onboarding Slide Deck:
+[![CRC Onboarding](/assets/pdfs/crc_onboarding_presentation_v3.pdf)](/assets/pdfs/crc_onboarding_presentation_v3.pdf) 
+
+Clincard Training Slide Deck:
+[![Clincard Training](/assets/pdfs/clincard_penn_chop_training_powerpoint.pdf)](/assets/pdfs/clincard_penn_chop_training_powerpoint.pdf) 
+
+Consenting Slide Deck:
+[![Consenting](/assets/pdfs/consent_review_09_14_2022.pdf)](/assets/pdfs/consent_review_09_14_2022.pdf) 
+
+MRI Safety Slide Deck:
+[![MRI Safety](/assets/pdfs/MRsafety%20presentation%20(1).pdf)](/assets/pdfs/MRsafety%20presentation%20(1).pdf) 

docs/LabHome/Onboarding/first_week.md

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+---
+layout: default
+title: First day/week tasks
+parent: Onboarding
+grand_parent: Lab Basics
+nav_order: 3
+---
+
+# First day/week tasks
+
+## New Hire Checklist:
+[![New Hire Checklist](/assets/pdfs/new_hire_checklist.pdf)](/assets/pdfs/new_hire_checklist.pdf) 
+
+
+
+## First day:
+1. Meet with Onboard@Penn in person
+    1. You can make an appointment online [here](https://kiosk.na4.qless.com/kiosk/app/home/17), but it is not needed.
+    2. Complete section 2 of Form 1-9.
+    3. You must bring original documents with you for identification. List of acceptable documents [here](https://www.uscis.gov/i-9-central/form-i-9-acceptable-documents).
+2. Get PennCard in person
+    1. You can make an appointment online [here](https://penncard.business-services.upenn.edu/appointments), but it is not needed.
+    2. It might take a couple of minutes for your PennCard to give you access to the buildings you need access to, so before you leave Richards it is a good idea to ask someone else in the lab to check their slack & be willing to come let you in if your card doesn’t work at first to get back into Richards.
+3. Complete additional Workday inbox onboarding tasks, such as your W-4.
+
+Both the Onboard@Penn & PennCard offices are located in the Penn Bookstore, up the escalator to the second floor. The offices are next to each other. The Penn Bookstore is about a ~10 min walk from Richards:
+3601 Walnut St, Philadelphia, PA 19104
+
+
+Onboarding@Penn Home Page for additional details:
+https://www.onboard.upenn.edu
+
+
+## First week:
+- Find your Science Sib! Schedule a meeting with them.
+- Coffee chats! Other lab members will reach out to you to grab a coffee and get to know them!
+- Add yourself to the [website](https://www.pennlinc.io):
+    - The password/instructions for creating your profile on the PennLINC front-facing website are on the #pennlinc_website slack channel.

docs/LabHome/Onboarding/index.md

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+---
+layout: default
+title: Onboarding
+parent: Lab Basics
+has_children: true
+has_toc: true
+nav_order: 1
+---
+
+
+# Onboarding
+
+
+

docs/LabHome/Onboarding/penn_hr_materials.md

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+---
+layout: default
+title: Penn HR Materials
+parent: Onboarding
+grand_parent: Lab Basics
+nav_order: 7
+---
+
+# Penn HR Materials
+
+
+### Link to the UPenn HR Site:
+https://www.hr.upenn.edu/
+
+### Neurodevelopment & Psychosis Section Faculty & Staff Handbook:
+[![Staff Handbook](/assets/pdfs/staff_handbook_v1.0.pdf)](/assets/pdfs/staff_handbook_v1.0.pdf) 
+
+### Penn Contact Information:
+[![Contact Information](/assets/pdfs/contact_info.pdf)](/assets/pdfs/contact_info.pdf) 
+
+### Penn Perks:
+[![Perks](/assets/pdfs/penn_perks.pdf)](/assets/pdfs/penn_perks.pdf) 
+
+### Retirement & Savings Guide:
+[![Retirement and Savings](/assets/pdfs/retirement_savings.pdf)](/assets/pdfs/retirement_savings.pdf) 
+
+### Benefits Enrollment Guide:
+[![Benefits](/assets/pdfs/benefits_enrollment.pdf)](/assets/pdfs/benefits_enrollment.pdf) 

docs/LabHome/Onboarding/required_online_trainings.md

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+---
+layout: default
+title: Required online trainings
+parent: Onboarding
+grand_parent: Lab Basics
+nav_order: 6
+---
+
+# Required online trainings
+
+## HIPAA & CITI Training
+
+**HIPAA Training**
+
+- **HIPAA** should be assigned to you in WorkDay in the first day or two, but if it is not, you can search for it under Learning in WorkDay by searching “Protecting Patient Information (HIPAA) (Annual Program)”.
+
+**CITI Modules**
+
+- You will complete **CITI** training here: https://about.citiprogram.org. You should register with your personal email, or if you already have an account, you can affiliate it with the University of Pennsylvania. You will need to complete the Basic Human Subjects Protections and can complete either the Social Behavioral OR Biomedical modules (don’t do both).
+- If you are working on a federally funded research project (which you most likely are), you will also need to complete the **Good Clinical Practice** module on the CITI website. You can complete either the Social Behavioral OR Biomedical module (don’t do both).
+
+*Once completed, send a screenshot of your HIPAA certification in Workday, and send the CITI certificates to Stace. You cannot receive access to any databases or attend any meetings where PHI is discussed until these trainings are completed.*
+
+## Additional Workday Trainings
+
+In addition to CITI and HIPAA training, you will most likely be assigned additional trainings in Workday.
+
+Sign into Workday using your Penn Key username & password (see instructions in ‘Tasks to do before you get here’)
+
+Workday —> Menu —> Learning —> My Learning
+
+- Your required learnings will show up here.
+- In order to see your learning history, click the ‘View Your Learning History’ and it will produce a transcript of the courses/learning you have completed.