HSLS MolBio Workshops

All classes will take place in Scaife Hall, Falk Library Classroom B.

This is the tentative schedule. Subject to change. 

The Summer 2024 Medical Student Training Program Schedule

Date	Time	Topic	Instructor(s)
June 6, 2024	4-5:30 pm	All of Us Overview	Richard Steinman, Ansuman Chattopadhyay
June 13, 2024	4-5:30 pm	All of Us Project Planning	Richard Steinman
June 20, 2024	3:30-5:30 pm	All of Us Cohort and Dataset Building	Alexis Cenname, Ansuman Chattopadhyay
June 27, 2024	3:30-5:30 pm	Integrating All of Us Data into Datasets	Alexis Cenname, Ansuman Chattopadhyay
July 11, 2024	3:30-5:30 pm	Statistical Methods, Clean Datasets, Quality Control of EHR Data	Alexis Cenname, Ansuman Chattopadhyay
July 18, 2024	3:30-5:30 pm	Finalize Statistical Methods, Clean Datasets, Quality Control of EHR Data	Alexis Cenname, Ansuman Chattopadhyay
July 25, 2024	3:30-5:30 pm	Student Project Presentations	Ansuman Chattopadhyay, Alexis Cenname, Richard Steinman

 

Week 1 (June 6, 2024)

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All of Us Overview

Pre-Class:   

• Watch the All of Us Researcher Workbench Webinar - NIH (43 minutes) 

In Class:   

• Course overview - PowerPoint Slides
• In class paired discussion, questions of interest to you that could use the AllofUs dataset 
• Begin your registration for AllofUs 

Homework:  

• Register and complete training for AllofUs Registered Tier and Controlled Tier access 
• Optional resources:
  • Watch AoU Researcher Workbench Introduction Video - HSLS (2 hrs.) 
  • All of Us Research Program. Diversity and inclusion for the All of Us research program: A scoping review. PLoS One. 2020 Jul 1;15(7):e0234962. PMC7329113 

Week 2 (June 13, 2024)

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All of Us Project Planning

Pre-Class:   

• Complete AllofUs Registration 

In Class:   

• Continued discussion/development of research questions using AllofUs

Homework:  

• Begin self-paced Canvas learning module on statistics and R (Week 1) – Applying Probability and Data with R to All of Us Datasets 

Week 3 (June 20, 2024)

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All of Us Cohort and Dataset Building

In Class:

• 3:30-4:00 R Self-Learning Module Assistance (as needed)
• 4:00-5:00 Lecture - PowerPoint Slides 
  • Review introductory All of Us material 
  • Discuss CohortBuilder and DatasetBuilder functionality 
  • Introduce HSLS coding templates and their purpose 
• 5:00-5:30  Active Learning 
  • Verify user registration 
  • Search Data Browser for key words pertaining to AoU research questions

Homework:

• Complete Week 2 of Applying Probability and Data with R to All of Us Datasets -- email Alexis (alc244@pitt.edu) if you run into an error.
• Create workspaces for research projects in All of Us Researcher Workbench

Week 4 (June 27, 2024)

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Integrating All of Us Data into Datasets

In Class: 

• 3:30-4:00 R Self-Learning Module Assistance (as needed)
• 4:00-4:30 Lecture - PowerPoint Slides
  • Walk through example of building cohorts, concept sets, and datasets (Atopic Dermatitis & Chronic Sinusitis) 
• 4:30-5:30  Active Learning
  • Create workspaces, cohorts, concept sets, and datasets for analysis 

Homework:

• Complete Weeks 3-4 of Applying Probability and Data with R to All of Us Datasets -- email Alexis (alc244@pitt.edu) if you run into an error.
• Finalize research project group
• Finish building cohorts, concept sets, and datasets in the AoU Researcher Workbench

Week 5 (July 11, 2024)

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Statistical Methods, Clean Datasets, Quality Control of EHR Data

In Class: 

• 3:30-4:00 R Self-Learning Module Assistance (as needed)
• 4:00-4:30 Lecture
  • Atopic Dermatitis and Chronic Sinusitis Analysis Using Jupyter Notebook - PowerPoint Slides
• 4:30-5:30  Active Learning
  • Begin cleaning datasets for analysis in Jupyter Notebook using Python or R

Homework:

• Complete Weeks 5-6 of Applying Probability and Data with R to All of Us Datasets -- email Alexis (alc244@pitt.edu) if you run into an error.
• Continue with dataset cleaning

Week 6 (July 18, 2024)

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Finalize Statistical Methods, Clean Datasets, Quality Control of EHR Data

In Class: 

• 3:30-4:00 R Self-Learning Module Assistance (as needed)  
• No Lecture (0 min) 
• Project Directions
• 4:00-5:30 Active Learning
  • Clean EHR data for merging
  • Appropriately merge AoU dataset for analysis 
  • Discuss possible statistical methods for analyzing research question 

Homework:

• Complete Weeks 7-8 of Applying Probability and Data with R to All of Us Datasets -- email Alexis (alc244@pitt.edu) if you run into an error.
• Work on project slides

Week 7 (July 25, 2024)

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Student Project Presentations

In Class: 

• 3:30-4:00 R Self-Learning Module Assistance (as needed)  
• No Lecture (0 min) 
• 4:00-5:30   Active Learning

  • Discuss/present results of student projects