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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.

Schedule

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

This is the tentative schedule. Subject to change. 

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

 

Course Materials

Week 1 (June 6, 2024)


All of Us Overview

 

Pre-Class:   

In Class:   

Homework:  

  • Register and complete training for AllofUs Registered Tier and Controlled Tier access 
  • Optional resources:

Week 2 (June 13, 2024)


All of Us Project Planning

 

Pre-Class:   

  • Complete AllofUs Registration 

In Class:   

  • Continued discussion/development of research questions using AllofUs

Homework:  

Week 3 (June 20, 2024)


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:

Week 4 (June 27, 2024)


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:

Week 5 (July 11, 2024)


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:

Week 6 (July 18, 2024)


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:

Week 7 (July 25, 2024)


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