Data Science Garage: Building Tools for Genomics Research

Where We Work

Knight Cancer Research Building @ South Waterfront

Across from OMSI and right by Tilikum Crossing

Scientific Problem

How can we find actionable insights in a disease as complex as cancer?

Scientific Problem

How do we integrate data to extract meaningful insights?

• ETL (Extract, Transform, Load)

  • FHIRizer – Transforms GDC, Cellosaurus, HTAN data into FHIR graph representation.

  • Snakemake & Airflow – Automate and orchestrate ETL workflows.

Bringing It All Together with Python

Data Standards, ETL, and Management

• Management

  • GRaph Integration Platform (GRIP) - a powerful  graph query engine designed to span across multiple database backends.

  • Gen3 – Data commons for storage, querying, and management.

• Standards

  • Pydantic – Validates and enforces FHIR schema.

  • GA4GH (Global Alliance for Genomics & Health) – Establishes global       standards for genomic data interoperability.

  • Pathway Databases (Pathway Commons, Reactome) – Structure & standardize biological context through molecular interaction graphs.

Management

ETL

Standards

Bringing It All Together with Python

Data Standards, ETL, and Management

GRIP & FHIR

Querying TCGA BRCA Data with subtype labels for classification

Subtype Classification with Neural Networks

ML modeling and Shapley Feature Extraction

Pathway Enrichment Analysis

Extracting Biological Insights from Gene Set Results

Nasim Sanati (she/her)
Computational Biologist
@teslajoy

Quinn Wai Wong (he/him)
Research Software Eng.
@quinnwai

Kyle Ellrott (he/him)
PI + Associate Professor 
@kellrott

Liam Beckman
Research Software Eng.
@lbeckman314

Brian Walsh (he/him)
Sr. Research Software Eng.
@bwalsh

Jordan Tagle (she/her)
Computational Biologist
@jordan2lee

Matthew Peterkort (he/him)
Research Software Eng.
@matthewpeterkort

Data Science Garage Team

Code + Stunning Sunrise + Local Coffee + Great Team

Follow us along @ https://ellrottlab.org/

Code + Slides!