CODE - COMPREHENSIVE ONCOLOGY DATA & ENGINEERING

CODE - Shared Resource,
Andrew Post, MD, PhD, Director
Andrew.Post@hci.utah.edu
(801) 585-0600

The Comprehensive Oncology Data & Engineering Shared Resource (CODE), provides comprehensive, cost-effective, and high quality information systems that enable Huntsman Cancer Institute (HCI)’s research community to collect and mine data from local, statewide, catchment area, and national sources. Originally called the Research Informatics Shared Resource and renamed CODE in 2025, the Resource has supported cutting edge cancer research at HCI since the Cancer Center’s founding more than 25 years ago. To achieve its mission, CODE staff have extensive expertise in key technological areas:

• Software engineering
• Database design and development
• Application and web development
• Natural language processing
• System design
• Data mining
• Electronic data capture systems
• Vendor product evaluation

CODE supports operations and workflow for all HCI Shared Resources and many other research support teams such as Research Administration, the Clinical Trials Office, the Research Compliance Office, the Oncology Research Information Exchange Network (ORIEN) program, Community Outreach and Engagement (COE), and Population sciences Research Infrastructure Systems & Management (PRISM). CODE’s software and database systems include:

• Cancer Clinical Research (CCR): supports data capture and integration for creating disease registries employed by HCI’s multi-disciplinary Disease Centers.
• Comprehensive Oncology Research Environment (CORE): integrates and exchanges data from multiple locally developed, third party, and vendor systems to enable seamless query and reporting across laboratory, biospecimen, medical record, chart-abstracted data, clinical trials, tumor registry, and population studies.
• CORE Browser (Comprehensive Oncology Research Environment Browser): a new CORE component that implements a web-based research data desktop for accessing and sharing raw sequencing data files and associated analyses stored in Amazon Web Services (AWS) Simple Storage Service (S3) buckets.
• GNomEx: next-generation sequencing laboratory information management system
• Molecular Profiling: clinical somatic testing results from major testing labs used by HCI
• Integrated Query (iQ): self-service query and reporting tool that encompasses nearly all CODE databases
• Research Subject Registry (RSR): study data capture and management system

In addition to these locally developed systems, CODE supports research use of critical data resources from University of Utah Health, and it supports third party and vendor software applications and integrates their data with locally developed tools. These include:

• Enterprise Data Warehouse (EDW): electronic health record data access for research
• Flatiron Health: real world dataset comprising abstracted and deidentified electronic health record data from cancer providers nationwide (identified HCI data abstracted by Flatiron is also available)
• HCI Tumor Registry: captures reportable cancers and treatments from HCI facilities
• LabVantage: Biospecimen management and annotation system, which supports the HCI Biorepository as well as specimen tracking within HCI research laboratories
• OnCore: clinical trials management system suitable for investigator-initiated trials
• REDCap: study data capture and questionnaire system
• SQL Server Reporting Services: data reporting software
• Tableau: reporting and dashboarding software
• Teleform: research questionnaire software
• System for Health Assessment and Population Equity (SHAPE): data visualization tools (Cancer InFocus and Tableau) for identifying cancer burden and control opportunities throughout HCI’s 5-state Mountain West catchment area.

CODE’s work follows industry standard methodologies and takes advantage of the best tools and resources. CODE uses Java (Spring and JEE) and Python (aiohttp) for backend software development, Angular for frontend development, multiple database technologies (SQL Server, MySQL, PostgreSQL, MongoDB), and Docker for deployment. Some of our key software is available as open source. Work is prioritized based on HCI needs as determined by the HCI Research Executive Committee, an internal CODE Advisory Committee comprised of stakeholders and leaders throughout HCI, and user feedback.

HCI CODE Shared Resource Governance
HCI Senior Director Oversight
Aik Choon Tan, PhD
Faculty Advisory Committee Chair
Aik Choon Tan, PhD
Faculty Advisory Committee Members
HCI Research Executive Committee

If use of this resource results in a publication, please acknowledge Huntsman Cancer Institute and our Cancer Center Support Grant by using the following text:

"Research reported in this publication utilized the CODE - Comprehensive Oncology Data & Engineering at Huntsman Cancer Institute at the University of Utah and was supported by the National Cancer Institute of the National Institutes of Health under Award Number P30CA042014. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH."