Clinical and Health Informatics Resources

The SMPH has developed a cloud-based, HIPAA-compliant computing environment called Platform X. Built within Microsoft Azure cloud environment, Platform X provides a safe and scalable data analytics space for SMPH researchers. Platform X isolates the environment for each project, and every research team has dedicated and private data storage and computing resources. Platform X securely delivers research data to the teams’ storage space and creates exclusive, team-dedicated compute instances tailored to the teams’ analytic needs. All data are encrypted at rest and in transit. The necessary computing resources are provided within the environment to conduct data analysis in place, without downloading data. The platform leverages cloud native services as well as Virtual Machines (VMs). Center for Internet Security (CIS) benchmarks are applied to safeguard the computing and data when VMs are in use. Firewalls control all outbound internet access, with extensive centralized logging and auditing. Alerts are generated when potential incidents are identified. Advanced identity governance controls are in place that go beyond what is available on the premise within the SMPH and UW-Madison overall. Disaster recovery plans and data lifecycle management are defined for each project based on specific requirements. Dedicated information security staff are responsible for implementing security and privacy control procedures according to the NIST 800-53 Revision 5.

SMPH has established a generalizable and adaptable ‘Real-World Data Collaborative’ (RWDC) environment within the Platform X using Infrastructure as a Code to support large projects with multi-dimensional data and data linkages. The cloud infrastructure and RWDC include the following components (Figure 1):

• Globus: facilitates secure file transfer from external sites either via web-based uploads or Globus-to-Globus (for large data) transfers. Additionally, Globus stores data transferred to or from Globus. Retains a copy of source data and any data egressed from the platform for inspection/audit.

• Copy Function: creates a working copy of the data ingested via Globus to the Internal Storage Account in the cloud.
• Azure Data Factory: orchestrates the code that processes data in Internal Storage Accounts and integrates those with other data sources and metadata that may exist in the SQL Database.
• Git: enables researchers to maintain their code in a version control system.
• Continuous Integration/Continuous Deployment (CI/CD) Pipelines: deploy code to Azure Data Factory.
• VMs: host a variety of software tools (e.g. R, Python) for researchers to conduct analyses.
  • Bastion provides a secure path for project team members to access the VMs within the Platform X using a Remote Desktop Connection.
• File Share: functions like a network where users across VMs share data and files.
• Backup Vault: all data in Storage Accounts, VMs, File Share, and SQL Database are routinely backed up.
• Security Center: monitors the environment for deviations from established control systems for compliance and suspicious activity. Makes recommendations to improve security posture and sends alerts when investigation is required.

This cloud-based infrastructure facilitates efficient and timely data sharing and submission to national repositories and promotes data sharing in compliance with NIH guidelines.

SMPH is developing an on-premises High-Performance Computing (HPC) environment called Platform R. Platform R is free to use for SMPH members. Housed within a local secure data center, Platform R provides capabilities and tooling for large dataset analytics. Platform R supports these workloads with managed compute, storage, and networking resources. Platform R’s initial HPC cluster, Sett, is comprised of 40 server nodes, 2408 CPU cores, and 25 TB memory. Sett utilizes Slurm to schedule and manage compute jobs. Shared storage, for short-term scratch use, makes 400TB of physical disk space available through a Ceph distributed storage system running on high-speed NVMe drives. Ethernet over fiber networking uses 25GbE connections between compute nodes and 100GbE within storage nodes. The platform additionally connects to UW-Madison facilities for research data inputs and long-term data storage. These connected systems include ResearchDrive, the UW Biotechnology Center, campus’ S3-compatible Object Storage offering, and Globus. Initially, Platform R was not designed to store electronic protected health information (ePHI), although it is being designed for future HIPAA compliance. The technical architecture of this environment is guided by NIST SP 800-223 IPD. PR will be connected to PX for scalability and on-demand bursting.

The Center for High Throughput Computing (CHTC) supports a variety of scalable computing resources and services at UW-Madison. Among the resources available through CHTC is the High throughput compute (HTC) environment with over 20,000 cores and dozens of GPUs. This resource, which is free and shared, is available to all UW researchers. CHTC also provides access points to utilize the resources across the nation. Alongside the standard access to HTC resources, CHTC offers buy-in options for priority access that may be required by high demand or specific needs of a researcher. CHTC’s Research Facilitation team provides users with tools and guidance to manage and automate compute workflow on their resources.

OnCore is a comprehensive Clinical Trial Management System (CTMS) that allows researchers to use one program to manage all components of clinical research, while maintaining consistency and compliance across the institution. Protocols are the foundation of all OnCore functionality and features. Protocol information must be entered in OnCore before building calendars, creating protocol budgets, enrolling subjects, tracking subject visits, or invoicing sponsors. The PC Console (Protocol Coordinator Console) is the central repository for protocol information. Protocol coordinators track protocol ID numbers, objectives, assigned staff, sponsors, participating institutions, regulatory information, investigational drug and device information, and other details of each research study.

Other key features:

• Subject Management: facilitates the tracking of study participants, including enrollment, visits, and other relevant data.
• Financial Management: helps manage budgets, invoicing, and financial aspects of clinical trials.
• Regulatory Compliance: assists in maintaining compliance with regulatory requirements and standards.
• Data Management: supports data collection, monitoring, and reporting throughout the clinical trial lifecycle.
• Integration: our instance of OnCore is integrated with the following external systems:
  • HealthLink EHR (Epic): Patient billing and demographics
  • eBinders (Florence): Regulatory binders
• Reporting and Analytics: provides tools for generating reports and analyzing data related to clinical trials.

Florence eBinders is an electronic system that replaces paper documents and physical binders for human subject research study documents. It is an efficient, 21 CFR Part 11 compliant way to electronically sign, manage, store, and share documents. Features of eBinders include the following:

• Document Management: helps organize and manage essential documents related to clinical trials, ensuring compliance with regulatory requirements.
• Collaboration: facilitates collaboration among study teams, sponsors, and other stakeholders involved in the clinical trial documentation process.
• Workflow Management: supports document workflows, version control, and electronic signatures to ensure document integrity and compliance.
• Regulatory Compliance: maintains compliance with regulatory standards and guidelines related to documentation in clinical trials.
• Site Access: enables secure access for participating sites and sponsors.
• Audit Trail: provides an audit trail of document actions and changes, enhancing transparency and accountability.
• OnCore interoperability: OnCore interfaces with eBinders, making it easier to create new binders and ensure appropriate access credentials are pushed to binders.
• Simple filing: send anything directly to your regulatory binder with the Florence ePrinter tool. This makes it easy for research teams to file PDFs, correspondence, and other important binder contents.

iLab (Agilent Technologies) is a cloud-based platform designed to facilitate core facility management and streamline research administration processes within academic and research institutions. Core facilities are shared resources within organizations that provide specialized services, equipment, or expertise to researchers.

Key features of iLab include:

• Core Facility Management: iLab helps manage core facilities by providing tools for scheduling equipment, tracking usage, and managing billing and invoicing.
• Service Requests: Researchers can submit service requests to core facilities through the iLab platform, streamlining the process of accessing specialized services.
• Resource Scheduling: The system allows for the scheduling of equipment, services, and resources within core facilities, helping to avoid conflicts and optimize utilization.
• Billing and Invoicing: iLab facilitates the tracking of resource usage and automates billing processes, helping core facilities manage financial transactions efficiently.
• Reporting and Analytics: The platform includes reporting tools to generate insights into resource usage, financials, and other relevant data.

REDCap (Research Electronic Data Capture) is a largely self-service, secure, web-based application used for building and managing data collection forms. REDCap provides data management functionality by allowing the development of electronic instruments and surveys to support data capture for research studies, including those that involve protected health information (PHI). REDCap can also be used to collect data for quality improvement and operational support projects.

REDCap provides:

• An intuitive interface (with optional data validation for data captured on forms and surveys).
• Audit trails for tracking data manipulation and export procedures.
• Export procedures for seamless data downloads to common statistical packages (e.g. SPSS, SAS, Stata, & R).
• Reporting capabilities.
• Procedures for importing data from external sources.

UW Health’s Health Link is a secure, web-based application for connecting private and referring physicians, skilled nursing and long term care facilities and their staff to Main Line Health’s electronic medical record. The Health Link tool and the underlying electronic medical records database and system are both developed by Epic Systems Corporation.

Health Link helps to integrate clinical care and research to support patient safety, protocol fidelity, and regulatory compliance. There are several self-service and custom tools available within Health Link to facilitate clinical research workflows such as:

• Assessing study feasibility
• Recruiting new participants
• Tracking enrolled participants
• Entering orders for participants
• Documenting research related care
• External research monitoring
• Communicating securely with research and clinical staff
• Billing for research

Much of Health Link research functionality is dependent on use of the clinical trials management systems, OnCore, which is interfaced with Health Link.