Enabling Data Driven Research

Enabling Biomedical Data Driven Research

Bringing you common infrastructure, and consultation services

Mission

Research IT exists to supply infrastructure, tools, and services used by researchers, patients/participants, and clinicians to collect and combine data to make discoveries and to improve human health and wellness.

What we do

Research IT is responsible for several of Stanford's centralized biomedical infrastructure like Stanford's Clinical Data Warehouse (aka STARR, fka STRIDE) and research data management platform like REDCap. Goal of these infrastructure is to advance Stanford's Precision Health mission. Our team designs, develops and maintains these systems. Aside from infrastructure components, Research IT offers a confidential consultation service to Stanford University biomedical researchers on topics related to technology integration; research data capture, management, and analytics; compliance, data privacy & security issues.  

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To common tools, and services

2018 Research IT news

Enabling Stanford mission

Nero Computing for HIPAA Compliant Big Data Analytics launched

Your secure workspace for team science

Research IT in collaboration with SRCC launches Nero Computing, a  secure Big Data analytics workspace for Stanford researchers

In collaboration with Stanford Research Computing Center, Research IT has launched Nero Computing platform, Stanford's first High Risk and PHI compliant research computing resource.

Nero is designed to support Big Data team science. Big Data research benefits from the availability of High Risk and PHI compliant environments, whether for analysis of social network data or health data. Nero brings the analytical communities across different disciplines together to work in a collaborative and secure environment.

Radiology imaging data now integrated with STARR

Researchers can now request large scale Radiology data from Hospitals along with Epic data

Research IT launches phase I of STARR-Radio, a new platform ability to bring Radiology data to Stanford researchers

Research IT has built a cloud scale radiology imaging repository that brings data from Hospital picture archiving and communication system (PACS) into a research archive.  Stanford has half a petabyte of historical radiology data and ~20% of this data is now in the research archive as part of phase I and we continue to add the rest. The data contains different modalties e.g. X-rays, MRI, CT, Ultrasound, Mammography, etc. Research IT has developed robust and scalable de-ID pipelines for X-rays, MRI and CT as part of phase I release and is continuing to build out for rest of the modalities. Researchers can request Research Informatics Center for access to the imaging data. 

STARR-Radio is being developed in collaboration with Research IT faculty committee and Google Healthcare team.

Multi-center PCORI funded study launched

Clinical Strategies for Managing and Reducing Long-Term Opioid Use for Chronic Pain

PCORI study launched to determine whether cognitive behavioral therapy or pain self-management classes are effective at alleviating pain and reducing opioid use among people with chronic pain

EMPOWER, a large PCORI grant funded multi-site trial, under leadership of PI Beth Darnall, was launched in early July 2018. Nearly  ~1300 participants from Stanford Pain Clinic, Stanford Primary Care, Intermountain Health Primary Care, Stieg Pain Clinic and Phoenix VA Primary Care will participate in the research study. This research involves a 3-arm Randomized Controlled Trial comparative effectiveness trial of two evidence-based behavioral treatments, cognitive behavioral therapy for pain and chronic pain self-management, within the context of voluntary, patient-centered opioid tapering. This research builds on Darnall team's first report on "Patient-Centered Prescription Opioid Tapering in Community Outpatients with Chronic Pain".

Research IT team (Teresa Pracht, David Tom and Garrick Olson) deployed an instance of HIPAA compliant CHOIR, customized for the PCORI study, on Google Cloud Platform, to support the multi-site collaborative research and analysis. The study team is using Research IT managed Stanford REDCap for storing study protocols.

Advances in AI in Medicine

Palliative Care Prediction model goes from research to bedside

Palliatve care prediction model developed by Stanford lab is deployed at the Stanford Hospital

Late last year, MIT press review published on a Stanford developed deep learning model for palliative care. Since then, the Shah lab, co-authors of the paper, have developed multiple other models.There is now a gradient boosted model (GBM) and a brand new probabilistic model. The GBM model was deployed at the Stanford Hospital in Jun 2018 (link).

Research IT team member, Tina Seto, worked collaboratively with Nigam Shah's lab and Stanford Health Care to develop the data pipeline that fed the models. First version of the model was developed using data in STARR datalake and the production model was developed using SHC Clarity data to reduce the data latency from 3 days to 1 day.

A new way to access STAnford medicine Research data Repository (STARR)

On Stanford Center of Population Health Science Data Center portal

With Stanford Center for Population Health Science

Under a new DASHER initiative, Research IT's Susan Weber has made a subset of de-identified STARR structured data (STARR-Tahoe) available on PHS Data Center portal. This allows for new way of exploring STARR data that did not exist before. In particular, you can quickly navigate through the metadata and table descriptions, and visualize the distribution of data associated with the variables. STARR-Tahoe will be updated at least annually. 

Stanford Center for Population Health Science (PHS), under the direction of Mark Cullen, Senior Associate Dean for Research, focuses on study of health determinants and outcomes in large populations. It sits at the intersection of medicine and public health, spanning basic and social sciences, enabling integrated research that encompasses virtually every domain of life and society. The Data Center at PHS hosts a diverse collection of high-value “marquee” data sets like Truven Marketscan and partners with several data owners around the world like Born in Bradford

A gold standard for sleep analytics

Alliance Sleep Questionnaire expanded for Stanford Technology Analytics and Genomics in Sleep Program

With Stanford Technology Analytics and Genomics in Sleep (STAGES) Program

Alliance Sleep Questionnaire (ASQ) Stanford Technology Analytics and Genomics in Sleep (STAGES) enrolled their first patient at Stanford Sleep Clinic in April 2018. Remaining 10 sites will go live soon. This is a significant expansion to the existing ASQ program. ASQ has been engineered by Sanjay Malunjkar at Research IT in collaboration with Eileen Leary, Sr. Manager for Clinical Research at the Sleep Clinic. ASQ first went live in Stanford Sleep Clinic in 2011 and has since enrolled 8,000 patients. The STAGES program will expand ASQ to 30,000 patients.

Here are some additional details on the STAGES research program from Eileen. The STAGES study is funded by the Klarman Family Foundation and will collect multi-modal data on 30,000 patients across 11 different sleep clinic sites (across USA and Canada). Sleep disorders and sleep dysregulation impact over 100 million Americans, causing enormous medical consequences including cardiovascular (arrhythmia, hypertension, stroke), metabolic (diabetes, obesity) and psychiatric (depression, irritability, addictive behaviors), to name only a few. Sleepiness costs millions due to workforce errors and accidents. Although the global market for just hypnotic products will reach $76.7 billion by 2019, our fundamental understanding of sleep remains a biological “black box”. This curtails our ability to identify etiologies and thus treat sleep disorders effectively. To address this unmet need, STAGES team proposes to conduct large-scale genomics studies, sleep phenotyping and automated PSG data analysis. The information will be crucial for our understanding of the genetic architecture of sleep and to improve detection, treatment and prevention of sleep disorders. To maximize research potential, all tools and data will be made available to the research community. Specifically, Stanford is responsible for collecting data for 30,000 individuals from multiple sites:

  • On-line sleep/medical history questionnaire (the ASQ, a branching logic questionnaire developed by Harvard University, University of Pennsylvania, University of Wisconsin-Madison, St Luke's Hospital, and Stanford University)
  • In lab nocturnal Polysomnography data (one night PSG)
  • Computerized Neurocognitive Battery (U Penn CNB)
  • Actigraphy over 2-4 weeks (Amazfit Arc)
  • 3-D craniofacial images.
  • Stored biological samples (DNA, plasma, serum) for future biomarker research
  • Genome Wide Association Study (GWAS) data

 

This study will be a landmark that will constitute a gold standard for the analytics of sleep. In collaboration with Prometheus Research, the STAGES program has built a comprehensive data platform to allow for easy data collection and management. 

Point of care clinical trials

Patient-centered opioid tapering with active behavioral treatment

With CHOIR Learning Healthcare Platform

Collaborative Health Outcomes Information Registry (CHOIR) team (Garrick Olson, Teresa Pacht, David Tom, and ex-team member Randy Strauss), working in close collaboration with Prof Sean Mackey, MD, PhD, Chief of the Division of Pain Medicine, delivered the point-of-care clinical trial feature on the CHOIR platform. This method was developed by Stanford University biostatistician Philip Lavori, PhD, and researchers from VA Boston Healthcare System in 2011 as an alternative to expensive, lengthy, double-blind, placebo-controlled clinical trials to compare drugs and procedures that are already in regular use. A layperson summary of the method can be found here and the publication is here.

Research IT is supporting a prestigious new $8.8M PCORI grant, led by Beth Darnall, PhD Clinical Professor of Anesthesiology, that will use a point-of-care clinical trial in patient-centered opioid tapering with active behavioral treatment. The study will include ~1000 participants from Stanford Pain Clinic, Stanford Primary Care, Intermountain Health Primary Care, Stieg Pain Clinic and Phoenix VA Primary Care.