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Images Now Available in CRI COVID Data Mart

By | News

In collaboration with the Human Imaging Research Office (HIRO), the CRI is for the first time making images available in our COVID-19 limited data mart. In addition to the structured data already in this data mart, which includes patient demographics, encounters, diagnoses, labs, medications, flow sheets, and procedures, researchers will now have access to HIRO imaging data. Chest radiographs are currently available, and chest CT scans will be added soon. These images are in the DICOM format, and access requires IRB approval for use of the limited data mart.

More information about these images is available in our Medical Imaging Tip Sheet. If you have any questions, please reach out to Julie Johnson at jjohnso3@bsd.uchicago.edu or join us for online office hours.

CRI Seminar Series returns for 2019-2020

By | News

The CRI’s annual series of free training sessions in informatics research tools and techniques returns for the 2019-2020 academic year with a schedule focused around the popular topics of REDCap, high performance computing (HPC), and clinical data analytics. Julissa Acevedo will teach her annual trio of sessions in various aspects of REDCap in November, February, and April, beginning with an introduction to the basics. The CRI’s Manager of Scientific Computing Mike Jarsulic will offer an overview of CRI computing infrastructure in January and an HPC tutorial to coincide with a planned upgrade in May. In March, Tomasz Oliwa, PhD, and Brian Furner will present a session in how to enhance clinical data analytics with the technique of natural language processing.

View the schedule here, and make sure to sign up for the email list to be notified when seminars are available for registration!

Welcome Dipti

By | News

The CRI welcomes our new director, Dipti Ranganathan.

In addition to leading our operations and strategic planning, Dipti also serves as Assistant Dean for Academic & Administrative Information Systems for the Biological Sciences Division (BSD), leading the implementation of new technology solutions to improve strategic decision-making and operational efficiency. She joined the BSD from University of Texas Southwestern, where she led strategic initiatives including technology support for clinical research, research administration, and academic and educational technology. Dipti has a Bachelor’s degree in Industrial Engineering and Operations Research from the University of California, Berkeley, a Master’s degree in Operations Research also from Berkeley, and a Master’s degree in Computer Science from the University of California, San Diego. She is a member of the American Medical Informatics Association and the Association for American Medical Colleges, Group on Information Resources. 

Our former director, Dr. Sam Volchenboum, has been named Dean for Master’s Education in the BSD. He will now lead efforts to develop Master’s education programs in the BSD, beginning with a program in health sciences informatics. The CRI will continue to work with Sam as a research partner.

CRI experts to present tutorial at AMIA 2019 Informatics Summit

By | News

The CRI’s Jorge Andrade, PhD, and Sam Volchenboum, MD, PhD, will join colleagues from Nemours Alfred I. duPont Hospital for Children and Columbia University to present a tutorial session at the American Medical Informatics Association (AMIA) 2019 Informatics Summit this March. 

The tutorial, titled “A Bioinformatics Tutorial for Analyzing Whole Exome Sequencing: Unstructured Data to Variant Interpretation,” will be attended by clinicians, biologists, biomedical researchers, and students who are using or planning to use high-throughput genomics data in their research. It will provide an opportunity to run whole exome sequencing (WES) bioinformatics pipelines for processing raw fastq files into variant call files via the CRI’s high performance computing cluster, as well as hands-on examples for interpreting WES variant data using publicly-available resources.

We are looking forward to joining our colleagues from other institutions and combining our expertise in bioinformatics analysis and high performance computing to offer a valuable experience to AMIA attendees.

CRI’s REDCap expert invited to teach for Vanderbilt’s REDCapU

By | News, REDCap

CRI Business Systems Analyst and resident REDCap expert Julissa Acevedo was recently invited to present for Vanderbilt University’s REDCapU, an online teaching tool to educate REDCap administrators so that they can better support their end users. Julissa presented on the topic of REDCap surveys for a webinar that was attended by 157 registrants from 120 institutions across 19 countries.

Julissa shares her deep knowledge of REDCap with researchers here through the CRI Seminar Series, training materials, and personal consultations.

In new partnership with NCI and Leidos Biomedical, CRI will add radiology images to neuroblastoma data commons

By | News

The CRI is expanding our Pediatric Cancer Data Commons (PCDC) with a new pilot project in partnership with Leidos Biomedical Research, Inc.

As part of the National Cancer Institute (NCI)’s DI-Cubed data integration project, we are using our expertise in data harmonization to develop a process to integrate medical imaging resources into the International Neuroblastoma Risk Group (INRG) Data Commons. This proof-of-concept study will focus on MIBG scans, an important imaging modality for neuroblastoma patients.

The DI-cubed Project is an effort to convert data from various clinical studies into a standardized format, and to demonstrate how this standardization can enable data from multiple studies to be combined, creating larger and more useful cohort sizes and making it possible to share data more easily between institutions. In addition to standardizing data from different sources, the project will bring together data from different domains, such as clinical data, imaging data, and genomic data. We are proud to contribute to this important national initiative. Read more about this project here.

Recent honors for CRI Director

By | News

CRI Director Sam Volchenboum, MD, PhD, is contributing his substantial expertise in pediatric oncology and biomedical informatics to several high-profile committees and advisory boards this year.

Sam has been appointed to two groups related to the National Cancer Institute (NCI) Cancer Research Data Commons (CRDC). He is a member of the Semantic Infrastructure Scientific Committee, a small committee that provides ongoing expert advice and direction for expanding the NCI’s Semantic Infrastructure to address the needs of the CRDC. He also serves on the Scientific and Technical Advisory Board for the CRDC. This Board provides input into the technical direction of the CRDC as well as guidance on how this important program can best serve the cancer research community.

In September, Sam was invited to and participated in the Biden Cancer Summit in Washington, DC. This summit brought together leaders from across regions, sectors, and disciplines to strategize on the best ways to continue improving the culture of cancer care and research. 

Sam’s expertise is being recognized within the University of Chicago, as well. He currently serves as Chair of the Board of Computing Activities and Services, a faculty statutory board appointed by the Provost, as well as sitting on the Provost’s IT Committee, which reviews IT projects and recommends allocations of IT resources in support of the University’s mission and institutional priorities.

CRI developing new community platform with Thirty Million Words

By | News

Building on our successful past and current work with Thirty Million Words (TMW), the CRI is helping build a new community platform for the initiative. TMW, directed by Dr. Dana Suskind, is an innovative, evidence-based intervention program designed to create a population-level shift in the knowledge and behavior of parents and caregivers to optimize foundational brain development in babies and young children, particularly those born into poverty.

Since the project began in 2014, the CRI’s applications development team has been a key collaborator in developing and supporting the informatics operations for TMW and associated studies. We are now expanding our work by building the infrastructure for the TMW Community Platform, a multi-year community-wide demonstration project that will implement TMW interventions through health and social service providers already working at scale in partner communities.

Under the leadership of Director of Applications Development Brian Furner and Sr. Programmer Seong Choi, the CRI is working with a selected development partner and the TMW team to build a technical platform that will facilitate the delivery of TMW interventions and the collection of data for analysis. The platform includes a web application that supports community and user management, participant enrollment and consent, delivery of newborn interventional content, and a dashboard to monitor implementation. Our team is also developing reporting infrastructure for the platform, as well as a demo version of the application that will be used to train TMW’s implementing staff. We expect to deploy the TMW Community Platform in July 2019.

CRI-built CTMS launches successfully

By | CTMS, News

We are happy to announce that ARTEMIS, the enterprise Clinical Trials Management System  developed by the CRI for the University of Chicago, went live today. Beth Martell, Executive Director of the Office of Clinical Research, joined the CRI team in our offices as the first study was entered into the system. 

With the system successfully deployed, our work on ARTEMIS is far from over. As clinical researchers at the University begin to use the system to initiate new trials, we will continue to refine it as well as developing and adding new functionality. CRI Director Sam Volchenboum commented, “I’m so proud to be a part of this amazing team. We built a clinical trials management system from the ground up, with a foundation like nothing else on the market. We’re one big step closer to creating a system that consumes and produces structured data from start to finish.”

CTMS Update: Autumn 2018

By | CTMS, News

The CRI’s successful development of a Clinical Trials Management System (CTMS) for the University of Chicago continues on pace this autumn as we prepare for the launch of the system. After a year of iterative work to develop and test key components, the project is now in the final user acceptance testing phase and is set for deployment in mid-November 2018. Once the CTMS is in production, all new clinical trials at the University will be initiated within it.

With our system, which includes a fully functional front end for budgeting and reporting in addition to managing clinical data, all information for University of Chicago clinical trials will be easily accessible in one place. The CRI has extended our relationship with Bad Rabbit Consulting and will continue to work closely with their research administration experts as we manage and further develop the CTMS after it is in production. We look forward to the successful deployment of this enterprise system that will unify, standardize, and modernize clinical research efforts across the BSD.