E-seminar: A Pragmatic Approach to Modeling Human Disease with Clinical Data

The Center for Translational Data Science will be hosting Dr. Theresa L. Walunas (she/her/hers) on Friday, September 17th at 12pm to host a talk titled “A Pragmatic Approach to Modeling Human Disease with Clinical Data.” Dr. Walunas is an Assistant Professor in the Division or General Internal Medicine and Geriatrics in the Department of Medicine at Northwestern University Feinberg School of Medicine.

Human diseases can be challenging to represent in animal models. But what is the alternative? "Real World" clinical data from electronic health records presents an opportunity to develop representations of complex human conditions, provided that the research community understands the strengths and challenges inherent to the data. Developing a pragmatic approach to using electronic health record data is the first step to unlocking its research potential. Data science and informatics professionals who understand this data and how to connect it to primary mechanistic and social science data will be essential to the future of research in this space.

CTDS is awarded a major federal contract to host a new COVID-19 medical imaging resource center

“A new center hosted at the University of Chicago — co-led by the largest medical imaging professional organizations in the country — will help tackle the ongoing COVID-19 pandemic by curating a massive database of medical images to help better understand and treat the disease.

Led by Maryellen Giger, PhD, of UChicago, along with leaders from the American College of Radiology (ACR), Radiological Society of North America (RSNA), and American Association of Physicists in Medicine (AAPM), the Medical Imaging and Data Resource Center (MIDRC) will create an open source database with medical images from thousands of COVID-19 patients. Funding is from the National Institute of Biomedical Imaging and Bioengineering at the National Institutes of Health (NIH).

The MIDRC is responding to an unmet need of the medical imaging community as doctors and scientists seek to better understand SARS-CoV-2, the virus that causes coronavirus disease 2019, or COVID-19, and its effects on the human body. By collecting and integrating images and their data via a dynamic, secure networked system, the MIDRC will provide a large-scale, open, common framework to enable technological advancements, guide researchers’ validation and use of AI (artificial intelligence), and translate clinical systems for the best patient management decisions.”

Full article from UChicago Medicine

E-seminar: From Combination Puzzles to the Natural Sciences with Dr. Forest Agostinelli

The Center for Translational Data Science is proud to announce that we will be hosting Dr. Forest Agostinelli on July 9th at 11am CST for a seminar on his work building AI agents that learn to solve puzzles and how this relates to the natural sciences. Dr. Agostinelli is an Assistant Professor at the AI Institute in the Department of Computer Science and Engineering at the University of South Carolina. He received his B.S. from the Ohio State University, his M.S. from the University of Michigan, and his Ph.D. from the University of California, Irvine under Professor Pierre Baldi. His group conducts research in the fields of deep learning, reinforcement learning, search, explainability, bioinformatics, neuroscience, and chemistry. In this talk, Dr. Agostinelli will present DeepCubeA, a deep reinforcement learning and search algorithm that can solve the Rubik’s cube, and six other puzzles, without domain specific knowledge. Next, he will discuss how solving combination puzzles opens up new possibilities for solving problems in the natural sciences. Finally, he will show how problems we encounter in the natural sciences motivate future research directions in areas such as explainable artificial intelligence and education. A demonstration of their work can be seen at http://deepcube.igb.uci.edu/.

Pride Month Presentation

On June 30th, the Center for Translational Data Science will be hosting UChicago’s Assistant Provost and Executive Director of the Center for Identity + Inclusion, Ravi Randhava, to speak at a special Pride Month Lunch and Learn. This presentation will focus on educating CTDS staff on LGBTQ history and campus/community resources. All of CTDS is welcome to attend this special remote session. Zoom information is available on the CTDS group calendar.

E-seminar: Childhood Cancer Data Lab: Researcher Audiences & Lessons Learned (So Far)

The Center for Translational Data Science is proud to announce that we will be hosting Dr. Jaclyn Taroni on June 11th at 11am CST for a seminar on different researcher audiences the Childhood Cancer Data Lab is intended to serve. Dr. Jaclyn Taroni has recently taken over the Director role at the Childhood Cancer Data Lab, a program of Alex's Lemonade Stand Foundation, after serving as the Principal Data Scientist for nearly 3 years. The Data Lab serves multiple pediatric cancer research audiences. In this talk, Dr. Taroni will cover the lab's current understanding of the needs of different audiences and share experiences building software products, creating training workshop content, and using large heterogeneous datasets to inform analyses of rare disease data.

Summer 2021 Internship Applications are now closed

Our summer internship application is now closed. Thank you to all who applied. We encourage you to apply for future opportunities with the University of Chicago.

Bronx Center for Science and Mathematics - Careers discussion

On April 23rd the Bronx Center for Science and Mathematics hosted Dr. Kyle Hernandez from the Center for Translational Data Science for a session on careers in bioinformatics. This presentation focused on defining the field of bioinformatics and its real-world application. He also discussed his career path and his work managing a team of bioinformaticians, research programmers, and clinical data specialists here at CTDS.

Summer 2021 Internship Applications are now open!

We are accepting applications for our 2021 Summer Internships! Interns will contribute toward biomedical research through analytical solutions and will develop technical skills across data engineering, data science, bioinformatics, and software engineering. Interns will have opportunities to learn from staff mentors with experience building petabyte-scale research infrastructure.

COV-IRT 1-Year Symposium & Panel Discussion

On March 31, 2021 the COVID-19 International Research Team hosted their virtual annual symposium. Keynote speakers included Dr. Duncan MacCannell from the CDC, Dr. Sharon Peacock from the University of Cambridge, David Jaffray and Andrew Futreal from MD Anderson Cancer Center, and Don Milton from the University of Maryland School of Public Health. Dr. Kyle Hernandez from the Center for Translational Data Science moderated a session with speakers from NASA Ames Research Center, Signature Science, Real Networks, and Baylor College of Medicine on modeling, masks, and microbiomes.

University of Georgia Institute of Bioinformatics Invited Seminar

On February 5th the University of Georgia Institute of Bioinformatics hosted Dr. Kyle Hernandez from the Center for Translational Data Science for a seminar on large scale bioinformatics in the Genomic Data Commons. His seminar defined the term “data commons” and discussed its application, focusing on the genomic data harmonization systems in the GDC. He also discussed the GDC Pipeline Automation System (GPAS), its core database and data import, as well as its workflow.

University of Arkansas - Data Science Career Panel

The University of Arkansas hosted Dr. Kyle Hernandez, Gina Kuffel, and Zhenyu Zhang from the Center for Translational Data Science on January 25th for a panel on the application of data science in a non-tenure track setting. Data scientists collect, process, and analyze data to examine and predict meaningful trends in a variety of fields. Creating insights from structured and unstructured information is a critical form of statistical application. Data scientists are often found in positions related to medicine, marketing, finance, and business.

Webinar: GDC Bioinformatics Pipelines

Date: Monday, September 30, 2019

Time: 2:00 PM - 3:00 PM (EDT)

Location: Web Conference (See WebEx information below)

Speakers:

Dr. Zhenyu Zhang, Ph.D, GDC Bioinformatics Manager, University of Chicago

Colin Reid, GDC User Services, University of Chicago

The GDC bioinformatics pipelines support the alignment of DNA and RNA sequence data against a common reference genome build, and the generation of derived data. GDC pipelines are implemented using data processing software and algorithms selected in consultation with the expert genomics community. This webinar will provide an overview of GDC bioinformatics pipelines and demonstrate how generated data is made available through GDC analysis tools.

Webinar: Gen3 Data Exploration

Join us as we walk through Gen3’s services and demonstrate how researchers can bring data into Gen3 and get access to a data ecosystem with open-source tools to drive scientific discovery. During this webinar we will demonstrate how to explore and analyze cancer cell line data in Gen3.

User Spotlight featuring Riyue Bao, PhD

View fullsize

Webinar: Using Jupyter Notebooks with Gen3

Join us as we walk through Gen3’s services and demonstrate how researchers can bring data into Gen3 and get access to a data ecosystem with open-source tools to drive scientific discovery. During this webinar we will dive into the details of data science with Gen3 and how Jupyter Notebooks work with Gen3