All posts by cpike

CRI to lead development of new BSD-wide clinical trials management system

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Following a competitive proposal process, the Center for Research Informatics has been selected to lead the development of an enterprise clinical trials management system to be used for clinical research efforts across the University of Chicago Biological Sciences Division. The project was officially launched last week at a meeting led by Dean Kenneth Polonsky and attended by the Advisory Group for the project, a broad group of information technology leaders from across the University.

Over the coming months, the CRI will lead the process of designing and building a new system and integrating it with the BSD information systems already in place. We are now building our team for this project – see the job opening for a Senior Program Manager here. As the development phase is completed, this team will lead a new branch of the CRI dedicated to maintaining the system and supporting BSD clinical informatics as a whole.

The CRI is excited to be taking on this ambitious, high-impact project and we look forward to keeping you updated as our team grows and work on the system progresses.

Coming soon: Gardner, our new HPC cluster

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This fall, the CRI will launch our new high performance computing cluster, named Gardner. Available to all BSD/UCM researchers and their collaborators, the new cluster will allow us to accommodate more users and run analyses even more quickly and powerfully.

Gardner will feature:

  • 2.0 GHz Intel Haswell processors across all nodes
  • Infiniband FDR interconnect (56 Gbps)
  • 97 TFLOPs  Actual Performance (Rmax)
  • 88 standard compute nodes (2464 total cores;  128 GB RAM per node)
  • 28 mid-tier compute nodes (784 total cores; 512 GB RAM per node)
  • 4 large memory nodes (112 total cores; 1.28 TB RAM per node)
  • 5 GPU nodes with NVidia Tesla K80 GPUs
  • 1 Xeon Phi nodes with 2 Knight’s Corner coprocessors
  • 350 TB Scratch Space

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“We are converging on a time when the whole world could become a big clinical trial”

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With a recent lawsuit drawing attention to inaccuracies in heart rate data gathered by Fitbits, do wearable health tracking devices have a place in clinical research? CRI Director Sam Volchenboum and Daphne Kis, writing in TechCrunch, look at both sides of the issue and advocate for a path forward that prioritizes both accuracy and usability.

Wearables and other forms of real-time tracking can transform large-scale studies of disease, giving researchers data that is more extensive and more accurate than what patients are able to remember weeks or months later. For example, this UChicago study of IBD patients uses Fitbits to track physical activity, allowing reseachers to find patterns and identify potential symptom triggers. But as Volchenboum and Kis note, “If we want better devices, we must do a better job of telling manufacturers what kinds of measurements and outputs we need. … Standards and data provenance aren’t sexy, but they are absolutely essential to any compelling future vision of clinical research.”

Science Life explores significance of CRI-enabled zebrafish research

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A story today in Science Life highlights the research on zebrafish antigen processing genes, conducted in part by the CRI Bioinformatics Core (read about our contribution here), that was recently published in the Proceedings of the National Academy of Sciences. Read the article to hear from the study’s lead author Sean McConnell, PhD, of the Department of Pediatrics about why these new discoveries are so exciting and how research on zebrafish may translate to advances in our understanding of the human immune system.

CRI Bioinformatics Core research published in PNAS

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A new publication in the Proceedings of the National Academy of Sciences highlights findings about novel antigen processing and presentation genes in zebrafish. This newly identified genetic diversity, discovered by de novo assembly, represents the most extensive diversity yet seen in the antigen processing genes of any species and fills in previously unrecognized knowledge gaps about the evolution of vertebrate adaptive immunity.

This research was enabled in part by our Bioinformatics Core. CRI Director of Bioinformatics Jorge Andrade, PhD, and Bioinformatician Kyle Hernandez, PhD, are co-authors on the paper. They produced the de novo assembly of the genome of a clonal line of zebrafish, using the CRI’s computing infrastructure for this complex data- and memory-intensive task. They then used many tools to determine which de novo scaffolds aligned near the chromosomal region being studied and aggregated these scaffolds to orient and order them across the region.

Read the full paper here, and see more publications enabled by the CRI here.

New publication highlights findings from 1,135 A. thaliana genomes

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A recent publication in the journal Cell details the findings of the first phase of the 1001 Genomes project, in which researchers sequenced and analyzed the genomes of 1,135 strains of Arabidopsis thaliana. This data has led to discoveries about the evolutionary and migratory history of A. thaliana and creates opportunities for new research about how genes and environment interact. Read about how CRI resources contributed to this study.

CRI’s Tarbell cluster used to unlock mysteries of ancient Himalayan populations

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In a study published in the Proceedings of the National Academy of Sciences, a team of researchers from the University of Chicago and other institutions used genomic analysis to provide new evidence for the prehistoric origins of modern Himalayan populations. Dr. Anna Di Rienzo of the Department of Human Genetics used the CRI’s Tarbell high-performance computing cluster, as well as the Computation Institute’s Beagle supercomputer, to sequence the genomes of eight individuals who lived thousands of years in the past and to analyze them in comparison with those of modern Himalayan dwellers. Read more about the study at Science Node.

CRDW fills 500th data request

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We’re celebrating a milestone for the Clinical Research Data Warehouse and the CRI team that keeps it running, as they recently filled their 500th data request since the service was launched in 2012. The datasets curated by this team have contributed to research across more than twenty departments and helped enable dozens of publications. Congratulations, CRDW team!

Watch a demonstration of the new INRG Data Commons

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At the 2016 Advances in Neuroblastoma Research meeting, CRI Director Sam Volchenboum presented a demo of the International Neuroblastoma Risk Group (INRG) Data Commons. The Data Commons, built by a UChicago team including the Center for Research Informatics and Center for Data Intensive Science, brings together phenotypic information and genomic data related to neuroblastoma. Researchers can perform complex cohort discovery, then conduct genomic analysis in a secure, high-performance environment. To learn more about how the Data Commons works, watch Sam’s demo above.

CRIO Bob Grossman launches NCI Genomic Data Commons

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The University of Chicago has publicly launched the National Cancer Institute’s Genomic Data Commons, developed by Chief Research Informatics Officer Bob Grossman. Representing two years of work by Dr. Grossman’s Center for Data Intensive Science and the CRI’s Bioinformatics Core, the GDC brings together genomic and clinical cancer data from multiple sources on a unified platform. Data that was formerly available only piecemeal is now centralized and standardized, making large datasets for cancer research far more accessible to scientists. The GDC is not only an unprecedentedly large repository of this data, it is also linked to tools for analysis and data sharing. Read more about the GDC here.

Vice President Joe Biden announced the GDC’s launch as part of the National Cancer Moonshot Initiative. By democratizing access to data and analysis tools and making it easier for researchers to collaborate, the GDC will contribute significantly to this effort to improve prevention, diagnosis, and treatment of cancer. The CRI is proud to have contributed bioinformatics expertise and resources to this important effort. Learn more about our contribution here.