SCIENCE ON DaLI

The following gives information about the research groups, projects, and publications related to DaLI

Supported Projects
Search for Dark Matter with Xenon-based Technology
Dr. Grandi’s research focuses on searching for dark matter by looking at rare interactions in specialized low-background detectors. As a member of the XENON-1T Collaboration, he developed two-phase noble liquid technology, where dark matter interacts with liquefied Xenon in a controlled detector which allows researchers to identify signals caused by dark matter particles among the overwhelming background caused by natural radioactivity (1-3]. A new, 3.3 ton Xenon detector (XENON1T) is in production at the Gran Sasso Underground Laboratory in Italy. The detector will be 100 times more sensitive than the current leading experiment. Data collection is set to begin in early 2016. The XENON1T detector (Figure 2) will generate approximately 200GB of raw data per day, and during calibration it will produce up to 30TB of raw data per day. Acquired data will be sent out to the European GRID and to a server hosted on DaLI where it will be made available to XENON1T collaborators. Once on DaLI, dedicated algorithms will process and reconstruct the scintillation events. Access to DaLI will afford a staging storage capacity and sharing capabilities, and the improved 1/0 capabilities afforded by the non-volatile memory of DaLI will improve processing times of the massive observational data.
Cosmological Research with the 10-meter South Pole Telescope
Carlstrom and colleagues lead the South Pole Telescope (SPT) collaboration. Through two surveys, SPT-SZ and SPT-pol, the SPT collaboration provided insights into the structure of galaxies and expanded the understanding of physics immediately following the Big Bang. The third generation detector SPT-3G will be installed in 2016 and will be 20 times more sensitive than the previous detector. This increased sensitivity will allow researchers to estimate the mass of neutrino particles and refine the Standard Model of Physics. These detectors are expected to generate over 600TB of data per year. DaLI will facilitate the transfer of SPT data from its base in Antarctica and accelerate simulation-processing throughput.
Particle Astrophysics with VHE Gamma-Ray Detectors
Wakely and collaborators conduct very high-energy (VHE) astrophysics research. The Cherenkov Telescope Array (CTA) will improve on the sensitivity of the current generation of telescopes by a factor of 10 and will produce as much as 200TB of data per year at peak operation. The two CTA detector sites (Chile and the Canary Islands) are remote and will not contain the infrastructure needed to support large-scale data hosting. DaLI will provide a storage platform with tight integration to high-performance computing clusters, enabling the Chicago group to serve as a US­based high-capacity distribution site and play a leadership role in developing advanced simulation and analysis methods.
The Sustainability of Riparian Forests in Expanding Amazonian Agricultural Landscapes and Disrupted Nitrogen Cycles in the Brazilian Amazon
Dr. Christopher Neill at MBL, in collaboration with Argonne National Laboratory (Argonne) and Woods Hole Research Center collect observational datasets in the Amazon to study the effects of land cover change, hydrology, and land-atmospheric processes. Their field sites collect real-time data on carbon exchange, stream flow, water levels, and records from climate stations, and game cameras. These data are paired with satellite images, and used to simulate the Amazon regional-scale climate. Climate model outputs can then be analyzed to ask a large range of questions about future Amazon climate, forest productivity, and crop production. Storage requirements for this work will be at minimum 250TB. DaLI will provide storage space for these datasets along with access to software to support the transfer and organization of the intricately related but incredibly diverse datasets generated by these field sites. DaLI will also provide compute resources to run climate simulations and storage for the simulation output files.
Arctic LTER: Climate Change and Changing Disturbance Regimes in Arctic Landscapes and Collaborative Research on Carbon, Water, and Energy Balance of the Arctic Landscape at Flagship Observatories in Alaska and Siberia
The MBL runs the Arctic and Plum Island Long-Term Ecological Research (LTER) sites. Sensors used by the Arctic and Plum Island LTERs measure a suite of ecosystems parameters along with landscape-level images and datasets derived from satellite remote sensing. Checking and managing sensor data, as well as the time required to input metadata and check data quality are currently major bottlenecks. DaLI will provide storage space to LTER investigators to enable them to benefit from the developed data management and sharing tools that include tools to assist in data transfer, publishing, and automatic metadata extraction.
Dimensions US-China: Collaborative Research: How historical constraints, local adaptation, and species interactions shape biodiversity across an ancient floristic disjunction
Dr. Gilbert’s group explores the biodiversity in the deciduous forests of eastern Asia and eastern North America. These forests were anciently connected and have a shared evolutionary and ecological history offering a unique opportunity to study the drivers of biodiversity across geographical space and through evolutionary time. The research team will reconstruct phylogenies using massively parallel sequencing methods for improved dating and biogeographic analyses. This is a collaborative effort between institutions across the United States and China. Current data volumes are -5TB and will increase significantly over the next three years to >100TB. Data storage capabilities are limited, resulting in data being spread over many different infrastructures, making cohesive data management a handicap for sharing and large-scale ecological analyses. DaLI will provide a stable storage infrastructure and novel compute architecture to perform large-scale phylogenetic analysis and reconstruction. DaLI will also provide tools that facilitate data sharing between collaborators.
ABI Sustaining: A visualization and analysis resource for comparative microbial ecology and CyberSEES: Type 2: Collaborative Research: A Computational and Analytic Laboratory for Modeling and Predicting Marine Biodiversity and Indicators of Sustainable Ecosystems
Dr. David Mark Welch at MBL heads VAMPS (Visualization and Analysis of Microbial Population Structures), a free, open-source, website (vamps.mbl.edu) that allows researchers using massively parallel sequencing data to analyze the diversity of microbial communities in an intuitive visual context. VAMPS hosts over 1300 projects encompassing more than 34,000 datasets, including those from the International Census of Marine Microbes, the Human Microbiome Project, the NSF Long Term Ecological Research sites, and the NSF Center for Dark Energy Biosphere Investigations. The database size is expected to double every 14 months resulting in a database of over 5 TB within 3 years, and if VAMPS accepts metagenomic data this estimate could increase by an order of magnitude. DaLI will provide VAMPS with storage resources for its growing data, as well as access to processors with 3D-Xpoint architecture that will dramatically improve the performance of memory intensive operations.
Methods for genomic analysis of massively parallel sequencing data
The Stevens group develops methods for genomic analysis of massively parallel sequencing data. These methods (Kiki, Ray, Spate) take advantage of supercomputers to assemble some of the largest metagenome datasets in the world. They currently store 1 PB of data and expect this number to expand dramatically in the coming years. The Stevens group will benefit from the data management tools and expandable storage provided by DaLI. Furthermore, access to the next generation 3D XPoint architecture on DaLI compute nodes will allow researchers to develop new algorithms for faster in-core memory intensive applications.
Single-cell RNAseq analysis to study molecular evolution
The Morgan lab at MBL uses single-cell RNAseq analysis of Reticulospinal neurons in frogs, lizards, and birds to study the molecular evolution of the startle response across species. Processing and analysis of this data requires extensive computing power and the size of datasets are rapidly increasing.
The Roles of Pioneer Neurons and Adhesion Molecules in Neuronal Migration
Advances in scanned imaging modalities such as confocal and light sheet microscopy are constantly increasing the speed, resolution, and sophistication of image measurements. An ongoing collaboration between Dr. Gordon Kindlmann, Dr. Victoria Prince, and the RCC has generated incredibly useful software for the real time acquisition, processing, and analysis of images acquired during light sheet microscopy(LSM) imaging sessions. This software transfers data from the light sheet microscope to the RCC’s High Performance Computing cluster. These images are processed and immediately made available for viewing via a web portal (see workflow in Figure 3), allowing the user to visualize the results of computationally-expensive analyses very quickly-during acquisition-and remotely monitor ongoing light sheet microscopy experiments which can last hours or days. These studies are expected to generate 20TB of data per year. DaLI will provide both the space and resources to analyze this invaluable data. It will provide a replicable platform for acquiring, analyzing in real time, and publishing data (minting DOis).
Enabling biological discovery through innovations in imaging and computation
The Oldenbourg Laboratory at MBL is developing a new type of light microscope, the LC-PolScope, which uses light polarization to gain insights into submicroscopic structural parameters and non-invasively create contrast where native structures are otherwise invisible. Development of analysis techniques for this instrument requires a concerted effort between experts in physical optics, computational image analysis, and biology. Currently, the complex computations required to process the image data are run on the local computer connected to the LC-PolScope, creating an acquisition bottleneck as these machines lack the computational power to quickly perform these operations. Access to DaLI resources via a high-bandwidth network will allow users to process the images during acquisition, and a shared project space on DaLI will serve as a collaborative platform that will facilitate the development of novel image analysis techniques.
Cell polarization and tissue morphogenesis from molecular interactions
The Munro Laboratory combines quantitative microscopy with detailed agent-based computer simulations to explore how cell polarization and tissue morphogenesis emerge from molecular interactions. Because individual simulations are expensive to run, the ability to store detailed simulation outputs, which can later be “mined” for insights, is critical. However, limitations on data storage and retrieval prevent the long-term storage of these outputs. DaLI will provide the necessary storage to enable these researchers to expand their research towards larger-scale quantitative experimental and computational analysis of cell and tissue dynamics.
The Role of Gesture in Word Learning
Professors Goldin-Meadow and Brentari are interested in how sign language, gestures from hearing and deaf communities, and informal languages such as homesign systems play a role in the acquisition of language. Over several decades, they have collected an extensive video data of 100 children aged between 14 months through 10 years. They captured naturalistic interactions at home and detailed motion capture videos of actions. Organizing and annotating these complex datasets is a major undertaking. In a collaboration with the Center for Gesture, Sign, and Language, the RCC has developed cyberinfrastructure to support the management and distribution of this data in a centralized Sign and Gesture Archive (SAGA). Through DaLI, a server-side data flow can be created to allow users to annotate videos on the server, perform data analysis, and collaborate and share the expected 42TB of data far more efficiently. Data in the Brentari lab is generated from a PhaseSpace 8-camera IMPULSE system.
The first analysis of the role of serotonin in regulating behavioral quiescence and locomotion of the nematode C. elegans in a state-dependent manner
Dr. Biron and collaborators record videos to track the behavior of the nematode C. e/egans over 12-24 hour periods. This increased imaging time allows them to dissect complex behavioral patterns such as lethargus (a sleep-like behavior). Their experiments produce 100-200GB of raw data per day of imaging session. A major limitation on the experimental throughput stems from the problems of storage, access, and backup of about 20TB of raw data per year. The researchers plan to scale up their data acquisition to 100TB per year, but lack the infrastructure to manage such large volumes of data. DaLI will enable this scaling by integrating their acquisition instrument directly with storage space on DaLI.
Topological Vortex Dynamics
Irvine Lab performs three-dimensional visualization at high speeds and high resolution to study the dynamics of linked and knotted vortices in water. In the next three years they predict to generate 150TB of video data. Processing of these videos is time-consuming and often creates a bottleneck that slows acquisition. DaLI would provide the resources to integrate these cameras with HPC resources to carry out computationally and data intensive tasks significantly faster and meet the storage needs for the newly generated data.
Development of Compact, Fast Waterproof Hyper-Spectral Imager & Multi-Channel SpectroPolarimeter for Marine Studies of Coloration and Patterning
The Hanlon Laboratory at MBL studies Rapid Adaptive Coloration in cephalopods and fishes. Dr. Hanlon’s group has developed an innovative light-field sensing instrument that enables dynamic characterization of light in aquatic and other moist environments. The Hanlon laboratory has no formal large-scale storage capacity, and they currently store 19TB of data across multiple desktop drives, with a projection to add an additional 2-3TBper year. DaLI will provide this project with comprehensive data storage resources as well as tools to facilitate the transfer of data from this novel instrument in the field to secure storage on DaLI.
Integrative analysis of ingestive biomechanics and dental microwear in evolutionary and ecological context and Integrative Investigation of the Evolution and Biomechanics of Mandibular Form in Hominids
The Ross Laboratory studies the organization, function, and evolution of vertebrate feeding systems using in vivo measurement of 3D jaw kinematics, muscle activity, bone strain, and cortical neuron activity, combined with computational methods for modeling bone deformation, muscle architecture dynamics, and motor control. One project, that examines the role of primate sensorimotor cortex in control of ingestion, chewing, and swallowing, involves collection of up to 16 channels of physiological data, synchronously with video and neural data. Recent NSF MRI funds have allowed Dr. Ross to acquire a Biplanar Digital Videofluoroscopy Instrument for X-ray Reconstruction of Moving Morphology (XROMM), allowing digital video to be included in this dataset. To facilitate the acquisition and analysis of these datasets, the RCC has worked with the Ross lab to develop the XROMM Data Management Software(XDM). The XROMM equipment was acquired through an NSF MRI grant. The XDM software guides users through an interface that selects experimental files for upload, automatically extracts useful instrument metadata, then stores those files in a key/value store that organizes the data and can be used to view and query data, populate a MySQL database, and automatically upload data to a national repository (the XROMM database at Brown University).
Inaugural Neuroimaging Workshop on the Dynamic Social Brain
The Center for Cognitive and Social Neuroscience is a resource for more than 50 faculty members across more than a dozen departments at UChicago. Research in cognitive and social neuroscience relies heavily on imaging technologies, which yield multi-GB datasets that take countless hours of processing for each participant and scan. Scientists at the RCC and the Center have developed the Chicago Electrical Neuroimaging Analytics (CENA) toolbox, a working HPC prototype for electrical and neuroimaging processing that greatly accelerate this process. For the purposes of data provenance, each processing step and dataset iteration are saved, resulting in up to 1 TB of data per study. Consequently, the Center’s dedicates considerable effort to the storage and analysis of these structural, electrical, and functional brain imaging data. The Center seeks to accommodate resources for the storage and analysis of 75-100 studies in the coming 3 years. DaLI will provide much needed storage space and data management resources for these datasets. The use of the XDM software tools developed at RCC for the Ross lab will facilitate the management of interdisciplinary datasets.
How large neuronal ensembles in the cortex act together to control, coordinate, and learn complex movements of the arm and hand
Hatsopoulos and collaborators work to understand how large neuronal ensembles in the cortex act together to control, coordinate, and learn complex movements of the arm and hand. Using multi-electrode arrays, each of which is composed of 100 microelectrodes, correlated with XROMM 3D X­ray fluoroscopy, a 14 camera Vicon motion capture system for collection behavioral data, and a miniature fluorescence microscopy for fluorescence imaging of neural activity. The researchers generate 10 TB of data per year, and have currently collected >50TB. The XDM software available on DaLI will facilitate the transfer and organization of these datasets while providing essential storage capacity and compute resources for these experiments.
Visual code for natural motion and prediction
The Palmer Laboratory uses new computational techniques to study the visual code for natural motion and prediction. Dr. Palmer has built a new natural motion database by making high-speed, high-pixel-depth recordings of natural scenes. By tracking the neuronal response to these videos the Palmer lab seeks to understand how moving objects are tracked and how this information is used to make predictions. Their current bottlenecks involve computation and analysis of data from more than 100 simultaneously recorded neurons, and they would like to expand this to about 1000 concurrent neurons to run real-time clustering during electrophysiology experiments. DaLI will provide tools for tighter integration of these electrophysiological instruments with HPC resources and resources for making the natural motion database available to the broader research community.
Computational investigation of molecular phenomena underlying experimental electrochemical characterization of polymer electrolytes
Juan de Pablo, Paul Nealey, and Shrayesh Patel’s joint project proposes the use of an ensemble of molecular simulation techniques to investigate phenomena governing ion transport behavior in various polymer electrolyte systems. The simulations will be used to inform upon the molecular basis of existing experimental characterizations as well as to guide future synthesis and characterization of polymer electrolyte materials.

Publications
  • “A Search for Light Dark Matter Interactions Enhanced by the Migdal effect or Bremsstrahlung in XENON1T”, E. Aprile et al. (XENON Collaboration), arXiv:1907.12771, Submitted for publication to Phys. Rev. Lett. (2019)
  • “Light Dark Matter Search with Ionization Signals in XENON1T”, E. Aprile et al. (XENON Collaboration), arXiv:1907.11485, Submitted for publication to Phys. Rev. Lett. (2019)
  • “XENON1T Dark Matter Data Analysis: Signal Reconstruction, Calibration and Event Selection”, E. Aprile et al. (XENON Collaboration), arXiv:1906.04717, Accepetd for publication on Phys. Rev. D (2019)
  • “XENON1T Dark Matter Data Analysis: Signal & Background Models, and Statistical Inference”, E. Aprile et al. (XENON Collaboration), arXiv:1902.11297, Phys. Rev. D 99, 112009 (2019)
  • “The XENON1T data acquisition system”, E. Aprile et al. (XENON Collaboration), arXiv:1906.00819, JINST 14, no.07, P07016 (2019)
  • “First detection of two neutrino double electron capture in 124Xe – the longest half-life ever observed directly”, E. Aprile et al. (XENON Collaboration), arXiv:1902.11002, Nature 568, 532–535 (2019)
  • “Constraining the spin-dependent WIMP-nucleon cross sections with XENON1T”, E. Aprile et al. (XENON Collaboration), arXiv:1902.03234, Phys. Rev. Lett. 122, 141301 (2019)
  • “First results on the scalar WIMP-pion coupling, using the XENON1T experiment”, E. Aprile et al. (XENON Collaboration), arXiv:1811.12482, Phys. Rev. Lett. 122, 071301 (2019)
  • “Dark Matter Search Results from a One Ton-Year Exposure of XENON1T”, E. Aprile et al. (XENON Collaboration), Phys. Rev. Lett. 121, 111302.
  • “A hydraulic mechanism of tongue base retraction during swallowing in primates.” Journal of Experimental Biology (Submitted for publication) Orsbon, C.P., Gidmark, N.J., Gao, T., Ross, C.F. (2019)
  • “Joint angular excursions during cyclical behaviors differ between tetrapod feeding and locomotor systems.” Journal of Experimental Biology Granatosky, M.C., McElroy, E., Laird, M.F., Iriarte-Diaz, J., Taylor, A.B. and Ross, C.F. (2019) doi.org/10.1242/jeb.200451
  • “Dynamics of motor cortical activity during naturalistic feeding behavior.” Journal of Neural Engineering. 16(2): 026038. Liu, S., Iriarte-Diaz, J., Hatsopoulos, N.G., Ross, C.F., Takahashi, K., Chen, Z. (2019) doi.org/10.1088/1741-2552/ab0474
  • “Dynamic musculoskeletal functional morphology: Integrating diceCT and XROMM.” Anatomical Record 301(2):378-406. Orsbon, C.P., Gidmark, N.J., Ross, C.F. (2018) DOI: 10.1002/ar.23714
  • Munakami, M., Takahashi, K., Runesha, H.B., Ross, C.F., “Development of XROMM Data Management (XDM) tool for an integrated workflow for big image/video data in orofacial research (abstract/poster)”, SfN satellite meeting on “Neural mechanism of feeding and swallowing and its application to neuro-rehabilitation”, Annual Meeting for Society for Neuroscience, Chicago, IL, Oct. 2019
  • Papadourakis, V., Suminski, A., Takahashi, K., Hatsopoulos, N.G., “Shared and non-shared neural subspaces between action execution and multi-sensory action observation (abstract/poster)”, The annual meeting, Society for Neuroscience, Chicago, IL, Oct, 2019
  • Gupta, S., Sheen, S., Papadourakis, V., Takahashi, K., Hatsopoulos, N.G., Suminski, A.J., “Examination of snared and non-shared neural subspaces in the primary motor cortex between active movement and brain machine interface control (abstract/poster)”, The annual meeting, Society for Neuroscience, Chicago, IL, Oct. 2019
  • Balasubramanian, K. , Papadourakis, V., Liang, W., Takahashi, K., Best, M., Suminski, A., Hatsopoulos, N.G., Propagating patterns of activity across motor cortex facilitate movement initiation (Preprint available at bioRxiv – doi:https://doi.org/10.1101/549568)

 

Acknowledgement Statement

Please using the following statement in your publications to acknowledge DaLI:

“This research was supported in part by the NSF through resources provided by the Research Computing Center at the University of Chicago, under NSF grant award 1661523″