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Biomedical Informatics - Equipment

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Biomedical Informatics shared resource is enabled by the equipment groupings listed below. The equipment supports the research computing initiative of the Institute. The Biomedical Informatics shared resource also supports the Institutional file servers.

Equipment Brand Model CPU Memory Storage Quantity Purpose
Oncore
Server HP ProLiant DL360p Gen8 2 x Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz (8 cores, 16 threads) 32GB 2.4TB 2 OnCore Database Server and Test VM Host
Server HP ProLiant DL360p Gen8 2 x Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz (8 cores, 16 threads) 16GB 900GB 1 OnCore Application Server
Server HP ProLiant DL360p Gen8 2 x Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz (8 cores, 16 threads) 16GB 2.4TB 1 OnCore Backup Server
SEER
Server Dell PoerEdge R620 2 x Intel(R) Xeon(R) CPU E5-2640 v2 @ 2.00GHz (8 core, 16 threads) 96GB 4TB 2 SEER VM Host
Server HP ProLiant DL360 G7 2 x Intel Xeon  Intel  2.50 GHz (6 cores, 12 threads) 72GB 4TB 2 SEER VM Host
Server Dell PowerEdge R710 2 x Intel(R) Xeon(R) CPU E5649 @ 2.53GHz (6 core, 12 threads) 64GB 4.5TB   SEER VM Host
Server NetApp FAS2240-4,HA,24x3TB,Dual CTL2     6.5TB 1 SEER VM Storage
PMI / Data Warehouse
Server Dell PowerEdge R620 2 x Intel(R) Xeon(R) CPU E5-2620 0 @ 2.00GHz (6 cores, 12 threads) 96GB 2.2TB 2 Data Warehouse Database Server
Server Dell PowerEdge R920 2 x Intel(R) Xeon(R) CPU E7-8893 v2 @ 3.40GHz (6 core, 12 threads) 256GB 2.2TB 1 Informatica VM Host
Server Dell PowerEdge R620 2 x Intel(R) Xeon(R) CPU E5-2620 0 @ 2.00GHz (6 core, 12 threads) 160GB 2.2TB 1 BioFortis VM Host
Server Dell PowerEdge R620 2 x Intel(R) Xeon(R) CPU E5-2660 v2 @ 2.20GHz 96GB 8TB 1 Extract VM Host
Server Dell PowerEdge R610 2 x Intel(R) Xeon(R) CPU E5645 @ 2.40GHz (6 core, 12 threads) 32GB 32GB 1 Caisis VM Host
Others
Server HP ProLiant DL560 4 x Intel(R) Xeon(R) CPU E5-4607 0 @ 2.20GHz 96GB 1TB 1 Research Fileserver
Server HP Z820 2 x  Intel® Xeon® E5-2670 2.60 20MB 1600 8C 256GB 8TB 2 Research Computational Node
Server HP Z820 2 x  Intel® Xeon® E5-2670 2.60 20MB 1600 8C 64GB 8TB 1 Research Computational Node
Storage HP StorageWork D2600     36TB 2 Research Storage
Storage Dell EqualLogic PS6500E     144TB 2 Research Storage

Biomedical Imaging

TMA Analysis Workstation
TMA-Analysis Workstation

  • High-res digital camera with RGB liquid crystal filter (Olympus DP70 and DP71) to digitize specimens
  • Computer-assisted microscopy (Olympus AX70 and BX40 with six-way robotic stage/motorized turret) to support telemicroscopy and telepathology applications
  • Informatica-based extraction transformation and load interface (ETL) to automatically populate a secure, IRB-approved, Oracle-based Clinical Data Warehouse with data elements originating from the multi-modal data sources. During recent empirical, benchmark experiments this interface was able to reliably process and load all of the associated data for 5,000 breast cancer cases into the Warehouse in ~12 minutes
  • Nuance multispectral imaging system for accurate spectral classification and unmixing. It can be configured for either bright-field or fluorescence microscopy in the visible (VIS) wavelength range of 420-720nm (up to 950nm for fluorescence-only systems) to allow systematic investigation regarding the use metamerism, manifold shortcuts and digital staining applications

Multi-Spectral Imaging Workstation
Multi-spectral Imaging Workstation

  • Nikon Eclipse 90i fully automated bright-field/fluorescent microscopic imaging station with Photometric Coolsnap ES2 camera to support quick, reliable subsampling of specimens for presentations and publications
  • Olympus VS120 bright-field/fluorescent whole slide scanner with 100 slide capacity and standalone processing workstation which generates high-resolution digital images from microscopy samples within minutes while optimizing scan speed, Z-positioning and efficiency

  • Image server and graphical interface within Rutgers firewall to allow secure review and annotation by consulting pathologists and collaborators or to allow quantitative analysis using a wide range of computational imaging tools that are made available through the shared resource

Research Computing
Bioinformatics supports the following file servers: HP ProLiants (three DL360p Gen8, one DL360p Gen7, and one DL560); Dell PowerEdges (four R620, one R710, one R920, and one R610); one NetApp FAS2240-4, HA, 24x3TB, Dual CTL2; two HP Z820; one HP StorageWork D2600; and one Dell EqualLogic PS6500E. Bioinformatics has application, database, and storage server hardware with redundancy to support both the Aria electronic medical record and the OnCore clinical trials platform. Bioinformatics is enabled by the Rutgers High-Performance Computing Group that has a National Institutes of Health (NIH) shared equipment grant funding a Lenovo NextScale with 132 compute nodes (128Gbyte, dual Haswell 10-core sockets), eight GPU nodes (same node spec but with twin K80 GPU's), 2PB (raw) IBM GPFS (now called Spectrum Scale) and FDR Infiniband arranged in a 1X fat tree. The GPFS will be connected to the network fabric over six IB ports. There is one large memory node (1.5TB memory and 48 cores). Bioinformatics uses this resource for computationally intensive projects such as molecular modeling, genetic epidemiology, Markov Chain Monte Carlo (MCMC) simulations in bioinformatics, machine learning, etc.

SuperComputer - CaliburnSuperComputer - Caliburn

Through a $10 million infrastructure grant awarded to Rutgers from the State, CINJ has established persistent, ready access to state-of-the-art, high-performance computing, cloud support, and direct access to the newly established SuperComputer named Caliburn (20,160 cores, 140TB RAM and 218 TB non-volatile memory, peak performance 677 Tflops), which is the second most powerful in the Big Ten and ranked #8 among U.S. academic institutions. Using these assets, our team is able to accelerate the pace of optimizing computational algorithms and conducting quantitative genomic and imaging experiments in parallel.

Computing equipment is distributed across several sites including a server room in the CINJ basement with fire suppression, raised floor, and independent air conditioning with humidity control; a separate rack of servers for critical clinical/research data is located in the Robert Wood Johnson University Hospital data center (24/7 controlled access, Federal/State hospital data center compliant) as the fail-over site; Rutgers Administrative Services Building (ASB). Access to these sites is ID restricted and video monitored. Servers have a redundant dual power supply with battery backup; there is a tape library for disaster recovery (tapes containing encrypted data are stored by an off-site vendor).

 

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