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 server.

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
  • High-resolution digital camera with RGB liquid crystal filter (Olympus DP70 and DP71) to digitize array specimens
  • Computer assisted microscopy system composed of Olympus AX70 and BX40 microscopes equipped with a Prior 6-way robotic stage and motorized turret
  • Network-based Oracle database system
  • Nuance multispectral imaging system which allows for accurate spectral classification and unmixing. It can be configured for either brightfield or fluorescence microscopy in the visible (VIS) wavelength range of 420-720 nm (up to 950 nm for fluorescence-only systems)
  • Nikon Eclipse 90i fully automated bright-field/fluorescent microscopic imaging station with Photometric Coolsnap ES2 camera
  • Olympus VS120 bright-field/fluorescent whole slide scanner with 100 slide capacity and standalone processing workstation
  • Image server within Rutgers firewall to allow visualization, sharing and annotation to digitized specimens.

In addition, the Biomedical Informatics Shared Resource has application, database and storage server hardware with appropriate redundancy in place for clinical operations supporting both the Aria electronic medical record and the OnCore clinical trials software platform. The Resource is enabled by the Rutgers University High Performance Computing Group that has recently acquired an NIH shared equipment grant funding a compute cluster composed of CPU and GPU compute nodes. The machine is a Lenovo NextScale (formerly IBM NextScale) with 132 compute nodes (128Gbyte, dual Haswell 10-core sockets), 8 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 6 IB ports.  In addition there is one large memory node (1.5TB memory and 48 cores).  The Biomedical Informatics Shared Resource uses this resource for computationally intensive projects such as molecular modeling, genetic epidemiology, Markov Chain Monte Carlo (MCMC) simulations in bioinformatics, machine learning, etc. The Resource’s Bioinformatics specialists work with two scientific application technicians and a software engineer associated with the Rutgers/IST HPC Group (and funded by the university) to help researchers develop, port or tune code onto the HPC platform.

Security: The Biomedical Informatics Shared Resource follows the best practice guidelines of the University for maintaining security. All enterprise server hardware is located behind secure firewalls on a private network. Remote access is provisioned to employees and vendors via VPN and all vendors are covered by a Business Associate Agreement as required by HIPAA. SSH/SCP/SFTP is used to secure internal communications. E-mail containing PHI data is encrypted automatically and/or manually by Zix. Other data in transit is secured via, encrypted large file transfer provided by the LiFT device by Accelion, point to point VPN, or via rsync through encrypted tunnel. Data at rest (onsite backup, offsite backup and archives) and all mobile device data are encrypted (AES 256 bit) according to policy. Strong passwords are enforced. SOP’s are maintained centrally, updated annually, and available for review.
 

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