Graduate Bulletin

Spring 2018


Facilities of the Biomedical Informatics Department and Graduate Program

The Biomedical Informatics Department has a strong foothold in computing and in biomedical sciences. Our Department was jointly established by the College of Engineering and Applied Sciences and the Stony Brook University School of Medicine.

BMI’s three locations on campus offer students and faculty front seats in key centers of collaborative activity. Each BMI Department location features extensive learning and research suites with faculty and administrative offices, Postdoctoral trainee stations, classroom and meeting space, and student labs equipped with desktop computers, each with 1TB storage space, 16GB main memory, and a 4-core CPU. The Department’s HSC Suites have opened in the Health Sciences Center HSC Level 3, and include the Chair’s suite and administrative center. A second BMI location with office, meeting and student lab is under construction in the Old Computer Science Building on West Campus. The third BMI Department suite will be housed with the Cancer Center in the new Medical and Translational Research (MART) building being constructed adjacent to the new Stony Brook Children’s Hospital. Virtual meeting solutions continue to keep all Department members together, and enable distance learning.

The Biomedical Informatics Department (BMI) has a cluster computing system dedicated to research, development, and education in high performance computing, systems software, and applications. The cluster system consists of 10 compute nodes and 10 storage nodes. Each compute node has 2 10-core Intel Xeon CPUs, 2 NVIDIA K40 Tesla GPUs, one Intel Xeon Phi co-processor, 256GB main memory, a 512GB SSD, and 2 1TB hard-disks. Each of the storage nodes has 2 6-core CPUs, 64GB main memory and 95TB disk storage in RAID 5 configuration. All the nodes in the cluster are connected to each other via high performance Infiniband Switches. The cluster system is housed in the Department of Computer Science. BMI also owns a small Virtual Machine server farm consisting of a Dell PowerEdge server with 4 8-core CPUs, 256 GB main memory, and 28TB disk storage. This server is used to host VMs for development and testing purposes.

In addition to BMI owned servers and computers, researchers have access to XSEDE resources ( through a scientific gateways grant. The XSEDE resources include Stampede which is a distributed-memory Dell Linux Cluster with over 6,400 nodes. Each node has 2 Intel Xeon E5 (Sandy Bridge) processors, 32GB memory, and an Intel Xeon Phi Coprocessor (MIC Architecture) with 8GB memory. The computation nodes are interconnected with Mellanox FDR InfiniBand technology. BMI’s Student and meeting space has wifi and wired connections available to the SBU network. In recent years the use of cloud computing has taken center stage in both translational biomedical informatics and bioinformatics and students will also be introduced to those resources.