Gerstein (Central/Main campus and West Campus)
The Gerstein laboratory is found in two connected buildings, namely Bass Center and Kline Chemistry Laboratory, and in the West Campus Collections Study Center Building. Wireless access is available throughout using Gerstein laboratory-maintained access points and University-managed data access points. There are 6 office rooms and a conference room in Bass Center, which comprise a total of ~2,100 sq. ft., and 3 office rooms in Kline Chemistry Laboratory, which comprise a total of ~300 sq. ft. The conference room is fully equipped for teleconferencing, having one 90” screen and one 70” screen, two video cameras, and various smart devices for automation. There are 51 gigabit-ready desk, each equipped with at least one 34” LED-LCD widescreen monitor. All office spaces are properly environmentally maintained for the comfort of users and maintenance of computing equipment. Facilities in the West Campus Collections Study Center Building include a 425 sq. ft. server room, and two rooms used for storage which jointly have ~300 sq. ft. of space. The server room utilizes 10-Gbit and Gigabit connections, and is upgradeable to 40-Gbit networking.
Mark Gerstein's office space is 178 sq. ft.
Gerstein Lab Computing Infrastructure and Resources
The laboratory maintains its own public IP space of 832 IP addresses and manages four domains (e.g. gersteinlab.org, molmovdb.org, pseudogenes.org, and partslist.org). It also has on-demand access for private IP subnet space provided by the University. The lab has a full-time administrator maintaining the network, servers and laptops.
The lab’s computing infrastructure can be logically partitioned into four units: Bass Center, West Campus Server Room, Yale High Performance Computing, and Cloud Block services.
1. The Bass Center unit logically consists of end-user laptops and devices, and wireless entry points interconnected by an HP Procurve 5300xl switch. The unit is fully gigabit capable and is connected to the Yale backbone, which has a 10-gigabit throughput. There are 8 color laser printers. Wireless access points are through 3 Tri-Band Gigabit wireless routers and Apple Airport devices. There are about 80 working Apple 15” and 13” Macbook Pro laptops in the lab. The private network has seven business class color laserjet printers. A number of open source software, programs created in-house, and proprietary software are used by the lab researchers for their needs.
2. The West Campus Server Room unit is a Gerstein lab-maintained computing facility. It logically consists of 8 standalone servers, and 13 hypervisor-type servers, which host virtual machines. The private and public networks in this unit are facilitated by a Juniper QFX5100-48S switch and a HP Procurve 5300zl switch interconnected by copper and fiber. All virtual machines reside in an NFS shared space within a Nimble CS300 storage appliance with a total of 94TB usable space. Backups are maintained in 2 Overland SnapServer XSR 120 NAS devices with a total of 167TB raw space.
The Gerstein laboratory maintains an OpenStack cluster in the West Campus Server Room. The cluster consists of 1 director, 3 controllers, 3 Ceph nodes and 5 compute nodes. The cluster has 163TB of total storage, 80 CPUs and a cumulative 625GB of memory. It is internally 10Gbit networked, which is facilitated by 2 Lenovo G8272 and Lenovo G8052 rack switches.
3. The Yale High Performance Computing logical unit is maintained by Yale IT personnel. The Gerstein laboratory has priority access to compute against 1.2 Petabytes of storage which is cross-mounted onto two clusters, namely Grace and Farnam, and against 403TB in Loomis. Grace is a 33 node cluster with 672 cores; Farnam has
20 nodes, 536 cores with mixed Intel family CPUs and GPUs.
4. The Cloud Block logical unit is composed primarily of cloud based services of Amazon Web Service and Google Apps for Education, and secondarily by other providers namely Dropbox, Git, Wordpress, and other cloud services of relatively smaller companies.
The Gerstein Lab uses Platform-as-a-Service and Application-as-a-Service offerings of Amazon Web Services to provide its most externally visible expressions. The main web servers, publications, downloadable documents, archives of group discussion are maintained within Amazon Web services.
Google Apps for Education hosts the Gerstein Lab email service. It also provides the Google Drive Application-as-a-Service used mainly for storage but also as a quick document search enabler. Dropbox is used routinely by the laboratory to facilitate the web sharing of documents. It is used in tight conjunction with Amazon Web Services. The Gerstein Lab maintains and share the code it develops primarily in Git. Wordpress is used for class lectures.