RESEARCH COMPUTING SERVICES

Fox Chase Cancer Center Research Computing Services (RCS) Facility maintains a highly diverse and technically sophisticated computing environment to facilitate cancer research throughout the institution. The facility offers a number of services, including sequence analysis, bioinformatics programming and support, database design and administration, computer system support, networking, web engineering, and general programming. The RCS collaborates with investigators with special or unusual computational needs, providing programming and systems to enable specific research projects.

BIOINFORMATICS, SCIENTIFIC SOFTWARE, AND DATABASES.  Several major categories of scientific software are installed and supported by RCS, including a number of programs written by the RCS staff. The software installed supports various disciplines, including sequence analysis, molecular modeling, biomathematics, laboratory data management, program and database development, and network management.

The facility provides major scientific software packages for use, including the ORACLE, SYBASE, and MS-SQL relational database management systems; mathematical tools such as IMSL, BMDP, SAS, Mathematica, and S-PLUS; desktop publishing programs such as MicroSoft Office and Excel, FrameMaker and the TeX electronic publishing system; extensive graphics software for digitalization, 2D and 3D display, drawing and graphing; INSIGHT/QUANTA/CHARMm for molecular display; Felix NMR spectra analysis; and the GCG "Wisconsin" package for sequence analysis.

Several major scientific databases are maintained locally for use in genetics, molecular biology, and molecular structure research. These databases are updated automatically where possible via the Internet. Nucleic acid and protein sequence data are contained in the GenBank™ genetics databank, the EST database of expressed sequence tags, the PIR protein database, the Swiss-Prot protein database, the TFD database of DNA transcription factors, the EPD database of eukaryotic promoter sequences, and others. Molecular coordinates are in two databases: the Brookhaven Protein Data Bank PDB containing crystallographic coordinates of macromolecules, and the Cambridge Structural Data Bank of crystallographic coordinates of small molecules.

RCS also maintains a large ORACLE relational database system. This system is extensively used by the entire Population Science division, where it is used to support ongoing family studies, epidemiology, and clinical trials in chemoprevention. Additionally, it supports data management in the Laboratory Animal, Cell Culture, and Hybridoma facilities, and a number of individual laboratories. RCS services for these projects include hardware, system, and security management; database modeling, database design, forms, and Inter/Intranet design for new projects; data analysis; and user account management.

Programming services are an important part of the RCS facility. RCS personnel are expert in software development for a variety of tasks relating to biological research. The facility focuses on mainstream programming and Rapid Application Design languages heavily used within the biosciences and Internet communities. These include C/C++, Java, Javascript, Perl, Python, Tcl/Tk, and several others comprising all major computer languages. Consulting expertise in the theory of algorithms and computation is also available. Application domains include sequence analysis, genome computing, graphics, laboratory management, and web interfaces. Services range from quick help on knotty programming problems to complete software design, implementation, and support.

As an example, the Cell Culture facility (in collaboration with SELLS) is provided with a web-based system, as shown in Figure 1, supporting data collection, storage, retrieval, and security. Data entry is done by platform-independent web screens with data being maintained in the ORACLE relational database system.

WEB.  RCS provides technical support and infrastructure for the Fox Chase Cancer Center web site at http://www.fccc.edu/. An Internet Programmer, Mr. Massimino, coordinates technology for the various campus web sites, providing the structure and support for research, medical, and administrative programs to communicate their work to the public, patients, faculty, and staff. Under Mr. Massimino's direction, the campus web has been crafted as a single architectural entity that can easily manage a diverse range of content and publication needs for a broad audience. To meet this goal, the architecture uses HTML frames for ease of administration and updating. Graphics are reprocessed for faster loading and easier reading, and a distributed publication system which takes advantage of Lightweight Directory Access Protocol (LDAP) services was developed and deployed to allow employees to create and maintain sections of content. The use of LDAP services together with HTML frames allows the site to address issues of security, review, and timeliness. A research-oriented and curated Web site for internal use is maintained by a group of faculty, postdoctoral fellows, and RCS staff, including internal information and hyperlinks to web resources.

HARDWARE.  RCS maintains and supports a large variety of computers, including desktop machines, high-performance servers, and specialized devices such as hand held personal information systems. The administration of integrated and complex systems running several modern operating systems requires a great deal of expertise and attention. RCS administers machines that run all common operating systems, including Microsoft Windows and NT, MacOS, and several variants of the Unix operating system. These complex systems require significant integration effort to ensure proper functioning.

The facility supports approximately 250 PCs and 215 Macs. This support includes installing software, troubleshooting, upgrading, testing new operating system and software releases, providing training, maintaining a help desk, automatic backups, automatic software inventories, Y2K assessment, and coordinating service contracts. The facility also supports approximately 50 server systems for specific services. High-performance Unix server systems deliver bioscience applications such as sequence analysis, structural biology visualization, data management, World Wide Web access, electronic mail, and a variety of other scientific software. Servers are typically small to mid-sized Unix or NT machines, depending on the demands of the particular application. RCS supports a number of laboratory-based high-performance workstations dedicated to individual investigators with special needs in scientific visualization, imaging, and informatics. Backup services for PC's, Macs, and server-class systems are available to all investigators.

Shared network printers are maintained at several locations throughout Fox Chase and are accessible from any networked computer. High-resolution color printers and a slide maker service are also available.

DATA NETWORKING.  RCS provides strategic support for the Fox Chase data network--a campus-wide network with more than 1700 devices. The facility has responsibility for the design, management, and implementation of both the physical and logical infrastructure involved with the provision of network services throughout campus. The group coordinates the core architecture of the campus electronic mail, web, and news systems, and manages network name and address spaces for various network protocols.

The backbone of this network is a Fiber Distributed Data Interface (FDDI), which functions at a capacity of 100 million bits/second, or approximately 2,000 times the speed of a traditional computer modem. During 1998, RCS commissioned a review of our network plant and future plans and strategic directions with an outside consultant. Options reviewed included gigabit Ethernet, ATM, ADSL, ISDN, and cable modems. Plans are now underway for an upgrading campus technology to higher speeds to support the emerging demands of medical imaging, real-time video, data mining, and other multimedia uses in the coming years.

During 1998, we also implemented a second, redundant T1 line to the Internet, bringing our connectivity to approximately 3 Mbits/sec., or approximately 100 times that available through a standard computer modem. This connection was deemed necessary due to the increasingly critical nature of high-speed Internet access in support of research.

We are in the process of implementing an improved firewall and remote access systems that will allow us to better manage the access to our environment from outside the Fox Chase Network. For Fox Chase employees to connect to the internal network in a secure fashion, we are providing a technology called "tunneling" or "virtual private network." Various Internet-based services have been deployed, such as a directory service based on LDAP and a secure file access and distribution service based on Secure Socket Layers (SSL).

STAFF.  RCS personnel are trained in several relevant disciplines. Staff expertise is available in bioinformatics, Internet programming, image analysis, network engineering, systems administration, database design and administration, algorithm design and analysis, and graphics programming. RCS staff pursue advanced training, and routinely explore emerging and advanced technologies to offer the greatest support for the multifaceted use of technology in a research environment.

Illustrations or unpublished data in these reports should not be used without permission of the author.

Fox Chase Cancer Center

Scientific Report 1998