Shared Equipment and Core Facilities
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core

Facility Director:

Stephen Johnson, Ph.D.
Vanderbilt Clinic 5
630 W. 168th St.
New York, N.Y. 10032
Tel: (212) 305-(5)1858
Fax: (212) 305-(5)3302
E-mail: sbj2@columbia.edu
Web page: http://www.cpmc.columbia.edu/homepages/johnson/

Facility Manager:

Ms. Janie Weiss
P&S Room 1-420
630 W. 168th St.
New York, N.Y. 10032
Tel: (212) 305-(5)7352
Fax: (212) 305-1667
E-mail: janie@columbia.edu
Web page: http://cancercenter.columbia.edu/staff.html#jw

Professional Staff:

Susan Kistler
Black Bldg. Room 130
630 W. 168th St.
New York, N.Y. 10032
tel: (212) 305-(5)3945
fax: (212) 305-1667
e-mail: susan@columbia.edu
Web page: http://cancercenter.columbia.edu/staff.html#sk

Richard Friedman, Ph.D.
Black Bldg. Room 130
630 W. 168th St.
New York, N.Y. 10032
tel: (212) 305-(5)6901
fax: (212) 305-1667
e-mail: friedman@cancercenter.columbia.edu
Web page: http://cancercenter.columbia.edu/~friedman/

Debra Hairston
P&S 1-420
630 W. 168th St.
New York, N.Y. 10032
tel: (212) 305-(5)7350
fax: (212) 305-1667
e-mail: debra@cancercenter.columbia.edu
Web page: http://cancercenter.columbia.edu/staff.html#dhc

Ilya Pisman
P&S 1-420
630 W. 168th St.
New York, N.Y. 10032
tel: (212) 305-(5)7350
fax: (212) 305-1667
e-mail: ilya@cancercenter.columbia.edu
Web page: http://cancercenter.columbia.edu/staff.html#ip

Location of Facility:

Black Bldg. Room 1-420
630 W. 168th St.
New York, N.Y. 10032

Description:

The Facility serves more than 120 research groups, representing over 500 faculty, research scientists, and students engaged in basic and clinical research. Facility staff provide guidance, consultation services, documentation, and assistance in obtaining appropriate commercial manuals. The Facility provides one-on-one introductory sessions, group tutorial seminars, and general advice for inexperienced computer users. A credit class on Biological Sequence Analysis is offered every Spring semester. With respect to computer and informatics needs, the goal of these efforts is to enable researchers to become self-sufficient.

The Oncoinformatics staff provide guidance and up-to-date documentation to the Cancer Center researchers so that they may effectively utilize their central system. The Oncoinformatics core offers central and distributed services to coordinate the flow of information among internal and external databases and to facilitate synergies across laboratory, clinical and population research. Informatics services integrate information across Cancer Center activities. The principal tools for achieving this are databases that establish linkages and Web sites that provide access to data, both locally and externally. These services include data modeling, analysis and mining, acquisition of software tools and user training. Technology services (area inside dashed triangle) provide infrastructure that make these activities possible. These services include assisting with network connectivity, establishing special-purpose Cancer Center servers, maintaining security of confidential information, and automating backup to prevent loss of data.

Investigators wishing to obtain an account to use the Unix server for bioinformatics analysis (e.g. GCG software) should complete the Account Application. Desktop support can be obtained following completion of the Work Request Form. The Center's Security and Policy Guidelines are also available.

Hardware and Software:

The Oncoinformatics Core's Compaq Alphaserver ES 40 system runs the Compaq Unix operating system and the Center has full responsibility for the day-to-day management of the server. The following hardware and software is available:

• Compaq Alpha Server ES40:
  
  
  • 512 Mb of physical memory
  • 1 Terabyte of data storage
  • 1 4-mm magnetic tape cassette drive
    
    
• Additional Hardware:
  
  
  • 2 Pentium PCs for campus desktop backups
  • 1 Overland Tape Library
  • 1 Tektronix Phaser 740 Color Printer
  • 1 Hewlett Packard Laser Jet 4050TN
    
    
• Software:
  
  
  • The GCG is a package of biological sequence analysis programs along with on-line versions of the major nucleic acid and amino acid sequence databases. Additional software packages that complement the GCG suite are also available.
    
    
  • The SYBASE relational database management system provides database management and database application development. Current development projects use Prolific's Jam as the front end for developing graphical interfaces to the SYBASE databases.
    
    
  • C, Perl, and FORTRAN compliers are available form program development and modification.

The Alpha server is connected to Columbia University's Health Sciences Campus network, thus providing access to the worldwide network of research-oriented computer systems and services: WWW, electronic mail exchange; inter-system file transfer; remote system login; etc.

Permitted Users: Both Columbia-Presbyterian Medical Center (CPMC) personnel and non-affiliates may use this core facility. Herbert Irving Comprehensive Cancer Center members are given priority.

Charges:

• Backup Service
  
  
  • Member: $350 / Machine
  • Non-Member: $400 / Machine
    
    
• Monthly Surcharge:
  
  
  • Member: $32.50
  • Non-Member: $42.50
    
    
• Consultation Fees
  
  
  • $50-$80 per hour
  • $60-$100 per hour

Revision Date: October 2002