GCG DNA/protein sequence manipulation programs
04/29/99 11:15 AM

Access:

Use a telnet program (e.g., telnet, smartterm, netterm) to logon to cuccfa at:

cuccfa.ccc.columbia.edu

User ID: shanley
Password: CALL JIM SHANLEY  (4-4337) FOR PASSWORD

Store your files on your own unix directory on either cubsps or cunix.  Storage costs for the cuccfa computer are prohibitive.

Connect charges are reasonable and are presently borne for Fairchild residents by the Biology Library.

A graphical user interface (seqlab) is available for many of the GCG program if your Mac or PC  is equipped with an X-Windows emulator. See below.

A non-credit course on GCG and related programs is given each year by Richard Friedman at P&S . E-mail him for information (friedman@cuccfa.ccc.columbia.edu).

From:

Richard Friedman,Ph.D.
Herbert Irving Comprehensive Cancer Center Computer and Informatics Resource Center (CIRC)
Columbia Presbuterian Medical Center 130 Black Building 7-6901
friedman@cuccfa.ccc.columbia.edu)

March 8, 1999

Information for new GCG Users on cuccfa:

To learn GCG we recommend that you use the following manuals, published by ourselves as well as GCG. The introduction to computing manual contains information every Cuccfa user should know including what software you need on your Mac or PC to connect to Cuccfa. Included are course handouts on various kinds of sequence analysis as well.  

Tutorial manuals from the CIRC, $30. - Introduction to computing on the Columbia University Cancer Center Computer and Informatics Resource Center's Dec-Alpha. - Tutorial introduction to the GCG software package for biological sequence analysis. GCG manuals from GCG - GCG Program Manual, Unix Version. $155. - GCG User's Guide, Unix Version. $55   In addition to these manuals, users will also need to obtain specific software to run GCG. GCG has traditionally been accessible only through a text based interface. However, a graphical user interface is now available that makes GCG as easy to use as a Macintosh or Windows program. This interface, called Seqlab, not only makes GCG much easier to learn and to use, but also contains a new cut-and-paste sequence editor. Using Seqlab requires X-Windows Server software for your Macintosh or PC. A three button mouse is useful with X-Windows.  

Software recommended for access to GCG from a Macintosh: - BetterTelnet, terminal emulation program (free) - Versaterm Pro, terminal emulation program ($75 from Synergy). This is the recommended program. - Fetch, file transfer program (free) and if you are using Seqlab, the following is also necessary - eXodus X Server software ($165 from Macwarehouse) - Microspeed 3 button ADB mouse ($39 from Macwarehouse)  

Software recommended for text based access to GCG from a Windows 95/98/NT machine: - Teraterm, terminal emulation program (free) - SmartTerm, terminal emulation program ($152 from Macwarehouse) - WS-FTP, file transfer program ($32 from Macwarehouse) and if you are using Seqlab, the following is also necessary - Exceed for Windows 95/98/NT ($327 from DSCi) * - Microspeed 3 button mouse for the PC ($15 from Macwarehouse) *  

To better use Seqlab (see previous paragraph), you need to obtain the following in addition to the software and manuals already mentioned. SEQLAB manuals from GCG * - Seqlab Guide, $55. * - Seqlab Tutorial, $35*  

All shareware/freeware software for both the Macintosh and Windows 95/98/NT can be obtained directly on the web from http://www.download.com or http://mirrors.apple.com. Teraterm can be obtained from http://spock.vector.co.jp/authors/VA002416/teraterm.html Selected Macintosh software can be obtained from Richard Friedman x76901 friedm

an@cuccfa.ccc.columbia.edu  

Vendor Information: GCG Genetics Computer Group University Research Park 575 Science Drive Madison, WI 53711 Att: Leslie Szymborski Phone:(608)231-5200 Fax: (608)231-5202 e-mail:leslie@gcg.com  

Synergy Software 2457 Perkiomen Ave. Reading, PA 19606 Phone:(610)779-0522 Fax:(610)370-0548 sales@synergy.com

MacWarehouse 47 Water Street South Norwalk, CT 06854 Att: Michelle Franchella Phone:1-800-696-1727 extension 7008 Fax: (203)855-1386

For Macwarehouse always mention that these are the prices for Columbia that Michelle Franchella quoted to Richard Friedman. DSCi 3775 Iris Ave. Suite 1 Boulder, CO 80301 USA Att: Peter Citarella Phone: 303 447 9251 Fax 303 447 1406 Email: peter@dcsiem.com