Requirements
A personal computer that is based on an Intel 80x86 or Pentium microprocessor (or compatible), at least 4 MB of memory, a hard disk drive, a graphics display, a mouse or other pointing device, and a CD-ROM drive.
MS-DOS operating system (version 3.1 or later), Microsoft Windows (version 3.1 or later, or Microsoft Windows for Workgroups, version 3.1 or later), and drivers that are supplied by the CD-ROM manufacturer.
Software Update Installation
Update installation requires the same steps as a new installation.
New Installation
The Entrez retrieval program is supplied as a PKZIP self-extracting archive. To extract the program, follow these steps:
• Insert the Entrez1 CD-ROM disc into the drive and make it the current drive (assumed to be drive D in the example below). Change the current directory to ENTREZ\WIN and type the command “install” followed by the name of the directory into which the software should be copied (C:\ENTREZ in the example). Then return to the hard disk.
The ENTREZ directory will now hold the ENTREZ.EXE and ENTREZCF.EXE applications, and ASNLOAD and DATA directories.
C:> d:
D:> cd entrez\win D:> install c:\entrez D:> c:
C:>
• Start Windows. For convenience, you may want to create a program group and program items (icons) for Entrez and EntrezCf in your Program Manager window, if they have not already been created. Refer to the Microsoft Windows User’s Guide for instructions.
• Start the EntrezCf configuration application, and follow the instructions in the Configuration section.
CONFIGURATION
EntrezCf allows you to tailor your Entrez installation to suit your particular computer and network resources. Press the Next button in the opening window, leaving Show advanced settings unchecked. EntrezCf should normally be able to find the asnload and data directories.
If it cannot, it will put up another window and ask you to enter the paths to these directories.
EntrezCf then displays a window asking where the data sources are located. You can choose between CD-ROM Drive, Hard Disk, and LAN Fleserver for each of the discs. If you choose Hard Disk or LAN Fileserver, you or your LAN administrator will be expected to have already copied the contents of the relevant Entrez discs, or mounted the discs on a remote disc changer.
Note that you should choose LAN Fileserver if you are using a remote disc changer, even if the data are still on CDs. Otherwise, Entrez will believe you have a local CD-ROM drive dedicated to your computer, and may attemp to eject discs when you link to a different database.
Press the Next button to move to the next screen.
If you have specified a CD-ROM drive for any of the discs, the next window asks for the number of CD-ROM drives on your system. On a PC with Microsoft Windows, it will also ask for the paths or drive letters (e.g., D:\) for those drives. The Macintosh uses the volume names to access the discs, and doesn't need this information. Entrez will swap discs among one or two CD-ROM drives, if necessary. A new feature of Entrez is that any disc can be placed in any drive.
If you have chosen Hard disk or LAN fileserver, another screen will appear, asking for the paths to the various data sources. This information depends upon where you have copied the data.
Press the Next button to continue with the configuration.
EntrezCf then asks for you to insert the Entrez1 disc. It will next display a window asking if you want to copy index files to your hard disk for faster document retrieval. Copying all of the index files will take up around 15 Mbytes of space on your hard disk.
Press the Next button to move to the final screen.
The final window allows you to save the settings or to back up and review (and revise) your configuration instructions. When you press the Save settings button, EntrezCf will copy any requested index files and will write the ncbi configuration file. You can then run Entrez.
TROUBLESHOOTING
Application Software Problems
As a general rule, if you have a problem that occurs when you get a new release of Entrez, you should delete the old software and extract the version on the disc. You may also need to delete the ncbi configuration file (see below). The problem may have been noticed or reported, and addressed in the most recent update of the application.
If Entrez or EntrezCf fail, the cause may be that the ncbi configuration file has become corrupted.
You should try reinstalling and reconfiguring after first deleting the existing ncbi configuration file. (On the Macintosh this file is named ncbi.cnf, and resides in the System Folder or the System Folder:Preferences folder. Under Windows it is named NCBI.INI, and resides in the Windows directory.) If there is a problem it is best to first configure without copying index files (after deleting the configuration file). If this solves the problem then you can run EntrezCf again to reconfigure with copying index files.
Printer fonts can now be specified independently from screen fonts. See the section on Customization below. The DISPLAY font is used for displaying (and printing) records in MEDLARS, GenBank flat file, and FASTA formats, and for the MEDLINE and Sequence ASN.1 formats. These reports do not word wrap, so the printer font should be adjusted if they print past the right margin. The MEDLINE Report and Sequence Report formats do perform word wrapping.
Disc Recognition Failure
On the PC, if Entrez cannot find the CD, and the Windows File Manager also cannot open the CD icon (or indicates that there are no files on the disc), the problem may be caused by Windows overwriting the memory onto which the CD-ROM driver is mapped. You should exclude this region from being considered as available memory. To do this, determine the memory addresses that the CD-ROM drive is using (check the manual for how to read the switch settings on the interface card or call the manufacturer). Then, configure your memory manager or DOS extender program to exclude these addresses (check the manual for what command options to use or call the manufacturer for instructions).
On the Macintosh, if the CD is rejected as not being a “Macintosh disc”, you may have an extension (e.g., DOS Mounter) that preempts recognition of the ISO 9660 disc. If so, you should drag the offending file out of the Extensions folder and restart the computer. Another possibility is that your Foreign File Access and ISO 9660 File Access drivers did not load properly. These are automatically installed along with the CD-ROM driver in the Extensions folder. However, under System 7.0, they must manually be dragged into the System Folder itself, and the computer must then be restarted, in order for them to work. System 7.1 can use them in the Extensions folder.
CUSTOMIZATION
The entrez configuration file has several possible sections. This file can be edited with a text editor, after it is first created by Entrez. (On the Macintosh it is named entrez.cnf, and resides in the System Folder or the System Folder:Preferences folder, while under Windows it is named ENTREZ.INI, and resides in the Windows directory.) The explanations below are for those configuration file elements that are not documented elsewhere or set under program control:
[Section] Explanation
Key=Value
[PREFERENCES]
MAXLOAD=200 Maximum number of documents that can satisfy a Boolean query and still be retrieved.
MINPIXELWIDTH=300 Specifies the minimum display width and height (in MINPIXELHEIGHT=300 pixels) of MEDLINE and sequence reports.
SHOWASNPAGE=TRUE Adds an “ASN.1” folder tab to the MEDLINE and sequence reports. All MEDLINE and sequence data are stored in Abstract Syntax Notation 1 (ASN.1), and all other report formats are generated from this form.
[FONTS]
JOURNAL=Geneva,10,i These entries allow you to override the default font
... specifications used by the Entrez application. A
printer
font can be specified after the screen font and a vertical
bar (e.g., “Geneva,10,i | Times,12,i”).
[SAVE]
PATH=C:\SAVEHERE\ Path for saving files with the Save and Save All menu commands. Default is the current directory, i.e., the directory in which the Entrez application is located.
DEFREFFILE=ENTREZ.REF File name for saving MEDLINE records with the Save and Save All menu commands. Default is entrez.ref.
DEFSEQFILE=ENTREZ.SEQ File name for saving sequence records with the Save and Save All menu commands. Default is entrez.seq.
The PC/Windows version of Entrez allows you to set the TMP environment variable to specify the path to the directory in which temporary files will be created. You can add a statement setting this variable in your AUTOEXEC.BAT file. This is useful for installations that allow Entrez to be run over a local area network.
CREDITS
CD-ROM Data Coordination
Greg Schuler
Entrez Application Software
Jonathan Epstein, Chris Hogue, Jonathan Kans, Tom Madden, Jim Ostell, Greg Schuler, Alex Smirnov, Jinghui Zhang
Entrez Documentation
Diana Airozo, Jonathan Kans, Renata McCarthy, Rose Marie Woodsmall Data Specification (ASN.1)
Mark Boguski, Steve Bryant, Mark Cavanaugh, Colombe Chappey, Andrzej Elzanowski, Scott Federhen, Rand Huntzinger, John Kuzio, Detlef Leipe, Catherine Lukens,
Hitomi Ohkawa, Francis Ouellette, Greg Schuler, Karl Sirotkin, Tatiana Tatusov, Carolyn Tolstoshev, Jinghui Zhang
Neighbor Analysis
Brandon Brylawski, Hervé Récipon, John Wilbur Graphic Design
Greg Schuler
Production, Distribution and Support
Diana Airozo, Dennis Benson, Jim Fleshman, Lisa Hackett, Renata McCarthy, Barbara Rapp, Steven Rosenthal, Greg Schuler, Rose Marie Woodsmall Project Direction
David Lipman
ACKNOWLEDGMENTS
Sequence data have been incorporated from GenBank journal scanning and direct submission (the NLM’s Division of Library Operations); EMBL Nucleotide Sequence Database (European Molecular Biology Laboratory Data Library); DDBJ (DNA Data Bank of Japan); GSDB (Genome Sequence Database); SWISS-PROT Protein Sequence Database (Amos Bairoch and EMBL); PIR International (National Biomedical Research Foundation, Martinsried Institute for Protein Sequences, and Japan Institute for Protein Information Database); PRF (Protein Research Foundation, Osaka); PDB (Brookhaven National Laboratory Protein Data Bank); dbEST (NCBI);
and from sequences in patents published by the European Patent Office and the U.S. Patent and Trademark Office. GenBank contractor support has been provided by Management Systems Designers, Inc., UNISYS Corporation, ComputerCraft Corporation, and KEVRIC Company, Inc.
MEDLINE bibliographic data has been provided by the NLM’s Division of Library Operations and Office of Computer and Communications Systems.
The NCBI would like to acknowledge the following sources for their contributions to the map information in the GenBank Genomes division:
Drosophila Physical Map Bill Gelbart and Wayne Rindone, Harvard Human Genetic Map Ken Buetow, CHLC
Human Physical Map Lincoln Stein, Whitehead Institute, MIT Human Radiation Hybrid Map Kathleen McKusick and David Cox, Stanford Mouse Genetic Map Prakash Nadkarni, Yale, and Janan Eppig, Jackson Labs