The Business Master (3rd Edition)

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JEPRS User's Guide, page 1 Table of Contents Introduction to JEPRS . . . . 3 Adding References . . . . . 48 What is JEPRS? . . . . . . 3 Suggested Format . . . . 50 Features & Requirements . 4 Entering Sample References 54 Registration & Distribution 6 Further Help and Questions 7 Formatting References . . . 57 Pre-Defined Settings . . 57 Setting Up JEPRS . . . . . . 9 Starting Formatting . . 61 Files on Disk . . . . . . 9 Installation . . . . . . 10 Searching . . . . . . . . . 63 Starting JEPRS . . . . . 11 Pre-Defined Settings . . 63 Creating Your Own Starting a Search . . . 68 Database . . . . . . . 13 Maneuvering Through Utilities . . . . . . . . . 71 JEPRS . . . . . . . . 13 Importing . . . . . . . 71 Exiting The Program . . 16 Exporting . . . . . . . 74 Compressing the Database 76 The Main Menu . . . . . . . 17 System Information . . . 17 Format Styles: A Tutorial . 78 Comma-Delimited Output . 82 On-Line Help System . . . . 19 Context-Sensitive Help . 19 Printer Definitions: Tutorial 84 Sample Laser Printer Quick Start Tutorial . . . 21 Definition . . . . . . 84 Listing References . . . 21 Dot Matrix Example . . . 89 Adding References . . . 22 Searching References . . 23 Global Defaults . . . . 24 Appendices: Formatting References . 25 Importing References . . 27 JEPRS' Files . . . . . . . 90 Exporting References . . 29 Upgrading Version 1.x to 2.x 95 Global Defaults . . . . . . 31 Converting Format Files to a Editing Printer Definitions 35 Config File . . . . . 95 Editing Format Styles Running JConvert . . . . 96 (Journal Definitions) 39 Practical Uses: Number Files 98 Listing References . . . . 45 Editing & Updating References . . . . . . 46 Index . . . . . . . . . . . 101 JEPRS User's Guide, page 2 JEPRS! The Journal & Editorial Personal Reference System User's Guide Version 2.5 _______ ____|__ | (R) --| | |------------------- | ____|__ | Association of | | |_| Shareware |__| o | Professionals -----| | |--------------------- |___|___| MEMBER Disclaimer of Warranty JEPRS version 2.5 June, 1990 This software and documentation are sold "as is" and without by Louis M. Miranda warranties as to performance of P.O. Box 822894 merchantability or any other Dallas, TX 75382 USA warranties expressed or implied. Because of the various hardware After 01 September 1992 and software environments into Please Contact: which this program may be put, no Louis M. Miranda warranty of fitness for a 400 Selby Avenue #301 particular purpose is offered. St. Paul, MN 55102 Good data processing procedure dictates that any program be thoroughly tested with non- critical data before relying on "JEPRS" and "The Journal & it. The user must assume the Editorial Personal Reference entire risk of using this System" are trademarks of program. Any liability of the Louis M. Miranda; seller will be limited Program and Documentation are exclusively to product Copyr. 1985-1992 Louis M. Miranda replacement or refund of purchase price. JEPRS User's Guide, page 3 C H A P T E R O N E _________ Introduction to JEPRS #################################### This chapter of the JEPRS User's Guide will provide you with background information on the capabilities of the program. You will come away with an appreciation of what JEPRS can do, compatibility with other programs, new features of version 2.5, computer system requirements, and registration and shareware distribution information. ##################################### ************** What is JEPRS? ********** JEPRS (pronounced ``Jeepers!'') stands for the Journal and Editorial Personal Reference System. It is a program that maintains a database of references to articles published in journals, books, and/or magazines. You can add, edit/update, list, search, import, and export your reference citations. Also, print your references in virtually any style imaginable, including underlining, boldface, italics, superscripts, and subscripts. Lastly, JEPRS can read reference codes you place in your WordPerfect 5.0 and 5.1 manuscripts as well as PC-Write 3.0 manuscripts; it can then automatically generate a bibliography from those reference codes and produce a WordPerfect or PC-Write compatible output file; and then it can go back and replace your reference codes in your original manuscript with either an author/year citation or sequentially numbered citations. Why should you use JEPRS instead of some other program? There are three very good answers to that question: >> It's powerful. The combination of importing, exporting, searching, formatting, and word processor file capabilities of JEPRS are simply unequaled. JEPRS is very much the equal of programs costing many times more. >> It's easy to use. JEPRS is run by pull-down menus and pop-up dialog boxes, so you don't have to remember arcane commands. It also has most of its defaults pre-defined, so you don't have to wade through screen after screen of questions. In addition, JEPRS sports a context-sensitive help system-just press the [F1] key for instant help. JEPRS User's Guide, page 4 >> It's inexpensive. At a cost of only US$49.95, JEPRS is a great bargain. >>>>> Compatibility with Other Programs <<<<< JEPRS maintains its own proprietary database files that are not readable by any other program. Nonetheless, it can be compatible with virtually any reference management system you may be using now. That's because the combination of JEPRS with Med2Go can read any of the following file formats: Comma-delimited MedLine BRS/Colleague ERIC PsycLit JEPRS can also write any of the following file types: Comma-delimited MedLine This makes it possible to trade references among the various programs that you and your colleagues may be using. For example, JEPRS can import MedLine/NLM files from Current Contents on DisketteTM. Likewise, JEPRS references output to a MedLine file can be read into most commercial reference management systems. And comma-delimited files can be read into most commercial generic database systems, such as dBase, Excel, and Paradox. ************** Features & Requirements ********** >>>>> New Features of Version 2.5 <<<<< Several enhancements to JEPRS version 2.0 have occurred with version 2.5. These have been listed in the file called WhatsNew.Doc, but the major points are reiterated here: >> WordPerfect and PC-Write Support. JEPRS can now directly output WordPerfect 5.x and PC-Write 3.0 files. So now you can take advantage of your word processor's advanced capabilities, such as line justification, advanced formatting, and printer downloadable fonts. >> Automatic Bibliography Generation. Simply enter special codes into your word processor manuscript (such as {J#123} ), and JEPRS can automatically read the codes and generate a bibliography that includes the references you specified (such as #123). In addition, JEPRS will then go back and replace the codes with sequential numbers (1, 2, 3, ...) or author/year citations (Miranda, et al. (1990)). JEPRS User's Guide, page 5 >> Mouse Support. Use of a mouse is now supported at all menus, and in the Help screens. (Mouse support is not available for text editing.) >> Adding/Editing References. When adding or editing/updating references, entering text is now much easier. That's because multiline fields (such as authors, journal, and keywords) can now be edited in one line, without having to press [Enter] to go to the next part of the field. >> Importing: Med2Go. Registered users of JEPRS now receive a free utility called Med2Go. Med2Go lets you translate Comma-Delimited, ERIC, BRS/Colleague, and PsycLit files into MedLine files. The MedLine files can then be directly imported into JEPRS using the Utilities/Import Menu. >> Sorting. When viewing results from a search, and when formatting output, you can now sort the references by author, year, or journal. Sorting is also much faster than in version 2.0. >> Periods After Author Initials. If you enter your authors' initials without periods, you can now define your format styles such that periods will be automatically inserted. In other words, JEPRS can now convert ``Miranda LM'' to ``Miranda L.M.''. >>>>> System Requirements <<<<< JEPRS is made to run under DOS (version 2.0 or higher) on IBM PCs, PS/2s, and compatibles. JEPRS itself requires only 320 kilobytes of RAM, so any computer with 384k or more can run the program. A hard disk is not required for proper operation, but searches are considerably faster on a hard disk compared to floppies. In an average JEPRS database you could probably store 300 references per 100 kilobytes of disk space (i.e., you could probably store 1000 references on a 360k floppy or 4000 references on a 1.44 megabyte disk). JEPRS User's Guide, page 6 ************** Registration & Distribution ********** >>>>> Registering JEPRS <<<<< JEPRS is distributed as ``shareware''. Shareware is simply a method of distributing the software. There are many shareware programs that meet or exceed the capabilities of similar commercial programs. The shareware concept means that you are free to try the program for a 30 day evaluation period at no charge. If, at the end of that time, you decide you like it enough to continue using it, then you are obligated to pay a registration fee to the author, just like any software you purchase in a store. It is not public domain, and it is not free. Unregistered copies display Unregistered Version on the bottom right side of the >Main Menu.< When you register, you will receive information on disabling that message, and also disabling the >Opening Screen<. The registration fee is ridiculously small considering the amount of work JEPRS can do. The current fee is only $49.95. Registration has several advantages: The latest version of JEPRS. The latest version of Med2Go. A 60-page laser-printed User's Guide (this is a printed version of the JEPRS.Doc file). Six months of free customer support (by US Mail and CompuServe Mail). Update Notices. Registered users are always kept up-to-date with reports of minor releases (to fix bugs or add small numbers of features). Major updates are planned about once a year. The latest version of Peruse. Peruse is a free utility (written by a fellow ASP member) that lets you easily look through any text file you have on your computer. You can use a mouse to scroll through the text in any direction. There is on-line hypertext help, and a customization program too. To order/register your use of JEPRS, print out the ``Order.Doc'' file that's included on the disk, and fill out the information requested. Or, when you see the >Opening Screen< when JEPRS first starts, press [F1] to see ordering information, then press [PrintScreen] to print out the form on your printer. >>>>> Shareware Distribution <<<<< If you want to distribute JEPRS to other users (friends and business acquaintances, for example), you are free to do so as long as you distribute all the files that you received, in their original JEPRS User's Guide, page 7 condition (that is, unmodified by you) at no charge. For commercial distributors and bulletin board system operators, please see the file called ``Vendor.Doc'' on the distribution disk, for distribution requirements. >>>>> ASP: The Association of Shareware Professionals <<<<< ASP, the Association of Shareware Professionals, is a professional group for shareware authors who are committed to the shareware concept. It also provides benefits to users such as yourself: Members of the ASP must adhere to a code of ethics. Also, ASP Member shareware programs must not be `crippled': they must be fully-functioning versions of the software. In addition, users have the opportunity to bring unresolved complaints with authors to the ASP Ombudsman who can make final decisions. If an author is a member of ASP, it is a good indication of two things: 1) The author's commitment to the program, and 2) The general quality of that program. How can you be sure that a program is written by an author who is a member of the ASP? Just look for the ASP logo: _______ ____|__ | (R) --| | |------------------- | ____|__ | Association of | | |_| Shareware |__| o | Professionals -----| | |--------------------- |___|___| MEMBER This program is produced by a member of the Association of Shareware Professionals (ASP). ASP wants to make sure that the shareware principle works for you. If you are unable to resolve a shareware-related problem with an ASP member by contacting the member directly, ASP may be able to help. The ASP Ombudsman can help you resolve a dispute or problem with an ASP member, but does not provide technical support for members' products. Please write to the ASP Ombudsman at P.O. Box 5786, Bellevue, WA 98006 or send a Compuserve message via CompuServe Mail to ASP Ombudsman 70007,3536. For more information on the ASP, or on shareware in general, enter ``Go Shareware'' at any CompuServe ! prompt. ************** Further Help and Questions ********** Questions and comments regarding JEPRS' operation are always JEPRS User's Guide, page 8 welcomed. Feedback from users is the best way I have of finding out what features you want to see in future versions. Every major new feature has been requested by a user of the program. Your voice counts. ================================================================== Customer Support Louis M. Miranda 400 Selby Avenue #301 St. Paul, MN 55102 CompuServe Mail: 73567,471 =================================================================== If you cannot reach me by mail, please try to contact me via CompuServe. If you do not have access to CompuServe, please try to contact me through the ASP: Executive Director Assoc. Shareware Professionals 545 Grover Road Muskegon, MI 49442-9427 Thank you for your support of JEPRS! JEPRS User's Guide, page 9 C H A P T E R T W O _________ Setting Up JEPRS #################################### This chapter provides information on setting up JEPRS on your own system. In addition to a listing of the major files on the distribution disk, this chapter will tell you how to: install JEPRS on your own computer; start the program (including command-line options); maneuver through the menus; create your own database; and terminate the program. ##################################### ************** Files on Disk ********** Here is a list of the major files that make up the JEPRS system, and a short description of their use (A complete list of files is in the ``ReadMe.Doc'' file): >> JEPRS.Exe. This is the JEPRS program itself; entering JEPRS at the DOS prompt (C:>) starts the program. >> ReadMe.Doc. This file contains the most basic information for starting JEPRS. It also lists all the files you should find on the distribution disk. >> JEPRS.Doc. The file you are reading now: The User's Guide to JEPRS. This is the main documentation file for the program. It contains background information on JEPRS, system requirements, registration information, setting up the program, tutorials on JEPRS' main functions, and a detailed listing of each menu's options. >> WhatsNew.Doc. New features of the latest version of JEPRS are listed in this file. >> Order.Doc. Printing this file on your printer produces a form you can use to register your copy of JEPRS, as well as make comments about the program. >> JEPRS.Hlp. Contains the text for JEPRS' context-sensitive help screens. If JEPRS can't find this file when it is running, you will JEPRS User's Guide, page 10 not be able to get on-line, context-sensitive help by pressing the [F1] key. >> Ref1.JPR. A sample database file for JEPRS. It contains the actual text of the database. >> Ref1.JPK. The `key' file that goes along with the Ref1.JPR database file. You cannot use a database file without a key file. >> JEPRS.Cfg. A sample config (`configuration') file that contains 30 formatting definitions, printer control codes, default directory and file name information, and user-definable Global Defaults. ************** Installation ********** Before installing JEPRS, make a copy of all the files on the program disk. Never use your original disk to run the program. This is especially true with a shareware program like JEPRS, since you must distribute the software exactly as you received it. If you are upgrading from version 1.0 or 1.1, please see the chapter in the Appendix on converting Format files to Config files. >>>>> Floppy Drive Systems <<<<< If you don't have a hard disk, simply use your new copy disk of JEPRS as your working disk; there's no need for any special installation procedures. If you are updating a previous version of JEPRS, copy the following files from the new version's disk onto your present working disk: JEPRS.Exe JEPRS.Hlp ReadMe.Doc WhatsNew.Doc The only file that is absolutely necessary to copy is ``JEPRS.Exe''; however, if you want the >Help< screens to work, you must also copy ``JEPRS.Hlp'' to your work disk. >>>>> Hard Disk Systems <<<<< If you have a hard disk, follow these instructions to install JEPRS on your hard disk. Once you make a copy of the original disk, insert the copied disk into one of your floppy drives. Now make sure your default drive is the hard disk (that is, if your hard disk is drive C:, then enter C: at the DOS prompt). Now enter the following commands at the DOS prompt (these commands will create a new directory called ``JEPRS'', and copy all the files on this disk to that directory): C:\> cd \ JEPRS User's Guide, page 11 C:\> md JEPRS C:\> cd \JEPRS C:\JEPRS> copy a:*.* This assumes that your disk is in floppy drive A:. Substitute a:*.* above with whatever your floppy drive is (e.g. b:*.* if your disk is in floppy drive B:). Now enter dir at the DOS prompt to see if all the files are there. If not, go through the procedure again just in case you missed a step or entered something else by mistake. ************** Starting JEPRS ********** You start the program by simply entering the command ``JEPRS'' at the DOS prompt, like this: C:\JEPRS> JEPRS If all goes well, three short messages will scroll onto the bottom of the screen and the >Welcome Screen< will appear. Press [F1] to get ordering information, or any other key to go to the >Main Menu<. (Once you have registered your shareware version of JEPRS with the author, you will be provided with a way to disable the opening screen.) If you are starting JEPRS without a database (for example, when you are creating a new one), you will get an error message stating that JEPRS can't find the database files; this is normal. Just press [F6] to create your own database (see below for detailed instructions on creating your own database), [F4] to specify a new name, or [F10] to exit the program. >>>>> Command Line Options <<<<< There are several command line options that you may use when starting JEPRS. These include 1) Config file name and 2) Screen color options. The general format for entering these options is: C:\JEPRS> JEPRS <Config filename> /opt where <Config filename> is a valid filename for your config file, including a path if necessary, and /opt is any combination of screen color options (see below). >> Config Filename. If for some reason you wish to use a different name for the Config file (in other words, you're not calling it JEPRS.Cfg or it's not in the current drive and/or directory), then you can specify its name on the command line, like this: C:\JEPRS> JEPRS MyRefs.Cfg This tells JEPRS to use MyRefs.Cfg as the Config file, which must be in the current directory. If you wish, you may also specify the drive JEPRS User's Guide, page 12 and/or directory it is in, if this is not the current one. For example, if you keep MyRefs.Cfg in a directory called C:\PRINTER, then start JEPRS like this: C:\JEPRS> JEPRS C:\PRINTER\MyRefs.Cfg This tells JEPRS not only the name of the file, but also in which subdirectory it is located. >> Screen Color Options. In addition to Config filenames, you can specify one or more options dealing with the appearance of text on the screen. The /opt shown in the command line above is any combination of: /A -> amber monitor with color video card /G -> green monitor with color video card /B -> turns blinking off in formatting /C -> turns colors off in formatting Actually /A and /G are the same command, but both options are provided so that they are somewhat mnemonic. These two commands put the program into Black and White Mode (see the >Global Defaults Menu<); that is, all text is black, white, or gray, so that it can be properly displayed on any monitor. The /B option turns off the blinking attribute of italicized text when displaying output from the >Format Menu< on the screen. The /C option turns off the color attributes of boldface and underlined text when displaying output from the >Format Menu< on the screen. Boldface is normally displayed as white on cyan, and underline is normally blue on black, but both become black on cyan when this option is invoked. You can mix and match options in any combination; so if you want to use your Config file called MyRefs.Cfg (in the subdirectory called C:\PRINTER); you hate blinking characters; and you are using an amber monitor with a CGA video adaptor, you could start JEPRS like this: C:\> JEPRS C:\PRINTER\MyRefs.Cfg /B/A >>>>> Running Under Microsoft Windows <<<<< JEPRS and Med2Go can be run under Microsoft Windows without any modifications. You must run them as ``DOS applications'', though, since they are not Windows-specific applications. Here is how to set up JEPRS with its own icon in Windows version 3's Program Manager. Use the mouse to select the Program Group you want JEPRS to appear in. Then at the Program Manager menu choose [F]ile/[N]ew, then click on Program Item and choose [OK]. Now the Program Item Properties dialog box appears. At the [D]escription, enter ``JEPRS'', and at the [C]ommand Line, enter the path and filename for JEPRS. For example, if JEPRS is on drive C: in the directory called \JEPRS, then enter ``C:\JEPRS\JEPRS.Exe''. You can JEPRS User's Guide, page 13 also include command-line options here (described above). For example, if your JEPRS Config file is called MyRefs.Cfg, then you would enter the following at [C]ommand Line: C:\JEPRS\JEPRS.Exe C:\JEPRS\MyRefs.Cfg You can also add a special icon for JEPRS. Click on the button that says Change [I]con... and the Select Icon dialog box appears. At [F]ile Name, enter the path (drive and directory) where your JEPRS files are, specifying a file name of JEPRS.Ico. To use the same example as before, if your JEPRS files are on drive C: in the directory called \JEPRS, then enter ``C:\JEPRS\JEPRS.Ico'' at [F]ile Name. Then click on View [N]ext to see what the icon looks like. Now keep clicking on the OK buttons until you are back at the Program Manager. You'll notice that the J! JEPRS icon is now displayed in your program group. To start JEPRS, simply double-click on this J! icon. ************** Creating Your Own Database ********** When using the tutorial, JEPRS automatically uses the sample Ref1.JPR and Ref1.JPK database files. Now you probably want to create your own database. Once at the >Main Menu<, press [F2] to go to the >Global Defaults Menu<. Press [F]iles and then [R]eference file; now enter the name that you want for your database file (for example, MyRefs.JPR) and press [Enter]. JEPRS will then ask you for the name of the matching Key file, and it will automatically provide you with a default name (such as MyRefs.JPK, in this example). You can use the arrow keys, [Home], [End], [Insert], and [Delete] to edit the name any way you wish. After you press [Enter] to accept the name, JEPRS will pop up with an error message-don't worry, just press [F6] and JEPRS will create new Database and Key files with the names you specified. Then press [Esc] twice to return to the >Main Menu.< And now one last thing: save the new Database & Key file names into your Config file so you won't have to go through this whole procedure everytime you start JEPRS. Do this now by pressing [F2] to return to the >Global Defaults Menu<; then press [D]efaults, then press [S]ave defaults + filenames. So from now on when you start JEPRS with the Config file, it will automatically look for your new MyRefs.JPR and MyRefs.JPK files. ************** Maneuvering Through JEPRS ********** JEPRS User's Guide, page 14 >>>>> Screen Design <<<<< The screen is basically divided into 5 sections; since every menu has this same basic layout, let me describe some background about it. >> Menu Title. The topmost line on the screen always contains the menu title. This is meant to give you some idea of where you are in the program, and what you can do. >> Menu Line. The second line from the top contains a list of the actual commands you have available to you. When the menu line is active, the first letter of each command is highlighted and one of the commands is completely highlighted. This is to let you know that you can just press the highlighted letter to invoke the command, or if you just press [Enter] then the command that is completely highlighted is automatically invoked. You can change the highlighted command by using the left and right arrow keys, or by pointing the mouse at the command name and pressing the left mouse button. >> Format/Terms/Filename Area. In the middle left of the screen, one of three lists are displayed: either a list of possible format styles for formatting, a list of the terms you are using for searching, or the directory & file names you have programmed into the Config file. On the >Main Menu<, for example, the file names are listed. >> Messages Window. On the bottom left side of the screen, there is generally a messages window. It has basically two functions: To provide you with a short description of what you can do, and a list of the function keys you can press and what their functions are. >> Defaults/Information. The right side of the screen lists the current local or global defaults, and sometimes some additional information. >>>>> Menus & Prompt Boxes <<<<< When you are at any of JEPRS' menus, you can change the highlighted command with the cursor keys, but no matter what alpha-numeric key you press, it is not actually displayed on the screen. That's because you are entering input for a Menu. You select a menu item in any of 3 ways: >> Arrow keys. Use the arrow keys to highlight the item of choice, and then press [Enter]. >> Highlight letter. Press the highlighted letter of the function you want to invoke. >> Mouse. Use the mouse to point to the item you wish to invoke, then press the left mouse button. JEPRS User's Guide, page 15 The mouse buttons have the following keystroke equivalents: =================================================================== Left mouse button = [Enter] Right mouse button = [Esc] Both mouse buttons = [F1] (Help) =================================================================== The other type of input is for a Prompt. An example of a prompt is when you enter Search Terms on the >Search Menu<. The screen shows the prompt ``Enter Search Terms:'' and a reverse video box is displayed. Often, there is a default value already present; in that case, just pressing [Enter] will cause that default value to be used. Alternatively, you can just start typing your new entry, and the default one will be replaced by what you type. (The mouse is not functional at a prompt where you have to enter anything other than a yes/no answer.) One nice feature about prompts and their default values is that in addition to either taking them as they are or completely replacing them, you have the option of editing them. In order to edit text displayed at a prompt (as oppposed to replacing it), the first key you press must be an editing key which must be one of: [RightArrow] [LeftArrow] [Ctrl + RightArrow] [Ctrl + LeftArrow] [Delete] [Ctrl + End] [Insert] [Home] [End] If you press one of these keys before pressing an alpha-numeric character key, then you can edit the text displayed after a prompt. For example, let's say you're entering a file name on the >Global Defaults Menu< and the old file name is C:\Lou\Lab\JEPRS\OldFile.JPR There are two ways to change the file name to ``NewFile.JPR''. The first (hard) way is to just start typing the whole name in: C:\Lou\Lab\JEPRS\NewFile.JPR The second (easier) way is to edit the file name: 1. When the old file name is displayed, press the [End] key and then press the [LeftArrow] key until the cursor is under the ``O'' in ``OldFile''. 2. Now press [Delete] 3 times to delete ``Old''. 3. Just type in ``New''; the display should now read: C:\Lou\Lab\JEPRS\NewFile.JPR 4. Press [Enter] to accept your changes. JEPRS User's Guide, page 16 This saves you a whole lot of unnecessary typing, so keep it in mind whenever you need to change a default value at a prompt. ************** Exiting The Program ********** When you are done with JEPRS, return from wherever you are to the >Main Menu< (usually by pressing [Esc]), then exit the program as follows: 1. Press [E] . . . or . . . 2. Press [Esc] . . . or . . . 3. Use the arrow keys or the left mouse button to highlight >Exit<, then press [Enter] . . . or . . . 4. Click the right mouse button. When you do this, JEPRS will beep (unless you turned off the ``Error/Warning Beep'' on the >Global Defaults Menu<) and then ask you if you really want to exit the program; if you do, press [Y] (or point the mouse at the letter `Y' in the prompt box, and click the left mouse button); if you don't, press [N] (or any other key or the right mouse button). If you press [Y], you will be returned to DOS, and your screen colors will return to what they were before JEPRS started. Of course, the other way of exiting JEPRS is to simply shut off your computer-but don't do that. If you turn off your computer without exiting JEPRS, then you may lose data from your data files. So remember, always exit JEPRS properly before turning off your computer. JEPRS User's Guide, page 17 C H A P T E R T H R E E _________ The Main Menu #################################### Once you start JEPRS, and you pass the >Welcome Screen<, you are presented with the >Main Menu< from which you can enter any of JEPRS' commands. ##################################### ************** System Information ********** Notice the information on the right side of the screen labelled ``System Information.'' This provides some useful information to you regarding the environment that JEPRS is working in. It is also information that is useful to me if you discover any problems with the program. If there are any problems, it is very helpful if you copy down the information here (or press [][PrintScrn] to print it on your printer) and send it to me along with your problem. Each item is described briefly here: >> Error/Warning Beep. This tells you whether the error beep is turned on or off. You can change its setting on the >Global Defaults Menu<. >> Total Memory (RAM). This just informs you how much memory you have installed in your computer. Some IBM computers display one kilobyte less than they actually have (e.g., 639kb is displayed even if your computer really has 640kb installed). If you're using Windows 3.0, this figure reflects Windows' allocation of memory, and may not exactly reflect how much memory you have physically installed in your computer. Also, JEPRS cannot detect `extended' or `expanded' memory, so if you have this kind of memory, JEPRS doesn't know it's there and will not report it or use it. >> Memory Available. This tells you how much extra space JEPRS has available to it. The bigger your database, the smaller this number. Again, if you're using Microsoft Windows, you can edit your PIF file settings to increase or decrease the amount of space allocated to JEPRS. Memory Available will vary depending on how many TSR (``Terminate & Stay Resident'') programs you have in memory, and the JEPRS User's Guide, page 18 number of successful matches in your last search. If you have performed a search with a large number of matches, this can tie up memory; if you plan on sorting formatted output on the >Format Menu<, you can free up most of your memory by deliberately performing a search that will have only a few matches. >> Number of references in reference file. The total number of reference citations in your database file is reported here. When you start a new database, it should say zero, and when you Add or Import references, it should go up correspondingly. >> Number of relocated references. JEPRS stores your references in a very compact format. The only disadvantage to this method is that if you edit any of your references to make them longer, some disk space is wasted. When this happens, JEPRS increments the number of relocated references by one. After you have accumulated 20 or so of these moved references, it starts to take up valuable disk space. To see how to get rid of these unused references, see the >Utilities/Compress Database Menu<. >> Version number. For version 2.50, JEPRS was released to the public in December 1990. Always let me know what version you are using if you report a problem. >> Unregistered Version. If you see this on the screen, it means you are still evaluating the shareware version of JEPRS. Shareware means that you are free to try the program out for 30 days, after which you must either stop using the program, or register with the author. For information on registering with the author, please see the file called Order.Doc, or press [F2] (>Global Defaults Menu<), then Defaults, then Ordering information. When you register your use of JEPRS, the ``Unregistered Version'' text will change to ``Registered Version'', and you will be given information on how to disable the >Opening Screen<. >> DOS version. This tells you which version of DOS you are using (e.g., 2.11 or 3.21) to run JEPRS. >> Time and date. The current time and date are displayed on the bottom of the screen. >> Directory & Filenames. You can change any of these names at the >Global Defaults Menu<. JEPRS User's Guide, page 19 C H A P T E R F O U R _________ On-Line Help System #################################### In order to make your life as simple as possible, JEPRS provides you with on-line context-sensitive Help screens at the press of a key-the [F1] key. ##################################### ************** Context-Sensitive Help ********** At most points within JEPRS (whenever you see ``[F1]=Help'', and sometimes even if you don't), you have the option of pressing [F1] to get Help. General help is obtained by pressing [F1] while still at the >Main Menu.< To obtain help with any command on the >Main Menu<, invoke that command, and then press the [F1] function key. After pressing [F1], you should see the Help screen on the left portion of the display (so now you can see your Defaults on the right side of the screen at the same time). The Help facility provides context-sensitive help no matter where you are in the program. >>>>> Scrolling Through Help <<<<< After asking for help, several keys are displayed on the bottom of the Help window: [Up Arrow], [Down Arrow], [PgUp], [PgDn], [Home], [End], and [Esc]. Here is a short description of what each of these keys does: >> Up/Down Arrows. You can scroll through the text on the Help Screen by pressing the arrow keys. Each key press moves you up or down one line at a time. JEPRS stops when you have reached the beginning or end of Help. >> PgUp/PgDn. If more than one page of help text is available, you can use these keys to page through the text 20 lines at a time. >> Home/End. Pressing these keys will bring you to the very first or the very last page of the help text, respectively. JEPRS User's Guide, page 20 >> Esc. When you are finished looking at the Help screen, just press [Esc] to return to where you were in JEPRS before you asked for Help. >> Mouse Functions. New in version 2.5 is the ability to use a mouse. Pressing the right mouse button is the same as pressing [Esc]; that is, it exits you from Help. You can also use the mouse to point to any of the key labels at the bottom of the Help window, and then press the left mouse button to invoke the function. For example, if you place the mouse pointer on the key label [PgDn] and press the left mouse button, then the help text will scroll down one screen, just as if you had pressed the [PgDn] key on your keyboard. >>>>> The Help File <<<<< In order for Help to work, JEPRS must be able to find the file called ``JEPRS.Hlp''. If JEPRS can't find this file, it displays an error message: JEPRS.Hlp not found. Press any key to continue. when you try to get Help. The Help file must be in either the current directory or the directory specified on the >Global Defaults Menu<. Each Help file is specific for each version of JEPRS. Therefore, if you get an update (for example, you switch from JEPRS version 2.06 to version 2.50) you must replace the old Help file with the new one supplied with the update. Otherwise, Help will provide incorrect information. JEPRS User's Guide, page 21 C H A P T E R F I V E _________ Quick Start Tutorial #################################### Since JEPRS is so powerful, beginners can get bogged down trying to read the whole manual. So this chapter will take you on a quick tour of the capabilities of the entire program. After you complete this chapter, you should have a good feel for the overall capabilities of JEPRS. Parts of this tutorial assume you are using the sample files that came on your JEPRS distribution disk. ##################################### ************** Listing References ********** When you are at the >Main Menu<, simply press [L]ist to view the references in your database. You'll immediately notice that references are made up of any combination of: >> Title. >> Author. >> Journal. >> Volume (Issue). >> Page. >> Year. >> Citation Type. >> Reference Number. >> Editor. >> Publisher. >> Keywords. Function keys that you can use are listed at the bottom of the screen. The [Page Up] and [Page Down] keys will list the previous and next references, respectively. When you know the number of the reference you wish to view, you can type in the number and press [Enter] to go immediately to that reference. You can also use the function keys listed to send the reference to a text file, number file, or your printer. (For more information on these files, see the Appendix.) This is also the place where you can edit or delete your references. When you press [F4], you enter the edit mode, and can JEPRS User's Guide, page 22 modify or erase the current reference. You edit references the same way you add them, so see the section on Adding References for information what keys you can use to edit references. If you're in edit mode, press [Esc] to go to the menu at the top of the screen, then select [A]bandon to return to the >List References< screen. Press [Esc] to return to the >Main Menu<. ************** Adding References ********** Press [A]dd at the >Main Menu< to go to the >Add References< screen. The screen looks very much like the >List References< screen, and identical to the edit mode screen. You can move around the fields, and within the fields, just like most other programs on the market today: use the editing keys on the right side of your keyboard. There is also a list of keys and their functions on the bottom of the screen. If you need more help moving around the screen, see the chapter on Adding References. New in version 2.5 of JEPRS is the ability to edit multi-line fields (such as the title, which can be up to 3 lines long) as if it were one extended line. That is, if you enter text that's too long to fit in the editing window, JEPRS will automatically scroll left and/or right to let you see all that you're editing. You can edit any of the fields on the screen with one exception: the reference number. This number is assigned by JEPRS and will never be changed. The reason is that you can use JEPRS to read your manuscripts and automatically generate a bibliography (a new feature in version 2.5); if you were allowed to change the reference numbers, then JEPRS might insert the wrong reference into the bibliography that it generates. A nice feature of JEPRS that is missing in many other programs is the ability to use foreign (i.e., non-English) characters in your database. The characters that JEPRS can use are those in the IBM ``extended ASCII'' character set. To insert an extended character (such as a greek `alpha'), first type [^P] (that is, hold down the [Ctrl] key and press the [P] key once) and then hold down the [Alt] key and enter the ASCII code on the number pad on the right side of your keyboard. Since the ASCII code for `alpha' is #224, you would hold down the [Alt] key and then press [224] and then let go of the [Alt] key. You should now see an alpha ( ) on the screen. When finished adding or editing the reference, press [Esc] to go to the menu at the top of the screen. For now, press [A]bandon and then [M]ain Menu to return to the >Main Menu<. ************** JEPRS User's Guide, page 23 Searching References ********** One of JEPRS' most powerful routines is its >Search Menu<. You can perform anything from a very simple search (for example: find all references that contain an author named Wright) to complex searches that include AND/OR/NOT Boolean logic (such as find all references written by Wright or Weintraub and appeared in Cell or Science or Nature and between 1989-1990 and contain the keywords Differentiation or Muscles). To perform a simple search, first go to the >Search Menu< by pressing [S]earch at the >Main Menu<. The actual searching is done by pressing [G]o. But before you do that, you have to tell JEPRS what to search for. The fields to search through (for example, Authors) and the text to search for (for example, ``Wright'') are called `Terms' in JEPRS. So, to specify your Terms for a search, press [T]erms at the >Search Menu<. JEPRS asks you to ``Enter Search:''. This is where you enter the field to search through. The messages window displays a list of fields you can enter (as well as the Boolean operators you can use). For a simple search, just enter one field letter. Try entering an `A' for Authors, and then press [Enter]. Next, JEPRS gives you a blank line to enter the text to search for. Since, we'll be looking for all authors with the name `Wright', enter `Wright' and press [Enter]. Now you're back at the menu. To start the search, just press [G]o. While no matches are found, JEPRS will display the status in the Messages window. Once any matches are found, JEPRS automatically switches to the >Search Results< screen. It continues to update the display as new references are found. When it's done searching, you can use the up & down arrow keys to move the cursor to each reference. The bottom of the screen lists each function key you can use. For example, you can use function keys to mark, print, and view each reference. To view a reference in its entirety, just press [Enter] when the cursor is at that reference. That will bring you to the >List< screen, where you can view or edit the found references. >>>>> Advanced Example <<<<< Let's say you have to give a lecture on muscle cell determination and differentiation. You know you have many papers in your database that were authored by Wright, Emerson, Lassar, and Weintraub. The only problem is that, while each of these people publish papers of interest, they do not necessarily publish papers together. Most programs only allow you to perform searches using and (that is, ``find all papers by Wright and Emerson and Lassar and Weintraub'') which JEPRS User's Guide, page 24 won't work in this case. But JEPRS can handle this with no problem. Try the following search by pressing [T]erms at the >Search Menu< and entering the text as follows: Enter Search: A/A/(A+A)+Y Wright Emerson Lassar Weintraub 1985-1990 This is a search for (author = Wright) or (author = Emerson) or (author = Lassar and author = Weintraub) and (year = 1985-1990). Lassar & Weintraub are placed in parentheses since they are often authors on the same papers. This kind of a search, which would be an extremely common occurrence, is actually not possible in many other reference management programs. And don't think that JEPRS only allows you to do this with authors; you can do it with any and all of the searchable fields (see the Messages window after pressing [T]erms at the >Search Menu< to see a list of the searchable fields, or consult the chapter on Searching). ************** Global Defaults ********** In addition to the `local' [D]efaults that JEPRS provides on the >Search<, >Format<, >Import<, and >Export Menus<, JEPRS provides >Global Defaults< that affect your entire JEPRS session. This includes specifying printer settings, the word processor you use, whether you want error beeping turned on or off, color vs. monochrome mode, etc. To get to the >Global Defaults Menu<, press [F2] at any of the >Search<, >Format<, >Import<, or >Export Menus<. To specify the word processor that you will use (JEPRS currently supports WordPerfect 5.x and PC-Write 3.0), choose [D]efaults/[W]ord Processor Type; then select either [W]ordPerfect or [P]C-Write. Then press [Esc] once to return to the menu. Now select a printer by choosing [U]se Printer #; a pop-up menu will list the available printers. Choose the one that most closely resembles your printer; if none of them does, you'll probably want to look at the chapter on Global Defaults later on in this User's Guide. To make sure your choices are saved in the Config file, choose [S]ave Defaults+Files at the [D]efaults menu. From now on, whenever you start JEPRS with this Config file, these defaults will be automatically selected for you. One more thing about the >Global Defaults Menu<: you can temporarily access DOS without exiting JEPRS. To do this, press [G]o To DOS and you will get the DOS prompt; the normal DOS prompt is modified to remind you to type `EXIT' and press [Enter] to return to JEPRS. (If you do not have enough memory, you will get an error JEPRS User's Guide, page 25 message; don't worry, just press any key to continue.) Now press [Esc] until you return to the >Main Menu<. ************** Formatting References ********** The whole point of owning a reference management system like JEPRS is to format the references in a variety of format styles. So what can JEPRS do in terms of formatting? Quite a bit, actually. At the >Main Menu<, press [F]ormat to go to the >Format Menu<. As with searching, formatting is started by pressing [G]o. But you'll want to specify some parameters before you start. First of all, you'll want to tell JEPRS which of the 30 format styles to use. So press [F]ormat at the >Format Menu< to access the format style selection menu. Use the up & down arrows and the [Page Up] & [Page Down] keys to select the style you want (the arrowhead will move to show you which one is currently selected). Then press [Enter] to confirm your choice, and you will be returned to the >Format Menu<. JEPRS lets you specify the source and destination of the references. To specify the source of the references to format, press [I]nput, and then choose from the pop-up menu; for now, choose [R]eference file, and then press [Enter] twice to accept the defaults (first and last references, inclusive). To specify the destination of the formatted references, press [O]utput, and then choose from the menu; for now, choose [S]creen, and then press [Y]es; and press [Esc] to return to the >Format Menu<. Now press [G]o to start the formatting. The screen will clear, and the formatted references will start to scroll across the screen. Press [Scroll Lock] to halt the screen (JEPRS is probably one of the few programs you use where the [Scroll Lock] key actually has a function). To re-start the formatting, just press the [Scroll Lock] key again. You'll notice that the text appears in different colors, unless the Global Default for [F]ormat screen colors has been turned off. Since your PC screen can't display italics, underlining, subscripts, and superscripts, I have resorted to displaying each of these attributes in a different color. Normal text is black on cyan, bold is white on cyan, and underlined is blue on black. If you send this to your printer (using [O]utput=[P]rinter), then these attributes would appear on the printed output (but make sure your printer is set up first, at the >Global Defaults Menu<). If you stopped the text from scrolling, then press [Scroll Lock] to get it going again. Then press [Esc] to abandon formatting, and answer [Y]es to the dialog box that asks you if you really want to terminate formatting. This will return you to the >Format Menu<. JEPRS User's Guide, page 26 The >Format Menu< is where you do all formatting in JEPRS, except for exporting references in MedLine format. If you wanted to send the output to a PC-Write 3.0 or WordPerfect 5.x file, then you would specify [O]utput=[W]ordProcFile. Likewise, direct printer output would be sent by specifying [O]utput=[P]rinter. >>>>> Automatic Bibliography Generation <<<<< Beginning with version 2.5, JEPRS can ``read'' your manuscript and automatically generate a bibliography based on the reference numbers you place in the manuscript; it can then go back and replace those numbers with either (a) Author+Year or (b) Sequential Number citations. Only WordPerfect 5.x and PC-Write 3.0 are supported for this feature. An additional limitation is that JEPRS cannot replace citations that occur in WordPerfect Text Boxes (JEPRS can find the references there, but it cannot go back and replace them with citations). You specify the manuscript file that you want JEPRS to read by entering its file name on JEPRS' >Global Defaults Menu< (under [F]iles/[W]ord processor input file). To automatically generate a bibliography in this manner, you first go into your manuscript using your word processor (either WordPerfect 5.x or PC-Write 3.0), and wherever you want a reference citation, you enter {J#0000}, where `0000' is the JEPRS reference number you want to cite. For example, if you want to cite JEPRS reference number 144, then you would enter {J#144} into the manuscript. Then save the file and exit your word processor. Now start up JEPRS, and at the >Main Menu< press [F2] go to the >Global Defaults Menu<, press [F]iles/[W]ord processor input file, enter the name of your manuscript file and press [Enter]; then press [Esc ]to get back to the >Global Defaults Menu<. (If you haven't already specified your Word processor type, do that now at the >Global Defaults Menu<: press [D]efaults/[W]ordProcessorType, and then select your word processor.) Now press [Esc] until you return to the >Main Menu<. Press [F]ormat, then [I]nput, then [W]ord Processor file. (Now select your [O]utput and [F]ormat Styles as you normally would.) When you press [G]o to start, JEPRS will search through your word processor manuscript for the codes you entered, and automatically generate the bibliography. After first asking for confirmation, JEPRS will then go back into your file and replace the codes you entered (such as {J#144}) with either an Author+Year citation or Sequential Numbers. JEPRS will not, however, modify your original manuscript. It creates a copy of your original manuscript, and modifies only the copy. So now use your word processor to retrieve the modified copy to see what it looks like. JEPRS names the modifed copy as *.New; in other words, if your manuscript was called CHAP_ONE.DOC, then JEPRS will name the modified version CHAP_ONE.NEW. How does JEPRS know whether to replace your codes with Author+Year JEPRS User's Guide, page 27 or Sequential Number citations? The Format Styles specify whether Author+Year or Sequential Numbers are used. You can go back and modify your Format Styles by pressing [F2] to go to the >Global Defaults Menu<, then select [D]efaults/[J]ournal Definitions, and then select the number of the format style you want to use. Press the [Tab] key until you are in the field called ``Replace WP Code With:'', and then choose [A]uthor+Year or [N]umbers. Then press [Esc] to go to the menu at the top of the screen, and press [S]ave to save the format. Now press [Esc] until you return to the >Main Menu<. ************** Importing References ********** In this section of the chapter, I will describe how to use both PaperChase and ISI's Current Contents on Diskette to create MedLine formatted Import files, and then show how to add the Import file into your JEPRS database file. The basic concepts provided in this section of the chapter should be applicable to you even if you use other on- line or CD-ROM based systems. See the additional documentation on Med2Go to see how to convert other format types (ERIC, Psyclit, and comma-delimited) to MedLine, so that JEPRS can import them. >>>>> Creating an Import file with PaperChase <<<<< PaperChase is an easy to use, menu-driven, on-line system for accessing the National Library of Medicine's MedLine reference database. PaperChase is available through CompuServe Information Services (Go PCH), and also directly through Beth Israel Hospital in Boston, Massachusetts. Your local medical center library would probably have information on accessing this system. I will now assume that you have successfully completed one or more on-line searches with PaperChase. While still logged on to PaperChase, choose `P' from the Main Menu for ``Put all references on print queue''. Then choose `E' for ``Exit PaperChase to print''. A menu is then displayed for Print Options. At this menu, choose #2 ``National Library of Medicine format'' (this is the MedLine format). The final menu in PaperChase will be titled ``Include on Printout . . . ''. You have 4 choices: 1) References only 2) References plus abstracts 3) References plus Medical Subject Headings 4) References + abstracts + Medical Subject Headings Remember that the system charges extra if you download abstracts, but there is no extra charge for Medical Subject Headings. Therefore, I would suggest you always use #3 or #4. If you do, then when you import the file into JEPRS, JEPRS will convert the Medical Subject Headings into Keywords automatically. JEPRS User's Guide, page 28 After choosing #3 or #4 above, PaperChase then gives you instructions for downloading to a file. Follow these instructions exactly, and make a note of the filename you used for your downloaded references. This filename will become the Import file for JEPRS. Now go ahead to the section called ``Retrieving an Import File into JEPRS''. >>>>> Creating an Import File with Current Contents on Diskette (CCOD) <<<<< Current Contents on Diskette (CCOD) is a PC-based system for looking at weekly updates of the scientific literature. This section of the tutorial will teach you how to create a MedLine formatted Import file while using CCOD version 1.3. It will then describe in detail how to bring that Import file into your JEPRS database. Start CCOD the way you normally do (usually by entering `CC' at the DOS prompt), then load one of your weekly issues of Current Contents into the program by selecting [C]CIssue, then [O]pen Back CC Issue . . . , then choose the specific issue you want from the menu and press [Enter]; it will then verify your choice and tell you it's ready; at that point, press any key to continue, then [Esc] to the >Main Menu<, then press [S]earch, then [S]earch Session. Now define a new search profile or run an old profile, then press [F5] to view the results of your search. Press [V]iew to switch back and forth between full-screen and 1-line entries. Use the arrow keys to move the highlight bar around, then press [I] (for P[I]C) at each reference you want to import into JEPRS, or press [M]arkAll if you want to import them all. To create the actual MedLine formatted file, continue as follows. Press [F]ile, and at the pop-up FILE menu, choose [S]ave, and then [A]ll records (that means all P[I]Ced records). Select [F]ile Format, and then [N]LM-MedLine; at File [n]ame, enter the name of the file to contain the exported references (this will become JEPRS' Import file). Now choose [A]ppend/Overwrite, and select either [A]ppend or [O]verwrite, depending on whether you wish to save previous references in the export file. Finally, press [Enter] to start the export. >>>>> Retrieving an Import File into JEPRS <<<<< Start up JEPRS the way you normally do. Press [U]tilities, then press [F2] to get to the >Global Defaults Menu<. Press [F]iles, and then [I]mport file, and then enter the name of the Import file (the file you just sent your references into, using either PaperChase or Current Contents on Diskette). Remember that you can enter just a filename, or a whole file specification, including drive and directory information. For example, JEPRS comes with a sample MedLine file called ProComm.Log. After entering the Import filename, press [Enter]. Press [Esc] once to return to the >Global Defaults Menu<, and once again to return to the >Utilities Menu<. JEPRS User's Guide, page 29 At the >Utilities Menu<, press [I]mport to get to the >Import Menu<. Look at the right side of the screen: is the default called ``Edit references before importing'' set to Yes or No? If Yes, then when you press [G]o to start importing, JEPRS will stop at each reference and allow you to discard it or edit it before importing it; if No, then JEPRS will import all of the references in the Import file at once. For the purposes of this tutorial, set this to [N]o. Press [G]o to start the importing process. I have noticed that CCOD has a quirk: It capitalizes the first letter of each word in the title and every other letter is lowercase. Not only is this inconsistent with most other programs, they even go so far as to capitalize an abbreviation, such as `ATP', like this: `Atp' which is obviously wrong. Because of this quirk, I suggest you set [D]efaults/-[E]dit references before importing=[Y]es at the >Import Menu< in JEPRS. This allows you to modify your reference citations during importing. Of course, if this quirk doesn't bother you, then you can set [E]dit references before importing=[N]o, if you wish. Importing was easy, wasn't it? So easy, in fact, that you may not have noticed something. Some reference management programs require you to ``clean up'' your Import file before actually importing it. But JEPRS is smart enough to gloss over all the useless information (it just ignores the small amount of text that PaperChase and other systems add to the file). This is just part of JEPRS's continuing philosophy of making your life as easy as possible-let JEPRS do the hard work for you. ************** Exporting References ********** JEPRS has the capability to export references in the MedLine format, which is done at the >Export Menu<, available through the >Utilities Menu<. It can also produce comma-delimited output at the >Format Menu<. This part of the tutorial will show you how to use the exporting function of JEPRS. >>>>> Creating a Number File in a Search <<<<< You may be wondering what a Number File and a Search have to do with exporting references! Actually, neither are required for exporting, but they do show some of the flexibility and advanced features of JEPRS. Therefore, I'll include them in this section of the tutorial chapter. Let's say you are talking with a colleague, and she wants to find out more about the work of a scientist named Wright. You mention that you have a database full of Wright's references, and volunteer to give them to your colleague. This calls for exporting the references from JEPRS User's Guide, page 30 JEPRS. The easiest way to do this is to do a search for ``Wright'' in authors, send the numbers of the found references to a Number File, and then use the Number File as the source for the reference numbers in a JEPRS Export. To do this, press [S]earch at JEPRS' >Main Menu<. At the >Search Menu<, press [T]erms, then enter an [A] (for Author search) and press [Enter]. Then enter Wright and press [Enter] again. Then press [G]o to start the search. When the search is finished, press [F5] to Mark all the found references, then press [F8] to send them to a Number File. (If you get an error message stating that the file already exists, press [F4] to specify a new file name, and call it ``Wright.Num''.) Now press [Esc] twice to return to the >Main Menu<. >>>>> Exporting the Found References <<<<< Now that you've sent the references you found in a search to a Number File, you can export them. When you're at the >Main Menu<, press [U]tilities and then [E]xport to get to the >Export Menu<. Since the numbers of the references that you want to export are in the Number File, you'll have to specify that as the Input, or source of the reference numbers. So press [I]nput and then [N]umber file to tell JEPRS where to find the reference numbers. For now, leave the default output as the screen. Just press [G]o to start the exporting. Since you specified the screen as output, the references aren't really exported; they're just formatted and sent to the screen. To send them to an Export File, select [O]utput from the menu, then select [T]ext file and answer [Y]es at the menu. So where will JEPRS send the contents of the Text File? Actually, at the >Export Menu<, a Text File is a special case: it's called an Export File. You specify the name of the Export File at the >Global Defaults Menu<; the default name is JEPRS.Exp. That's where the Wright references have been sent. That's it for exporting; press [Esc] twice to return to the >Main Menu<. JEPRS User's Guide, page 31 C H A P T E R S I X _________ Global Defaults #################################### The purpose of the >Global Defaults Menu< is to allow you to modify virtually every aspect of JEPRS' working environment, to better suit it to your personal needs. Everything on this menu can be saved in your Config file; in this way, once you define your work environment, JEPRS will act the way you want it to. You won't have to modify these variables every time you start up JEPRS because it will read them in from your Config file automatically. ##################################### The >Global Defaults Menu< is accessible from the >Main Menu<, the >Search Menu<, the >Format Menu<, and the >Utilities Menu<. On the right side of the screen, you will see all the Defaults that are accessible from the [D]efaults choice on this menu. In addition, ``Available space on default drive'' tells you how many bytes of space are left to use on the current disk drive. If you're getting low on space, you might want to keep track of this number to make sure you don't try to add references if there is no space left on your disk. ``Total disk space on default drive'' tells you how many total bytes your drive is capable of holding. The next few sections of this chapter will explain how to go about changing, and then saving, the global defaults. >>>>> Files <<<<< This option allows you to change the names of any of the files that you are using in JEPRS. This prevents you from having to exit the program just to use a different data file, for example. Note that when you first start JEPRS, it immediately looks for the Config file on the current directory with the name ``JEPRS.Cfg'' (unless you specify a different name on the command line; see the chapter Setting Up JEPRS, especially the sections Starting JEPRS/Command Line Options). If JEPRS can't find the Config file, it uses default names for all of JEPRS's files. The default names are: Reference File: Ref1.JPR WP Input File: (None) Output WP File: (None) JEPRS User's Guide, page 32 Text File: JEPRS.Txt Number File: JEPRS.Num Config File: JEPRS.Cfg (or whatever you entered on the command line) Import File: ProComm.Log Export File: JEPRS.Exp In addition, you can enter a drive and directory name. If you do so, then anytime JEPRS goes looking for a file (for example, the Text file), it will first look in the directory specified in the Text file name; if none was specified, then JEPRS looks in the current default directory. If JEPRS doesn't find it there, then it looks in the directory specified in the Drive and directory name. On the other hand, when JEPRS creates files (such as Text and Number files) then it just uses the filename specified (and if no Drive and Directory was specified, then it uses the current DOS directory). >> Changing a file name. To change a file name, press the first (highlighted) letter of the file type, or just highlight the file type using the up and down arrow keys and then press [Enter]. You will be prompted for the new name of the file in a pop-up dialog box. Note that the old name is displayed there so that you can edit it. Edit the old name or just type in a completely new name, then press [Enter] when finished. The filenames you enter here are only temporary; if you want to make them permanent, you can save them in your Config file. For instructions, see the section below on [D]efaults/[S]ave defaults+files. If you change the name of the Reference file, you will be prompted for both the Reference and the RefKey file names, since they are specific for each other. JEPRS is smart enough to give the same name for each file, except for the extension (*.JPR for the Reference file, and *.JPK for the Ref Key file). You don't have to use *.JPR and *.JPK as the file extensions, but if you don't then JEPRS will not automatically use the same file names. >>>>> Defaults <<<<< When you select [D]efaults, a pull-down menu appears. Just like every other pull-down menu in JEPRS, use the up and down arrow keys and the [PgUp] and [PgDn] keys to scroll through the choices and press [Enter] to make a choice (or just press the highlighted letter). There are a number of items JEPRS lets you configure: >> Error/warning beep. This allows you to turn JEPRS' beeping on or off. Whenever you type an incorrect command, or at various other times when JEPRS wants your attention, it will beep at you. If for some reason you wish JEPRS wouldn't do that (you're working late at night for example), just select [N]o, and JEPRS will never beep at you. >> Text file formatting. There are several places at which JEPRS allows you to send formatted output to a Text file. In most cases, JEPRS User's Guide, page 33 JEPRS will send only your text, and not any printer codes. However, when you direct Output to a Text file at the >Format Menu<, JEPRS has the ability to include the printer codes. That way, you can send your output to a file, and then use the MS-DOS Print command to print it later (for example if the printer is already busy, or if you want to print it on a different machine). If [T]ext file formatting=[Y]es, then printer codes will be sent to the Text file; if [N]o, then printer codes will not be sent to the Text file. >> Use printer #. Beginning with version 2.0, JEPRS allows you to define up to 5 printers. This menu option lets you choose which of those printer definitions to use. After invoking this command, a menu of 5 printers is displayed. Use the arrow keys and [PgUp] and [PgDn] to move among the entries, and then press [Enter]. Or just enter the number of the printer you want to use. If you press [Esc], then your previous choice is not changed. If you will be routinely sending output to a word processor file instead of the printer, then there is no need to select a printer definition. >> Save defaults+files. Whenever you change any of the Global Defaults, they are retained in your computer's memory, but they are not permanently saved in your Config file. If you would like to save them, select this command from the menu. When your defaults and files have been successfully saved, the menu will automatically disappear. For a list of all the defaults that are saved with this command, see the appendix chapter on JEPRS' Files, especially the subsection called Config file. >> Journal Definitions/Format Style Definitions. Your Config file is capable of storing up to 30 Format Styles (that you use on the >Format Menu<). This option lets you change the definitions to anything you like. For more information on editing these definitions see the section below called Editing Journal Definitions/Format Styles. >> Printer Definitions. The Config file can store up to 5 Printer Definitions. This option permits you to edit your definitions to best suit your printer. For more information on editing your printer definitions, see the section below called Editing Printer Definitions. >> Colors for screen. This menu section lets you specify screen colors and attributes. When you choose this command, a sub-menu appears: you can then choose [T]ext color/B&W mode, [F]ormatting colors, and [B]linking. [T]ext color/B&W mode lets you choose a video mode. In color mode, JEPRS uses colors; in black and white mode, all the screen text is converted to black, white, and one shade of gray. Here is a brief list of recommendations: [Video Monitor Video Card Color Mode] JEPRS User's Guide, page 34 Color CGA, EGA, MCGA, VGA Color Amber, Green, or White CGA, EGA, MCGA, Mono B&W (any one-color screen, VGA Color including portables) There are some notable exceptions to these general rules. For example, both Compaq and Zenith have CGA cards that display different shades of gray on one-color monitors (amber, green, or white). In that case, the Color mode would probably look best. [F]ormatting colors affects the look of the screen when you format references at the >Format Menu<. If this is set to [C]olors for formatting, then normal text is displayed as black on cyan, bold text is white on cyan, and underlined text is represented as blue on black. If this is set to [N]o colors for formatting, then all text appears as black on cyan. [B]linking is similar to the [F]ormatting colors command, except that it controls how italic text is represented on the >Format Menu<. If this is set to [Y]es, then italic text is represented by blinking text; if set to [N]o, then blinking is turned off, regardless of italics. >> Form-feed to printer. Sometimes you may want to eject the last sheet of paper from your printer. This command allows you to do that without having to get up and walk over to your printer. Just press [Y]es to send the form-feed, or any other character to return to the pull-down menu. >> Ordering information. This choice presents you with details of how to order the latest version of JEPRS from the author. Remember: JEPRS is shareware, it is not free software. If you haven't already done so, you should register your use of JEPRS with the author if you are past the 30-day evaluation period. >> Word Processor Type. Version 2.5 of JEPRS now supports the reading and writing of WordPerfect 5.x and PC-Write 3.0 documents. Use this option to tell JEPRS what kind of word processor you use. This option is only necessary if you use [I]nput=[W]ordProcFile on the >Format Menu<, or [O]utput=[W]ordProcFile on the >Search Menu< or >Format Menu<. >>>>> Go to DOS <<<<< Go to DOS allows you to temporarily exit JEPRS and return to DOS (your computer's operating system). This would be useful, for example, to get a directory listing without having to exit from JEPRS. Whenever you use this command, however, don't forget to type ``Exit'' and then JEPRS User's Guide, page 35 press [Enter] to return to JEPRS. In fact, JEPRS will now modify your DOS prompt to remind you to return to the program. One thing to remember when using this option: Do not run a TSR (Terminate & Stay Resident) program (like SideKick) when you use this command. If you do so, and then return to JEPRS, your computer will likely crash. If you want to load a TSR program, you should exit JEPRS completely, by going to the >Main Menu< and pressing [E]xit. An improvement to the [G]o to DOS command in version 2.0 was JEPRS' use of the COMSPEC specification from your DOS CONFIG.SYS file. This change will not affect most users. But if you are a ``power user'' and you use a DOS command processor that is not the standard COMMAND.COM (such as if you use 4DOS or DR-DOS), then now JEPRS will successfully call this file via the COMSPEC specification. In previous versions, JEPRS just looked for a file called COMMAND.COM in the DOS path. ************** Editing Printer Definitions ********** A variety of printers are supported by JEPRS in the Config file which comes with the program. If your printer is not one of the pre- defined ones, or you want to add extra features, then you can easily modify any or all of the 5 available printer definitions. Note: If you plan on sending all of your JEPRS output to a Word Processor File, then there is no need to bother defining printer commands. Simply retrieve the Word Processor File into your word processor. =================================================================== ***** ADVANCED TOPIC: ***** Why five printer definitions? There are at least two reasons why you might want more than one printer definition. One easy example is that you have a laser printer at work and a dot matrix printer at home. By combining all your formatting and printing commands in one file, JEPRS prevents you from having to have a new set of Config files for each printer; you just modify the existing printer definitions to suit your needs. Secondly, you could specify one printer definition for Comma- delimited output. In this case, you would later direct this output to a Text file rather than your printer. =================================================================== To edit your printer definition(s), go to the >Global Defaults Menu<, choose [D]efaults/[P]rinter definitions. A pop-up menu will appear, listing the five pre-defined printer definitions. Choose one of the definitions by using the arrow keys and pressing [Enter] or just entering the number of the printer. Brief help is available by JEPRS User's Guide, page 36 pressing [F1]. If you want to use the current printer definition, just press [Esc]. After selecting a printer to edit, you are presented with the >Modify Printer Formats< screen. Here is where you can enter all your printer-specific information. Check your printer manual for the codes you need to enter for underlining, boldface, etc. >>>>> Entering Printer Codes <<<<< Many printer codes cannot be entered directly by the keyboard. For example, if one of your printer codes was <Esc>, you couldn't just press [Esc] to enter that code, because JEPRS would interpret that <Esc> as the command to go to the menu at the top of the screen. To enter a special printer code, first press ^P; that is, hold down the [Ctrl] key and tap the [P] key once. Then enter your code. (This is similar to the way WordStar and SideKick allow you to enter printer codes.) Let me give you a quick example. Let's say your printer manual tells you to enter the following code to turn underlining on: <Esc>&d3D . . . and the following code to turn underlining off: <Esc>&d@ You would enter the first code like this: ^P Esc & d 3 D . . . and the second code like this: ^P Esc & d @ .where each line represents a single character (that is, ``^P'' means hold down the [Ctrl] key and press [P], and ``Esc'' means press the [Esc] key). You can also enter codes by using the [Alt] key and the number pad on the right side of the screen. For example, some printer manuals tell you the printer commands in ``decimal'' format. In this system, for example, <Esc> is represented by the number 27; this is also the system used by the ``CHR$'' command in the BASIC computer language (that is, <Esc> would be ``CHR$(27)''). You can enter these by first pressing [^P], then while holding down the [Alt] key, pressing [2] and then [7] on the number pad (not the numbers on the top row of the keyboard) and then letting go of the [Alt] key. JEPRS User's Guide, page 37 >>>>> Modify Printer Formats <<<<< Here is a brief description of each of the fields listed on the >Modify Printer Formats< screen. >> Printer Number. You cannot change this number; it is set by JEPRS. This number allows you to pick this printer at the [U]se printer # command on the >Global Defaults Menu<. >> Printer Name. Enter the name of your printer. This name will appear next to the printer number on the printer selection menu. >> Printer Initialization Code. You can enter a code here that will be sent to your printer every time you send output to the printer at the >Format Menu<. For example, you may want to specify a certain font, or character pitch, or otherwise initialize your printer. >> Printer Reset Code. This code will be sent to your printer every time printer output is finished when you are at the >Format Menu<. >> Title. This text and/or codes will be sent to the printer as the title for the first (and only the first) page of output. You may want to enter something like ``Reference List'' or ``Bibliography'' in this space. If you choose [O]utput=[W]ordProcFile on the >Search Menu< or >Format Menu<, then this title will be sent to your word processor output file with a ``Large'' attribute (i.e., in WordPerfect 5.x, it will appear with the ``Large'' codes; in PC-Write 3.0, it will appear ``Double Wide''). >> Header. This text and/or codes is sent to the printer as the top line of every page of output. There is also one special code you can enter: ``\P''. If that code appears anywhere on the line, it will automatically be replaced with the page number (you can set the starting page number on the >Format Menu<). For example, you may want to enter something like: JEPRS output 18 Nov 1990, page \P >> Left Margin. Enter the number of characters you want JEPRS to skip to make a left margin. For example, if you enter ``0'', then JEPRS will start printing at the very left edge of the page; if you enter ``12'', JEPRS will skip 12 spaces before printing each line. >> Characters per line. This is the number of characters printed on each line before starting on the next line. Example: You're printing on 8.5 x 11 inch paper; your printer prints at 10 cpi (characters per inch); your left margin is 10 characters (= 1 inch); and you want a right margin of 1 inch. In this case, you should specify ``65'' as the Characters per line, since there is a total of 85 characters per line (8.5 inches x 10 char/inch), you have a left margin of 10 characters (1 inch) and you wanted your right margin to be 1 inch (85 - 10 - 10 = 65). JEPRS User's Guide, page 38 Things get a little tricky if your printer prints a proportionally spaced font (like a laser printer's Times Roman typeface). Since each character's width is different, you'll just have to play around with the line length number until you get a number that is large enough so that it doesn't leave too wide a right margin, yet small enough that it doesn't chop letters off the right hand side. And if you enter your Keywords in ALL CAPITALS remember that these are much wider than lowercase letters and you'll have to allow for this when printing. If you want to print keywords in ALL CAPS then I suggest that either you use a non-proportional (fixed-spacing) font or that you send the format to a Text file (instead of to the printer) or a Word Processor Output file. >> Pause after each page. For most printers, you would choose [N]o here. However, for printers in which you have to hand feed each individual sheet of paper, set this to [Y]es. When this value is [Y]es, then when JEPRS finishes printing one page at the >Format Menu<, it will ask you to feed the next sheet of paper and press [Enter] before it starts printing the next page. >> Top margin. This is the number of spaces to be skipped at the top of each page. For example, if your printer is set for printing 6 lines per inch and you want to leave a 1-inch top margin, then enter 6 here. >> Lines per page. Enter the number of lines per page, not including the top margin or header. Let's use the example again of a printer with 6 lines per vertical inch. On an 11-inch piece of paper, that's a total of 66 lines. If you set Top margin to 6, then you're left with 60 lines. But then JEPRS prints the Header and skips 3 lines automatically, so now you're down to 57 lines. If you want to leave a 1-inch bottom margin (6 lines) then you're down to 51 lines: this is the number you should enter for Lines per page. >> Form feed last page. If you want JEPRS to eject the final printed page from your printer, then choose [Y]es here. >> Underline/Bold/Italic/Superscript/Subscript On/Off. Enter the codes your printer requires to start and stop each of these special features. See the earlier section called Entering Printer Codes that describes how to use the [^P] key to enter codes here. >> Comments. This is two lines of text where you can enter any comments you want. These comments are for your information only; JEPRS ignores them completely when formatting. You might want to enter information like what your Initialization and Reset codes mean in English. >>>>> Saving Your Definitions <<<<< When finished editing your printer definition, press [Esc] to get to the menu at the top of the screen. As usual, you may press [H]elp JEPRS User's Guide, page 39 to get help. Otherwise press [S]ave to save your printer definition, press [E]dit to modify a different definition (see Advanced Topic, below), or press [Esc] to return to the >Global Defaults Menu<. =================================================================== ***** ADVANCED TOPIC: ***** Keeping Definitions in Memory or Disk If you don't [S]ave your definition, then it still stays in your computer's memory, but it will be erased under two conditions: 1. You exit JEPRS. 2. You choose a printer definition again. Let me give an example. Let's say you edited printer definition #2, and you're now at the menu at the top of the screen. Then you press [Esc] without [S]aving, so the modified printer definition #2 is still in memory and the original printer definition #2 is still in your Config file. If you then access the printer selection menu (either by pressing [U]se printer #, or by pressing [P]rinter definitions, at the >Global Defaults Menu<) and select #2 and press [Enter], then the original #2 is read in from your Config file and replaces the modified #2 that was in memory. On the other hand, if you're at the printer selection menu and you press [Esc] (instead of choosing #2 again) then the modified #2 is kept in memory and you can edit it (or [S]ave it) again. =================================================================== ************** Editing Format Styles (Journal Definitions) ********** You can create up to 30 different Format Styles/Journal Definitions in JEPRS. These various formats are used for selecting the style of output at the >Format Menu<. To edit any of them, go to the >Global Defaults Menu<, choose [D]efaults, and then [J]ournal definitions. A pop-up menu will appear from which you can select any of the 30 Format styles. To select one, use the up & down arrow keys, [PgUp] & [PgDn], and [Enter] to select. Or, just enter the number of the style you wish to edit. If you instead press [Esc], the previously selected style will be used. =================================================================== ***** ADVANCED TOPIC: ***** Using More Than 30 Format Styles JEPRS' ability to use up to 30 Format Styles within one Config file is more than enough for most users. However, sometimes people ask if somehow more than 30 can be accomodated. The answer is `Yes'. JEPRS User's Guide, page 40 You can do it by simply making copies of your Config file at the DOS prompt. Then when you start up JEPRS, specify the name of the Config file you want to use on the command line (see the section in Chapter Two called Starting JEPRS/Command Line Options for more details). For example, if your Config file is called JEPRS.Cfg, then use the DOS copy command to create another one with a different name: C:\JEPRS> Copy JEPRS.Cfg MyRefs.Cfg Remember to create these copies only after you have set up your printer definition(s) and other defaults. This way, you won't have to redefine them for each copy you make. =================================================================== Once you select a Format style to edit, you will be placed at the >Modify Journal Formats< screen. Here is where you can directly edit any aspect of the Format styles/Journal definitions. You can enter any normal text, any of the codes listed at the bottom of the screen, or any non-standard character by using the [^P] key (see the previous section, >Editing Printer Definitions< for information on entering special codes with the [^P] key). Here is a brief run-down of each field. >> Journal Name. Enter the name of the Format style. This name will be displayed on the pop-up menu that lets you choose among the thirty Format styles. >> Number. This is the number of the Format style. You cannot modify this number. >> Sort Reference. New with version 2.5 is the ability to sort output by author, journal, or year. If you choose [A]uthor, [J]ournal, or [Y]ear here, output references will be sorted by author, journal, or year, respectively, before being sent to the output device(s) selected at the >Format Menu<. If [N]one is selected, then no sorting is done. >> Indent Length. The number of characters each continuation line is indented beyond the left margin defined in the printer definition. If this number is zero, then no indenting is done: 1. SA Jones & ME Smith (1989) Fake references and you, Journal of Irreproducible Results If this number is set to 5, for example, then five spaces would be skipped on the 2nd and additional lines: 1. SA Jones & ME Smith (1989) Fake references and you, Journal of JEPRS User's Guide, page 41 Irreproducible Results If this value is set to anything other than zero, and you send output to the Output Word Processor File, then an <Indent> code will be placed in the file. >> Replace WP codes with:. If you select [I]nput=[W]ord Proc File at the >Format Menu<, then JEPRS can, at your option, go back into your word processor document and replace your JEPRS codes with either an Author+Year citation or Sequential Numbers. This option is where you select either [A]uthor+Year or [N]umbers. For example, if you select [A]uthor+Year and tell JEPRS to replace your codes at the >Format Menu<, then JEPRS would replace a {J#123} code with Miranda, et al. (1992). >> Periods for Initials:. New in version 2.5 of JEPRS is the ability to add periods after authors' initials. For example, if you have an author entered as ``Miranda LM'', then JEPRS can make it look like ``Miranda L.M.'' when it is formatted. To turn this feature on, select [A]dd periods; otherwise select [N]o periods. >> Journal/Abstract/Book. This is where you enter the codes (listed at the bottom of the screen) that tell JEPRS how to format your journal, book, and abstract articles. First, here's some basic information you should know about entering formats: The first set of characters you enter on a line (before the first space) will be used to connect the names of the authors if there is more than one. For example, if you start off the defintion with ``and '' (don't forget the space), then when multiple authors are listed for a reference they will be printed as ``WE Wright and LM Miranda''. On the other hand, if you start off the definition with ``& '', then multiple authors will be printed like this: ``WE Wright & LM Miranda''. I can't imagine using anything other than ``and '' or ``& '' to connect the authors, but if you do, realize that it can't be any more than 10 characters long and it can't have spaces within it. Any character that is not a special code will be printed exactly as is. For example, if your definition is ``and \L (\Y).\/\/'' then a sample output would be: WE Wright and LM Miranda (1988). (yes, that's right; the last two line feed characters (\/\/) create an extra blank line; also, the year is enclosed in parentheses, just as you specified in the definition). The best way to understand how definitions work is to print out sample ones using the >Format Menu<, and compare the output to the codes in the Format style definition. After comparing them carefully, you'll get a better feel for how the system works. JEPRS User's Guide, page 42 >>>>> Format Style Codes <<<<< Here is a complete rundown of what the special codes in the Format styles are for. >> \F. Place authors in output, first name first (e.g., ``LM Miranda, VK Lin and WE Wright''). >> \L. Place authors in output, last name first (e.g., ``Miranda, LM, Lin, VK, and Wright, WE''). >> \1. Place authors in output, last name first for the first author, first name first for each additional author (e.g., ``Miranda, LM, VK Lin and WE Wright''). >> \A. Place authors in output without any modifications (that is, don't add the ``and '' or ``& '' or extra commas). This would likely only be used for comma-delimited output. >> \T. Place title in output. >> \J. Place journal name in output. >> \N. Place reference number in output. For example, reference #22 would have a ``22'' in front of it, reference #67 would have a ``67'' in front of it, each regardless of its relative position in the output. (See also `\#', below.) >> \C. Place citation type in output (i.e., ``Journal'', ``Book'', or ``Abstract''). >> \Pa. Place page numbers in output. >> \E. Place editor in output. >> \Pu. Place publisher in output. >> \Y. Place year in output. >> \K. Place keywords in output. >> \#. Number output references sequentially. That is, the first reference printed (regardless of its number in the database) is printed with the number `1'; the second reference printed (regardless of its number in the database) is printed with the number `2'; and so on. (See also, `\N', above.) >> \/. Start new line. (That's a backslash followed by a forward slash, not a capital V). >> \<. Start optional inclusion. >> \>. End optional inclusion. What's an ``optional inclusion''? This is used to prevent printing any text that is dependent on one of JEPRS User's Guide, page 43 the fields being present. Let's say that the rules are that if you are referencing a book then the title of the chapter has to be in single quotes. So your definition in JEPRS might look like this: and \F. `\T' in: \J. That's fine if every book in your JEPRS database has a chapter title. A sample would look like this: WE Wright. `Muscle Cells' in: Cell Development. But if you had a book that didn't have chapter titles, the output would look kind of funny, like the next line: WE Wright. `' in: Cell Differentiation. That's not exactly a catastrophe, but it is undesirable. The optional inclusion codes allow you to get around a situation like this. In this case, you define your output this way instead (compare it to the prior definition): and \F. \<`\T' in: \>\J. Notice the `\<' and `\>' optional inclusion codes which surround ```\T' in: ''. What this tells JEPRS is that if the field inside the optional inclusion characters (in this case `\T', or the Title field) is empty, then don't print any of the characters within the optional inclusion. Therefore, the two examples above would print like this: WE Wright. `Muscle Cells' in: Cell Development. WE Wright. Cell Differentiation. And that is much nicer output. A major example is given in the chapter called Format Styles: A Tutorial (also look at the examples in the Config file provided). The next few codes are toggles. This means that you have to use them twice: once to turn on the function, and once to turn it off. You usually have to do the same thing in a word processor, like entering a command to start boldface, entering the text to be boldfaced, and then finally entering another code to stop boldface. >> \S. Toggle subscripts. >> \^. Toggle superscripts. >> \~. Toggle italics. >> \B. Toggle boldface. >> \_. Toggle underline. If you haven't entered the printer-specific sequences for these codes in the printer definition in your Config file, then they won't print on your printer. Once you've modified the Format styles to your specific needs, formatting with different format styles is simply a matter of choosing JEPRS User's Guide, page 44 one from a menu. >> Comments. The last two lines of the screen are where you can enter any comments you like. These are for your use only; JEPRS will not try to interpret them or use them for any other function. >>>>> Saving Your Definitions <<<<< When finished editing your Format style, press [Esc] to get to the menu at the top of the screen. As usual, you may press [H]elp to get help. Otherwise press [S]ave to save your Format style definition, press [E]dit to modify a different definition (see Advanced Topic, below), or press [Esc] to return to the >Global Defaults Menu<. =================================================================== ***** ADVANCED TOPIC: ***** Keeping Definitions in Memory or Disk If you don't [S]ave your definition, then it still stays in your computer's memory, but it will be erased under two conditions: 1. You exit JEPRS. 2. You choose a Format Style again. Let me give an example. Let's say you edited Format Style #2, and you're now at the menu at the top of the screen. Then you press [Esc] without [S]aving, so the modified journal definition #2 is still in memory and the original journal definition #2 is still in your Config file. If you then access the Format Style selection menu (by pressing [F]ormat style on the >Format Menu<, or by pressing [J]ournal definitions at the >Global Defaults Menu<) and select #2 and press [Enter], then the original #2 is read in from your Config file and replaces the modified #2 that was in memory. On the other hand, if you're at the journal definition selection menu and you press [Esc] (instead of choosing #2 again) then the modified #2 is kept in memory and you can edit it (or [S]ave it) again. =================================================================== JEPRS User's Guide, page 45 C H A P T E R S E V E N _________ Listing References #################################### The >List References< screen permits access to your references individually. Many times you will want to look up just a single reference or two. There is no need to do a search through the entire database if you already know the number of the reference you want to examine or edit. ##################################### Choose [L]ist from the >Main Menu< to get to the >List References< screen. Note: The >List References <screen can also be called from the Search Results screen. There are some subtle differences when using List from the Main Menu and List from the Search Results screen. See the Advanced Topic below for an elaboration of the differences. When you first reach the >List References< screen, JEPRS initially displays the most recently accessed reference in your database, and then asks you for a reference number. If there are no references in your database, JEPRS will automatically return to the >Main Menu<. Enter the number of the reference you wish to view; the corresponding reference in the database is subsequently displayed. JEPRS displays your reference in the standard screen format, allowing 3 lines for the title, 2 lines for the author, 2 lines for the journal, space for the volume, pages, year, and type, one line for the editor (if a book), 2 lines for the publisher (if a book), and 5 lines for keywords. If, by mistake, you enter the number of a reference that is not in the database (for example, a number larger than the last reference in the database), JEPRS displays the closest valid reference. You can use this to your advantage: If you enter a number larger than your database (such as ``99999''), JEPRS assumes you want to go to the end of the database, and will display the last reference. Also, realize that you are entering the numbers at a prompt, so you can use non-printing keys to edit the value. For example, if you displayed reference #122 then ``122'' will be displayed as the default value for the next reference; to look at reference #129, just press [End], then [BackSpace] once, then press [9] and [Enter] and #129 will be displayed. JEPRS User's Guide, page 46 >>>>> Function Keys <<<<< Several keys perform special functions-these are described on the bottom of the screen. Here is a run-down of each of those keys and their functions within the program. >> Esc. As you have probably come to expect by now, this key will end what you're doing and bring you back to the >Main Menu<. >> F1. As always, this will give you context-sensitive help, including a brief description of the function keys available on the >List References< screen. >> F4. Edit reference (see separate section, below). >> PgDn. ([Page Down] on 101-key keyboards) displays the next reference in your database. For example, if you first enter `142', JEPRS displays reference #142; if you then press [PgDn], reference number 143 will be displayed. >> PgUp. ([Page Up] on 101-key keyboards) displays the previous reference, just the opposite of [PgDn]. >> F8. Only the number (e.g. `6') of the current reference is sent to a Number File. This Number File can subsequently be used for input ([I]nput=[N]umber file) during formatting or exporting. >> F9. The displayed reference is sent to your printer in the currently defined Format Style (selected on the >Format Menu<). >> F10. Sends the displayed reference to a DOS Text File (again, in the currently-defined Format Style). Remember that [D]efaults/[T]ext File Formatting on the >Global Defaults Menu< determines whether printer codes are sent to this file. ************** Editing & Updating References ********** Editing references is essentially identical to adding references. See the next chapter, Adding References, for information on the function keys and menus used for editing and adding references. Since JEPRS does not have a Delete Reference option, >Edit Reference< can be used to remove an old reference citation and replace it with a new one. =================================================================== ***** ADVANCED TOPIC: ***** Listing in the Search Results Screen When >List References< is called from the >Search Results< screen, JEPRS User's Guide, page 47 there are a few minor changes in the workings of the function keys: >> Esc. This will bring you back to the >Search Results< screen, not the >Main Menu<. >> PgUp. Instead of displaying the previous reference in the database, the previous found reference is displayed. >> PgDn. Instead of displaying the next reference in the database, the next found reference is displayed. The changes in [PgUp]/[PgDn] function may not be intuitive, so here's an example: Let's say you performed a search that found the following references that matched your search terms: #3, #6, #88, #122, and #131 You press [Enter] at the >Search Results< screen while the cursor is on reference #88; this brings up the >List References< screen displaying #88. If you now pressed [PgDn], then instead of #89 being displayed, #122 would be displayed because it is the next found reference from the search. Likewise, pressing [PgUp] would display #6, since it was the previous found reference. Well, what if you really did want to see reference #87? Don't worry-you can still enter `87' at the prompt. =================================================================== JEPRS User's Guide, page 48 C H A P T E R E I G H T _________ Adding References #################################### One of the first things you'll want to do after starting your own database is to add references to it. This part of the program is where you enter new references at the keyboard (your other option is to automatically load references in various formats from a text file using the >Import Menu<). ##################################### Press [A]dd at the >Main Menu< to get to the >Add References< screen. You're presented with the standard screen format used for adding, editing, and listing references. It displays: [Field] [Size or Value] Title 3 Lines Author 2 Lines Journal 2 Lines Volume 13 Characters Pages 13 Characters Year 4 Characters Type Journal/Book/Abstract Number 1-64,000 Editor 1 Line Publisher 2 Lines Keywords 5 Lines The menu at the top of the screen is initially inactive. As usual, the function keys are listed at the bottom of the screen. The cursor is JEPRS User's Guide, page 49 first placed on the Title field. >>>>> Function Keys <<<<< The function keys used for moving around your text generally perform the same function they would in a word processor or text editor: [Key] [Function] [F1] Context sensitive help with adding your references. [Esc] Activate menu at top of screen. [Tab] Move cursor to the next field. [Shift+Tab] Move cursor to the previous field. [Right Arrow] Move cursor one character right. [Left Arrow] Move cursor one character left. [Ctrl + Move cursor one word right. Right Arrow] [Ctrl + Move cursor one word left. Left Arrow] [PgUp] Move cursor to the Title field. [PgDn] Move cursor to the Keywords field. [Home] Move cursor to the beginning of the current field. [End] Move cursor to the end of the current field. [Ctrl+End] Delete from cursor to end of line. [BackSpace] Delete previous character. [Del] Delete character over the cursor. [Ins] Toggle editor between Insert Mode and Overwrite Mode.* *-See the bottom right corner of the screen; there is text there that says `Insert' or `Overwrite'. When in Insert Mode, any characters to the right of the cursor are pushed aside when you type in new characters. In Overwrite Mode, characters to the right of the cursor are written over and erased by the characters you are entering. JEPRS User's Guide, page 50 New in version 2.5 is the ability to edit multi-line fields as a single, scrollable line of text. For example, when you first go into editing mode, you start in the Title field; this field is 3 lines long, but the screen shows a box surrounding a single line of text. As you enter more text into this box, you'll see the text start to scroll to the left when you reach the right side of the box. When you use the control and arrow keys (see table) to move around the field, you'll see the text scroll left or right, depending on which direction you're moving in. When you are editing a multi-line field (i.e., Title, Author, Journal, Publisher, or Keywords), JEPRS displays a helpful hint alongside the title of the text box. For example, when you are editing the Keywords, the title says ``Enter keywords, separated by semicolons(;)''. >>>>> Saving or Abandoning the Reference <<<<< When you are done adding or editing your reference, press [Esc] to activate the menu at the top of the screen. Once you do this, you have one of three choices: >> [S]ave reference. Your reference is added to the database on disk. >> [A]bandon reference. The reference you just edited is ignored (it is not saved to disk) and the reference entry form is cleared. >> [E]dit. You are returned to the reference you were just editing, in order to continue modifying it. >> [H]elp. This brings up a help screen. Once you have chosen [S]ave or [A]bandon, the next menu provides you with two choices: >> [C]ontinue. Go back to the >Add References< screen to add another reference. >> [M]ain Menu. Return to the >Main Menu< (pressing [Esc] here will do the same thing). ************** Suggested Format ********** Most of the time, JEPRS doesn't really care how you enter your references into the database-the fields are all basically just text fields, so you can enter anything you want. (The only field it does care about is the Authors-you should follow closely the suggestions provided below.) However, in order to make the formatted output as JEPRS User's Guide, page 51 consistent as possible, here is a list of suggestions for how you might enter your references into each of the fields: >> Title. The first letter of the first word of the title is capitalized. Do not place a period at the end of the title. >> Authors. This is the only field where you must pay strict attention to the guidelines. Authors are entered last name first, followed by a space and then the initials. There is no space between initials (this is crucial), but periods can be used if you like, and dashes are OK for hyphenated initials. Spaces and dashes are OK between multi-part last names (e.g., `da Vinci' or `Weaver-Jones'). For multiple authors, place a comma and a space after each author (this is crucial), except the last author. Do not place an ``and'' or ``&'' before the last author-JEPRS can do this for you when formatting. Here are some examples of correct and incorrect Author entries: [Author Entry] [Problem] Lin VK-I Correct. Lin V K-I Wrong: Extra space. Wright WE, Lin LM Correct. Wright WE & Lin LM Wrong: Don't use `and' or `&' in authors. da Vinci L Correct. da Vinci, L Wrong: Extra comma. >> Journal. It is generally easier and takes less typing to enter standard abbreviations for journals, rather than full names (e.g. ``Mol Cell Biol'' instead of ``Molecular and Cellular Biology''), but this is not required. When formatting bibliographies/reference lists, some publications want the full journal name cited, while others want the abbreviation. JEPRS cannot switch between the two: you must be consistent and enter one style or the other and leave it up to that publication's proofers to enter the full text or make the abbreviations. >> Volume. If you wish to include the issue number, you may want to do it the way MedLine does, by enclosing it in parentheses (e.g., volume 112, number 8 would be 112(8) in MedLine) but this is not required. See note for novices under Year. >> Pages. There are a variety of ways of entering the pages. You can enter just the first page; the first page, a dash, and the last JEPRS User's Guide, page 52 page; or the first page, a dash, and the `significant digits' of the last page. For example: 134 or 134-139 or 134-9 Note that MedLine does it the last way (134-9), if you want to maintain consistency with MedLine. See also the note for novices under Year. >> Year. No requirements. A note to novice computer users: although a lowercase `L' (l) and a one (1) and, likewise, an uppercase `o' (O) and a zero (0) may look very similar to you, they are very different things to a computer! If, for example, you enter the year as l988 (using a lowercase `l'), and then use JEPRS' >Search Menu< to find all years equal to 1988 (using a one `1'), JEPRS will not think that is a match. Keep that in mind when entering the Volume, Pages, and Year. >> Type. New in version 2.5 is a pop-up menu, making it easier to select either [A]bstract, [B]ook, or [J]ournal. The reference type is useful for 2 reasons: (1) it functions to limit your search to, for example, only books or only journal articles; (2) it is also required for proper formatting on the >Format Menu<, since JEPRS can format references differently, depending on whether they are an [A]bstract, [B]ook, or [J]ournal. =================================================================== ***** ADVANCED TOPIC: ***** Non-English Characters You can add and search for ``foreign'' (non-English) characters in the PC's extended character set; On the >Add Reference< and >Edit Reference< screens, you can add any character to your reference that your PC can display; characters not on the keyboard (such as ` ' or ` ' or ` ') are entered by holding down the [Alt] key and entering the ASCII code of the letter or symbol on the numeric keypad. For example, to enter a ``beta'', hold down [Alt], press [2], [2], [5], and then let go of the [Alt] key, and you should see ` ' on your screen. On the >Search Menu<, you can search for the extended characters you have entered into your references. (However, you cannot search for the box-drawing characters, such as .) When using these extended characters, and then searching for them, keep these facts in mind: 1. Make sure your printer can print them! Not all printers can print the PC's extended character set. 2. Realize that when searching, `a' is not the same as ` ' (that is, non-English characters do not match the English ones); if you entered ` ' in your reference, then you must use ` ' when searching for it. 3. Whether searching is set to [C]ase-sensitive=[N]o or [Y]es, JEPRS will not convert lowercase extended characters to their uppercase equivalents. JEPRS User's Guide, page 53 For example, if you turn [C]ase Sensitivity off, and search for `L one', then JEPRS will convert that to `L ONE' before searching; it will not convert it to `L ONE'. =================================================================== >> Number (#). This is automatically assigned by JEPRS. Neither you nor JEPRS can ever change it. >> Editor. Some people prefer entering the full name, some use just the first initials and full last name; whatever you do, just maintain consistency. Don't end it with punctuation. >> Publisher. Generally, you would enter the publisher's name and city. Don't end it with punctuation. =================================================================== ***** ADVANCED TOPIC: ***** Keywords: Uppercase or Lower? The only disadvantage to using all uppercase keywords is in printing formatted output using a proportionally-spaced font (there is no problem when using a fixed-spacing font or in sending output to a Word Processor File). That's because JEPRS determines a line is full of text based on the number of characters in the line, not the width of the characters. Look at the following example: THIS IS A TEST OF FIXED SPACING This is a test of fixed spacing THIS IS A TEST OF PROPORTIONAL SPACING This is a test of proportional spacing ******NOTE: for users reading this from the JEPRS.Doc file, the above tests of "fixed" and "proportional" spacing will not display correctly.****** With a fixed-spacing font, both the all-uppercase and the mixed- case lines take the same amount of space; but with a proportional font, the all-uppercase line is much longer. This would force you to make your line width much smaller, subsequently displaying the rest of the reference (which would be mixed uppercase and lowercase) with a very wide right margin. Of course, if you plan on importing MedLine files, these have their keywords in all uppercase already, so you'll have to deal with this problem eventually. My recommendation would be to use a fixed-spacing font when printing out the keywords (for example, just to get a listing of your entire database) but you can use a proportional font when printing bibliographies (because you usually don't print out the keywords for them anyway). On the other hand, if you plan on sending the output to a Word Processor File, then you can use any font and let you word processor worry about spacing JEPRS User's Guide, page 54 and line breaks. =================================================================== >> Keywords. Keywords must be separated by a semicolon (`;'). This is so that when you display or export your references, JEPRS can find a place to break the keywords into separate lines. Keywords can be entered in either all capitals or mixed upper- and lower-case; there is no particular advantage to doing it either way, since during a Search you can convert them to uppercase for comparison. ************** Entering Sample References ********** Here are some suggestions for entering the three (actually, four) types of references that JEPRS was designed to deal with. >> Entering a Reference for a Journal or Magazine Article. These types of articles generally have: an article title, several authors, a journal or magazine name, a volume number, page(s) of publication, year of publication, and any number of keywords you want to add. Let's say the reference was the article called ``Myogenin, a factor regulating myogenesis, has a domain homologous to MyoD'' by Woodring E. Wright, David A. Sassoon, and Victor K. Lin, that appeared in the journal Cell in 1989, volume 56, pages 607 through 617, and then you wanted to add some keywords. A sample entry might look like Figure 1. Some of the keywords in the example in Figure 1 have strange character doublets like `\S' and `\~'; these are JEPRS' formatting codes for subscripting and italicizing, respectively. So, when they keywords are printed on your printer, `C\S3\SH10T1/2' will come out as `C3H10T1/2', and `\~myc\~-homology' will come out as `myc-homology'. You can enter any of JEPRS' commands for boldfacing, underlining, italicizing, super- and sub-scripting right into your references; however, note that this feature is in addition to the >Format Menu< formatting options, so don't think you have to italicize every journal name in your database, because it should be done at the >Format Menu<. The formatting commands are described in the >Global Defaults< chapter, in the section on creating Journal Definitions. >> Entering a Reference for an Abstract. One of the various types of entries you may want to make is for a reference to an abstract. In the biomedical sciences, for example, abstracts of data to be presented at scientific meetings are generally published in a softcover book. The information for an abstract is similar to that of a book (see below), but quite different from a journal entry. The example in Figure 2 is from a poster presented at a Cold Spring Harbor Laboratory meeting in September, 1989. In this case, note that the `Journal' field becomes the symposium title, and the `Editor' is actually the organizers of the meeting. JEPRS User's Guide, page 55 >> Entering a Reference to a Book. The third major category JEPRS was designed for is book entries. If you plan on referencing a whole book as one entity (rather than chapter by chapter), see Figure 3 for a suggestion. Notice that the Title and Authors are blank, the Journal becomes the book title, the Volume is blank (unless, of course, it is a serial publication), the Pages are blank, and everything else is as expected. >> Entering a Reference to a Book Chapter. Sometimes, however, you will want to reference a specific chapter of a book, rather than the book as a whole. This is easily accomplished in Figure 4 by a slight modification of the Book definition in Figure 3. In the example in Figure 4, the chapter title is entered in the Title field, the chapter authors in the Author field, the book name in the Journal field, the `Book' type in the Type field, and the book editors in the Editor field. Just as in the Journal or Magazine example, JEPRS's special formatting characters are used, in this case italics for Drosophila. =================================================================== Title:Myogenin, a factor regulating myogenesis, has a domain ...... homologous to MyoD Authors:Wright WE, Sassoon DA, Lin VK ........ Journal:Cell ........ Volume:56 Pages:607-17 Year:1989 Type:Journal #:158 ....... ...... ..... ..... .. Keywords:Rat;myogenesis;cell differentiation; cell determination; ......... myogenin; MyoD1; L\S6\S; C\S3\SH10T1/2; \~myc\~-homology domain; \~myd\~; BUdR/Bromodeoxyuridine; =================================================================== Figure 1: A sample reference for a Journal article. =================================================================== =================================================================== Title:Developmental regulation of myogenin, a gene regulating ...... vertebrate myogenesis Authors:Miranda LM, Wright WE ........ Journal:Regulation of eukaryotic mRNA transcription ........ Volume: Pages:150 Year:1989 Type:Abstract #:855 ....... ...... ..... ..... .. Editor:W Herr, R Tjian, K Yamamoto ....... Publisher:Cold Spring Harbor Laboratory, Cold .......... Spring Harbor, NY USA Keywords:Rat;myogenesis;cell differentiation; ......... myogenin;MyoD1;L\S6\S;C\S2\SC\S12\S;Promoter \~myc\~-homology domain;TATA box;transfection; =================================================================== Figure 2. A sample reference for an Abstract. =================================================================== JEPRS User's Guide, page 56 =================================================================== Title: ...... Authors: ........ Journal:Year Book of Developmental Biology ........ Volume: Pages: Year:1989 Type:Book #:856 ....... ...... ..... ..... .. Editor:JM Schindler ....... Publisher:CRC Press, Inc., Boca Raton FL USA .......... Keywords:cell differentiation;developmental biology;mini-reviews;cell ......... determination;gene expression;cell biology;morphogenesis;pattern formation; =================================================================== Figure 3. A sample reference for a Book. =================================================================== =================================================================== Title:Genetics of \~Drosophila\~ embryogenesis ...... Authors:Mahowald AP, Hardy PA ........ Journal:Ann Rev Genet ........ Volume: Pages:149-77 Year:1985 Type:Book #:857 ....... ...... ..... ..... .. Editor: ....... Publisher:Annual Reviews, Inc., Palo Alto, CA USA .......... Keywords:cell differentiation;developmental biology; ......... cell determination;gene expression;morphogenesis;pattern formation;\~Drosophila\~; =================================================================== Figure 4. A sample reference for a Book Chapter. =================================================================== JEPRS User's Guide, page 57 C H A P T E R N I N E _________ Formatting References #################################### Formatting is one of several areas where JEPRS far exceeds the capabilities of most of its competitors. Formatted output can be boldfaced, underlined, italicized, superscripted, and subscripted, depending upon the capabilities of your word processor or printer. You can also specify page length, characters per line, a header, page numbering, and other parameters at the >Global Defaults Menu<. ##################################### At the >Main Menu< press [F]ormat. The >Format Menu< contains the commands [G]o, [F]ormat, [I]nput, [O]utput, [D]efaults, and [H]elp. As usual, the Help command can also be invoked by pressing [F1]. Of course, [Esc] brings you back to the >Main Menu<. ************** Pre-Defined Settings ********** JEPRS has the ability to set your [I]nput, [O]utputs, [F]ormat style, and [D]efaults to previously determined values. If you like these values as they are, you can skip over this section and get right on to formatting. However, if any of these are not to your liking, simply modify them as described here. >>>>> Formats <<<<< You can define up to 30 Format styles (also known as journal definitions) in your Config file (see the chapters Global Defaults and Format Styles: A Tutorial for information on modifying these styles). These format styles define how the formatted output from JEPRS will look. When you press [F]ormat while at the >Format Menu<, you can pick which format style to use. Use the up and down arrow keys and the [PgUp] and [PgDn] keys to scroll through the 30 available styles. When the arrow is next to the format style you wish to use, just press [Enter]. Or, just enter the number at the ``Format Style:'' prompt. If you decide you don't want to change the style, just press [Esc]. JEPRS User's Guide, page 58 If there is one format style that you use most often, you can save its number in your Config file as the default format style. Just go ahead and choose one of the available styles, and you will be returned to the >Format Menu<. Now press [F2] to go to the >Global Defaults Menu<. When you get to this menu, press [D]efaults, and then [S]ave defaults+files. Now whenever you use that Config file, the format style you just saved will be used as the default style. >>>>> Input <<<<< By default, JEPRS uses the keyboard for input. This means that when you press [G]o to start formatting, you would have to use the keyboard to manually enter the number of each reference that you want formatted. Sometimes this is not the best way to format your references. For example, you may want a whole subsection of your reference file (or the whole thing) formatted, or you may want to use a Word Processor File as input. Either of these are very easy to do. When at the >Format Menu<, press [I]nput. This will bring up a pull-down menu. Like every other pull-down menu in JEPRS, use the up and down arrow keys and [PgUp] and [PgDn] keys to move among the choices, then press [Enter] when the selection you want is highlighted. Or, just press the highlighted letter of your choice. Notice that when you make a selection, a yellow arrow appears next to that name on the right side of the screen. This is a reminder of your choice. Here is a list of the effects of selecting each of the inputs: >> Keyboard input. After pressing [G]o, you will be prompted to enter the number of every reference that you want formatted. >> Number file input. After pressing [G]o, JEPRS will look for the Number file, using the name specified on the >Global Defaults Menu<. This is just a text file containing numbers of references, with each number on a separate line. You can create this file yourself with a text editor or word processor (in the DOS Text or Non-document mode). In addition, JEPRS can create this file by pressing [F9] when at the >List Menu< or the >Search Results< screen. For more information on the Number file, see the chapter in the Appendix on JEPRS' Files. >> Reference file input. If you select this item at the pull-down [I]nput menu, then you are asked at which reference you wish to start and end. If you want to format the whole database, then just use the default values (which are the first and last reference in the database). Otherwise, you can enter any two reference numbers at which to start and end formatting. When you press [G]o, JEPRS will auto- matically format the references you specified. >> Word Processor file input. New in version 2.5 is JEPRS' ability to read WordPerfect 5.x and PC-Write 3.0 documents. After you press [G]o, JEPRS looks for the Word Processor Input File, using the name specified on the >Global Defaults Menu<. (You use your word processor to insert JEPRS codes into your document, such as {J#123}; see the JEPRS User's Guide, page 59 Advanced Topic.) JEPRS will then read through your Word Processor Input File, looking for the codes; in this example, it would generate output for reference #123. JEPRS can optionally go back and replace your JEPRS codes (such as {J#123} ) with either an author+year citation or sequential numbering. (You specify author+year or sequential numbering for each Format Style; see the chapter on Global Defaults, especially the subsection on Editing Format Styles for information on choosing between these two options.) After it reads through your Word Processor Input File and generates the bibliography, a pop-up dialog box appears on the screen, asking you if you want to replace the JEPRS codes. If you choose [N]o, then no further processing will be done. If you choose [Y]es, then JEPRS will create a new file which will be an exact copy of your Word Processor Input File, except that the JEPRS codes will be replaced by author+year or sequentially numbered citations. This new file will have the same name as your old file, except the extension will be *.New. For example, if your original Word Processor Input File was called MyFile.WP, then the revised version will be called MyFile.New. =================================================================== ***** ADVANCED TOPIC: ***** JEPRS Codes in Your Word Processor Documents Since JEPRS can now read WordPerfect and PC-Write documents, it is important to be very precise about entering the codes that JEPRS can read. The format is simple: Just type in a left squiggly bracket, followed by a capital `j', followed by the number or pound sign, followed by the JEPRS reference number, followed by a right squiggly bracket. For example, if you want to cite JEPRS reference #44, then you would type: {J#44} into your word processor document at the point where you wanted the reference cited. If you are using WordPerfect, keep in mind that you must use version 5.0 or higher, and that you should not use Text Boxes (JEPRS can find the codes if they are in a Text Box, but if you tell JEPRS to replace them with author+year or sequential number citations, then your document will become corrupted). You can use your word processor to surround the JEPRS codes with special features. For example, what if you need to have the codes replaced not just with sequential numbers, but superscripted numbers? Instead of just entering the JEPRS codes by themselves: {J#44} you can surround them with `superscript' codes from your word processor. For example, here is how the above code would look in WordPerfect's ``reveal codes'' screen if you put superscript codes around it: JEPRS User's Guide, page 60 [SUPRSCPT]{J#44}[suprscpt] The one thing you should keep in mind if you do this is that your word processor codes should be outside of the JEPRS codes' squiggly braces (as in the example above). =================================================================== >>>>> Output <<<<< When you select [O]utput from the >Format Menu<, a pull-down menu pops up to give you a choice of [S]creen, [P]rinter, [T]ext, or [W]ord Processor File. You can mix and match any combination of outputs. Check the right side of the screen under ``Output:'' to see which of the outputs are currently selected. >> Screen. Once you press [G]o to start, the formatted references will be displayed on the screen, continuously scrolling from bottom to top. >> Printer. Your formatted references will be directed to your printer. The currently defined printer will be used; check the >Global Defaults Menu< to see which printer that is. >> Text File. The references will be sent to the currently defined Text File (see the >Global Defaults Menu< to change the name of that file). Note that [D]efaults/[T]ext File Formatting on the >Global Defaults Menu< determines how the output references are formatted, in addition to the current Format Style. >> Word Processor File. Your specified references are sent to the [O]utput Word Processor File (>Global Defaults Menu<). This can be either a WordPerfect 5.x or PC-Write 3.0 file. You specify the file type at the >Global Defaults Menu< under [D]efaults/[W]ord Processor Type. >>>>> Defaults <<<<< There are two local defaults on the >Format Menu<: >> Page Start #. This number tells JEPRS how to number the pages on your output. JEPRS only numbers the output pages if you include the ``\P'' code in your header (see Printer definitions on the >Global Defaults Menu<). By default, it starts page numbering at page #1, but you can set this number to anything greater than zero. For example, if you set it to 23, then the first page of output will be listed as #23, the second page as #24, the third page as #25, and so on. JEPRS does not number your pages when [O]utput=[W]ord Processor File, since your word processor can do that for you. JEPRS User's Guide, page 61 >> Replace " with . . . . This default is useful for comma- delimited output. When you use comma-delimited output as a format style, then the fields are each enclosed in double quote marks and separated by commas. For example, if the year was `1989' and the author was `Wright WE' in one of your references, then they would appear in comma delimited output as: "Wright WE", "1989" However, there is the possibility that one of your references might itself contain a double quote mark. This would seriously interfere with your ability to import that reference into another database system (the additional double quote mark would mess it up). The [R]eplace " With . . . default allows you to change every occurrence of a double quote mark with some other character when it is output during formatting. So if you had a keyword that was: Open Reading Frame/"ORF" and you set the [R]eplace " With . . . default character to a single backwards quote (`), then JEPRS would send your formatted output like this: "Open Reading Frame/`ORF`" thereby avoiding the problem of extra double quotes in your output. ************** Starting Formatting ********** Once all the default values are set to your liking, just select [G]o to start the formatting process. Your screen will vary depending on the type of input and output you have selected. >> Keyboard Input. If you have selected keyboard input, then the very last line on the screen will prompt you for a reference number entry. Type in any number and press [Enter]. The number will automatically be incremented, so if you want to enter a sequential series of numbers, just keep pressing [Enter]. Since it is a prompt, you also have the option of editing the value displayed. If you have selected screen output, then the references will be displayed on the screen as soon as you enter the number. However, if the particular format style you have selected has [S]ort=[A]uthor, [S]ort=[J]ournal, or [S]ort=[Y]ear, then the references are displayed only after you have entered the last reference number and then pressed [F3] to start formatting. If you have not selected screen output, then a pop-up window will appear. This window will display the number of each reference as JEPRS is formatting it and sending it to the specified output(s). >> Reference File, Number File, or Word Processor File Input. If you have selected any of these files as input, then the screen will clear and the following will appear at the bottom: JEPRS User's Guide, page 62 [Esc]=Exit [ScrollLock]=Pause As usual, pressing [Esc] will terminate the current process and bring you back to the previous menu. Before it does, though, a pop-up dialog box will first ask you ``Terminate Formatting? (y/n)''; press [Y] to stop formatting or [N] to continue. If you have turned screen output on, the formatting references will scroll by on the screen quite rapidly. There is, however, an easy way to temporarily stop the screen: press the [ScrollLock] key on your keyboard (it's generally near the top right corner of your keyboard). If you do, the screen will pause, and the following message will appear at the bottom: Press [ScrollLock] to continue So, just press the key again to restart the formatting display of your references. If you have turned screen output off (and are using text file, word processor file, or printer output) then a pop-up box will appear displaying the current reference number being sent to the requested output device(s). JEPRS User's Guide, page 63 C H A P T E R T E N _________ Searching #################################### Once your database becomes fairly large, you will often not remember exactly which references it contains. You would probably like a system that allows you to search through your database to find the reference or group of references that you're looking for. JEPRS is quite flexible in this regard, and allows both very simple and quite complex searches. This chapter will describe how to go about searching through your database. ##################################### Press [S]earch at the >Main Menu< to go to the >Search Menu<. The menu at the top of the screen contains the commands [G]o, [T]erms, [O]utput, [D]efaults, and [H]elp. As usual, Help can also be accessed by pressing [F1]. And [Esc] brings you back to the >Main Menu<. ************** Pre-Defined Settings ********** All you need to do in order to perform a simple search is to specify one search [T]erm and then press [G]o to start (assuming all the pre-defined selections listed on the right side of your screen are to your liking). You cannot start a search without specifying any Terms; if you try to, you will get an error message. >>>>> Terms <<<<< Search terms specify the fields to be searched as well as the text that you want to match. To search for all papers by an author named ``Wright'', you would: Press [T]erms. Enter A to search through the author field. Enter Wright to search for this particular text. Once you press [T]erms, you are asked to ``Enter search:''; this is where you enter the letters corresponding to the field(s) to be searched. JEPRS lists the letters and their respective fields at the bottom of the screen (see table for field codes). JEPRS User's Guide, page 64 [Field Codes for Search Terms] [A]uthors [E]ditor [K]eywords [C]itation type [T]itle [Y]ear [P]ublisher [J]ournal You can perform mulitple searches by connecting the field codes with operators (see table for a list of operators). [Operators and their Significance] + AND - NOT / OR These are the Boolean logical operators. So if you want to search for papers by Author ``Wright'' and Title ``Myogenin'' then you would enter A+T for [A]uthor [+][and] [T]itle, then enter Wright, then enter Myogenin. [When you're entering the text, you must enter it in the same order as the field codes; that is, you couldn't enter ``Myogenin'' first and ``Wright'' second, otherwise it would look for ``Myogenin'' in the authors and ``Wright'' in the titles, giving you a nonsense answer. In order to help you along, JEPRS will make the current field code blink while you are entering the search text for it.] Thus your screen should look like this: Enter Search: A+T Wright Myogenin Because the Boolean logical operators are not always intuitive, let me give a brief explanation of each. If your search is A+T then both the author and the title you specify must be in the same reference citation in order for it to be considered a match. If your search is A-T then the author must be in the reference citation and the title must not be in that same reference to be a match. If your search is A/T then either that author or that title must be in the reference in order to be a match. Here are some additional tidbits to ponder: A+T is logically identical to T+A; that is, both an author an a title must be in the same reference. A/T is logically identical to T/A; that is, either an author or a title must be in the same reference. A-T is very different from T-A. In the first case, the author must be in a reference and the title must not be in a reference; in the latter, the title must be in a reference and the author must not. JEPRS User's Guide, page 65 JEPRS doesn't allow you to do a search like -A (in other words, find all references except those with a certain author). You can get around this by doing something like A-A; when asked for the first search text just press [Enter] (this will match all references) and then for the second search text enter the name of the author you don't want. This accomplishes the same thing as -A. JEPRS doesn't necessarily search for whole words. So if you specify a search for authors named ``STEIN'' it will also find ``STEINBERG'' and ``FRANKENSTEIN'' because they both have ``STEIN'' in them. There are three ways to try to get around this: (1) Make [C]ase Sensitivity=[Y]es and search for ``Stein''; then ``Frankenstein'' would not be a match; (2) Use a space, a comma, or other delimiter, for example ``Stein,''; then ``Steinberg'' would not be a match; and finally (3) if after performing your search you find that there are one or two common `contaminants', you can use [F4] (>Modify Search<) to specifically exclude them (e.g., -A Steinberg would get rid of all matches that had ``Steinberg'' in them). Of course in this case you would have to be careful to make sure that some of your references didn't contain both Stein and Steinberg as authors. >>>>> Advanced Example <<<<< Let's say you're preparing a bibliography on various subtopics within a more general field. This time, you're going to want to find all references dealing with DNA, but specifically eukaryotic cell transfection or prokaryotic cell transformation. You also want to exclude the older references, which will probably not be as much use to you. You also want to exclude all Abstracts, since they won't contain enough information to be really useful in this particular instance. This would be entered as: Enter Search: (K+(K/K))+Y-C DNA Transformation Transfection 1986-1989 A This search strategy tells JEPRS to look for all references that deal with (keywords = DNA and (keywords = Transformation or keywords = Transfection)) and (year = 1986-1989) but not (citation type = Abstract). =================================================================== ***** ADVANCED TOPIC: ***** Parentheses & Boolean Operators in Search Terms Placement of the parentheses is crucial in the advanced example. If you did not include the parentheses, and entered your search as simply K+K/K+Y-C, then that would have yielded a very different answer. This JEPRS User's Guide, page 66 can be demonstrated by listing some hypothetical references below: [Sample Reference Numbers & Their Keywords] 1 DNA; transfection 2 transfection; protein 3 DNA; transformation If you entered your search as (K+(K/K)), then references 1 & 3 would match (because 1 has `DNA' and `transfection' and 3 has `DNA' and `transformation'). If you entered your search as K+K/K (which would be equivalent to entering (K+K)/K, since JEPRS is just reading and interpreting from left to right) then references 2 & 3 would match (because 2 has `transfection' and 3 has both `DNA' and `transformation'). The Boolean logic operators can be very powerful, but they can sometimes be confusing, too. If you are in doubt as to how a search will be interpreted, use parentheses to force a particular interpretation. Too many parentheses can't hurt. =================================================================== >>>>> Output <<<<< When you select this option, a pull-down menu appears, allowing you to select any combination of [S]creen, [P]rinter, [T]ext file or [N]umber file. Check the right side of your screen to see which output(s) are currently selected. The default is [S]creen=[Y]es, everything else=[N]o. If you try to turn all the outputs off, JEPRS will beep and turn the [S]creen back on. >> Screen. Once searching begins, successful matches will be displayed on your screen in a compact, one-line format for each reference found. >> Printer. Successful matches will be sent to your printer in the currently-defined format style (see the >Format Menu< to select the format style). Note, however, that printer codes will not be sent to the printer. Also, the margins are predefined and cannot be changed. If you want to have formatted output (including boldface, etc.) sent to your printer, you must have output sent to your printer from the >Format Menu<, not the >Search Menu<. You can do this by using [O]utput=[N]umber file at the >Search Menu< and then using [I]nput=[N]umber file at the >Format Menu<. JEPRS User's Guide, page 67 >> Number File. Only the numbers of the successful matches will be sent to this DOS text file. This file can then be used as Input on the >Format Menu< and the >Export Menu<. See the chapter in the Appendix on JEPRS' Files for more information on the Number file. >> Text File. This is identical to having output sent to the Printer, except that it will be sent to the Text file (see the >Global Defaults Menu< for the name of the currently-defined Text file). All the caveats listed under ``Printer'', above, are also true for the Text file. In addition, [D]efaults/[T]ext File Formatting on the >Global Defaults Menu< also affects output to the Text file. >>>>> Defaults <<<<< There are a variety of local defaults that affect how the current search is executed. >> Begin. Specifies at which reference number the search will start. An example of its use would be if you had a database of 900 references and you knew that the paper you were looking for was in the last 300 or so references; then you would specify [B]egin at #600. This would cut down your search time significantly. The default value is 1 (the first reference in the database). >> End. This is just like Begin, but at the other end of the spectrum; just specify at what reference number you want searching to stop. The default value is the last reference in the database. >> Matches. This tells JEPRS to stop the search after this many matches have been found. Let's say that you know that a certain search, such as keywords for ``DNA'', will yield a lot of matches, but you only want to see the first 15 of them. Press [M]atches and enter ``15''. Then when you start the search, as soon as the 15th match is found, searching automatically stops. If fewer than 15 matches are found it will just search to the end of the database and then stop. The default value is the total number of references in the database. (If you have a very large database and you wish to sort it before displaying it, it is a good idea to use a Match number smaller than the database; this frees up memory for the sorting.) >> Case Sensitivity. When this is set equal to [N]o, then both your search text and the references in the database are converted to uppercase before being compared. That way you don't have to worry about entering ``DNA-binding protein'' or ``dna-Binding Protein'', since they will both be converted to ``DNA-BINDING PROTEIN'' for the search. If you wish to make the comparisons directly without converting to uppercase, then make [C]ase Sensitivity=[Y]es. You can make your choice `permanent' by saving this value in the Config file. That is, when you choose [D]efaults/[S]ave defaults+files at the >Global Defaults Menu<, the answer you entered here is saved and used whenever you use your Config file. JEPRS User's Guide, page 68 >> Sort. If this is set to [N]one, then JEPRS displays the references in the order they were found in the database. If you set [S]ort=[A]uthor, your matched references will be displayed alphabetically by the first author's last name. If [S]ort=[J]ournal, the found references are sorted by the Journal name. Finally, if [S]ort=[Y]ear, then the references are displayed in Year order. As with [C]ase sensitivity, this value can be saved in your Config file (see above). ************** Starting a Search ********** Once you press [G]o to start the search, the Messages window on the bottom of the screen will show you the number of references being searched as well as how many matches have been found. You can press [Esc] at any time to stop the search; if you do so, a pop-up dialog box will ask you to confirm your decision. Press [Y] to terminate the search, or press any other key to continue. Note that this terminates the search, it doesn't abandon it. So if any matches were found before you pressed [Esc], they'd be sent to the desired output after terminating the search. >> Text file, Number file, & Printer output. If any of these outputs have been selected, then once the search is completed, a pop- up box will display the number of each reference as it is being formatted and sent to the proper output. Again, you can press [Esc] here to terminate the output. >> Screen Output. If you have selected the screen as output, then as soon as any matched references are found, the window switches to the Search Results screen. As each matching reference is found, it is added to the Search Results in a compact, one-line format. Once the search is completed, the matches will be displayed in the Search Results screen in the order in which they were found in the database; unless, of course, sorting was turned on, in which case they will be sorted before being redisplayed. >>>>> Search Results Screen <<<<< The idea behind this display is that it presents as many references as possible, with the most useful information, in the least amount of space. This lets you scroll around the matching reference list, select specific references (or groups of references) you want to send to various outputs, view entire references, and edit references-all in one place. The function keys available are described here. Users upgrading from version 1.x: the key used for Modifying the search is different in version 2.5. JEPRS User's Guide, page 69 >> [Up Arrow]. This moves the cursor up one reference at a time. The screen is scrolled down one line if necessary. >> [Down Arrow]. Moves the cursor down one reference at a time. The screen is scrolled up one line if necessary. >> [PgUp]. Scrolls the screen up one page (if more than one page of matches have been found). >> [PgDn]. Scrolls the screen down one page (if more than one page of matches has been found). >> [Enter]. Displays the entire reference. What this actually does is bring up the >List Reference< screen, using the current reference number. In this way you are not limited to seeing only part of the matched references-you can see the whole thing. While at the >List Reference< screen, you can press the [F4] key to bring you to the >Edit Reference< screen where you can edit the reference (see the chapter in this User's Guide on Listing References for more information). Pressing [PgDn] or [PgUp] while at the >List Reference <screen will display the next or previous found reference, respectively. In other words, it won't display the next sequential reference in the database, it will instead display the next (or previous) reference on the list of matched references on the >Search Results< Screen. >> [Esc]. You will be returned to the >Search Menu<. At this point you may start a completely new search, or you can modify any aspect of the previous search. The latter is possible because JEPRS saves the search terms and default values from your last search. JEPRS will even save them if you go off to some other part of the program and then come back to search later. Of course, once you exit the program your search terms and defaults are lost. Once you return to the >Search Menu<, if you decide you want to redisplay your most-recent search, you can press [F3] to go back to your previous search. >> [F1]. As always, this will give you context-sensitive help. >> [F4]. This lets you modify your search by bringing you to the >Modify Search Menu<. The first time you modify your search, a short list of instructions is provided. Your previous search terms are displayed on the top left of the screen. The number of matches JEPRS has found for the current search is displayed in the upper right corner. When you are specifying terms for >Modify Search<, think of it as being added to your original terms. For example, if your original search was A+A but you found too many matches, you could modify your search with -K which would be equivalent to an original search of A+A- K. Notice that searching by >Modify Search< is usually very quick; that's because it doesn't search the entire database-it only searches those references that have already yielded a match (and that's the reason you can't use the or (/) operator, because then it would have to search the entire database). You can modify a search up to a total of 3 times. JEPRS User's Guide, page 70 >> [*]. Marks the reference that the cursor is sitting on. You can tell if a reference is Marked because it will have an asterisk (`*') next to the year. Marking a reference is used for output (see [F8], [F9], & [F10] below). >> [F5]. Marks all of the matched references. Even if more than one page of matches has been found, every matched reference on every page of the Search Results is marked. Marking a reference is used for output (see [F8], [F9], & [F10] below). Hint: To unMark all the references, press [F5], then press [F6]. >> [F6]. Reverses all the Marks. That is, all Marked references become unMarked, and all unMarked references become Marked. Let's say you have 20 matches and you want to send one subset to the printer and another subset to a Number file (for exporting). You would first manually Mark each reference that you want printed by using the [*] key, and then press [F9] to send them to the printer. Then you would press [F6] to reverse all the marks, and press [F8] to send the other subset of references to the Number file. >> [F8]. If no references are Marked, this sends the number of the current reference (where the cursor is sitting) to the Number file. If any references are Marked, then only Marked references are sent to the Number file (regardless of where the cursor is). >> [F9]. If no references are Marked, this sends the entire text of the current reference to the printer. If any references are Marked, then only Marked references are sent to the printer. The currently- defined format style (see the >Format Menu<) is used for output. Also, the line width is pre-defined at 65 characters per line. >> [F10]. If no references are Marked, this sends the entire text of the current reference (where the cursor is sitting) to the Text file. If any references are Marked, then only Marked references are sent to the Text file (regardless of where the cursor is). The currently-defined format style (see the >Format Menu<) is used for output. Also, the line width is pre-defined at 65 characters per line. In addition, the [D]efaults/[T]ext file formatting on the >Global Defaults Menu< affects the output. JEPRS User's Guide, page 71 C H A P T E R E L E V E N _________ Utilities #################################### The >Utilities Menu< contains three functions that, while very useful, are generally used less often than those functions listed at the >Main Menu<. Here, JEPRS allows you to import references, export references, and compress your database. ##################################### ************** Importing ********** JEPRS has the power to import references in three different formats from a variety of different sources. These are formats generally used only by Ph.D.s, M.D.s, and others in biomedical fields. >>>>> Formats <<<<< JEPRS supports three different import formats. You can select any one of them from the ones listed on the screen. The formats and their potential sources are: >> MedLine. This is a ``standard'' biomedical reference format defined by the USA's National Library of Medicine (NLM). Most commercially available reference management programs and on-line biomedical database systems support this type of file. For example, PaperChase (an on-line system of Harvard University-affiliated Beth Israel Hospital in Boston) allows you to search through the National Library of Medicine's main bibliographic database and download these references to your own computer. One of the (several) formats they support is MedLine. MedLine output is also produced by IBM PC-based programs, such as ISI's Current Contents on Diskette (CCOD). Just like PaperChase, CCOD allows you to save files in MedLine format. >> CL-MedLine. This format is slightly different from the standard MedLine format. It is produced by a program called CL-MedLine from a company called CLSI, Inc. CLSI, Inc. has recently announced that CL- MedLine is being discontinued. Therefore, future versions of JEPRS JEPRS User's Guide, page 72 will no longer support this format. >> BRS/Colleague. Though this format looks a little like MedLine, it is really quite different. An on-line database searching system called BRS/Colleague produces these formatted files. Note: Keep in mind that you can generally import these files immediately into JEPRS without modifying them at all. For example, you sometimes get extraneous commands and other text mixed in with your actual references when you download these files from the on-line databases. Some other programs actually make you ``clean-up'' these files before importing them. But not JEPRS! JEPRS is smart enough to ignore anything that isn't a real reference. >>>>> Defaults <<<<< Two local defaults are available from the menu: >> Remove subheadings from keywords. MedLine and other files tend to have a lot of information most people consider superfluous. This includes keywords for source of grant support (US government vs. private funding), and subheadings for keywords. Those subheadings can be useful for PaperChase searches, but tend to be less so in JEPRS. Therefore, if you set this value to [Y]es, then these terms will be stripped from your references before being added to your database. >> Edit references before adding to database. In most programs, once you starting importing, you have an all-or-none situation: import all the references in a file, or don't import at all! You have the option in JEPRS of importing them one at a time. If this default is set to [Y]es, then as each reference is read in from the file, it is displayed on JEPRS' >Edit Reference< screen. At this point, you have the option of: discarding the reference and moving on to the next one; saving the reference as is; or editing the reference and then saving it. See below for more details. >>>>> Starting an Import <<<<< After verifying that the Format and Defaults are set to your liking, you are almost ready to start importing. The one last thing that must be taken care of is the name of the Import file. There are two ways to go about this, depending on whether you always import a file with the same name, or always use different names. If you always import a file with a standard name (such as MedLine.Txt) then you can go to the >Global Defaults Menu< (by pressing [F2] while at the >Utilities Menu<) and specify its name on the [F]iles/[I]mport file menu. Then go to [D]efaults/[S]ave defaults+files. In this way, the name of the Import file will be saved in your Config file, and you will not have to bother changing it every time you import a file. If, on the other hand, the file will have a different name every time, see the advanced topic, below. JEPRS User's Guide, page 73 =================================================================== ***** ADVANCED TOPIC: ***** Using a Different Filename for each Import The other way of specifying an Import filename is if you have a different file name every time you perform an Import. In this case, it would be annoying to have to remember to go to the >Global Defaults Menu< and specify the filename for the Import file every time you performed an Import. What you can do is take advantage of JEPRS' intelligence: Go to the >Global Defaults Menu< (by pressing [F2] at the >Utilities Menu<) and this time specify a ``fake'' filename at the Import filename prompt. Choose a name that you know you will never use, like FakeFile.XYZ. Again, choose [D]efaults/[S]ave defaults+filenames to save this filename into your Config file. (Why are we saving a fake filename?! Read on . . . ) Now whenever you are at the >Import File< menu and you press [G]o to start importing, a dialog box will pop-up to tell you there is a file error, since JEPRS can't find your fake file called FakeFile.XYZ. Then all you have to do is press [F4], enter the real filename, press [Enter,] and you're done. =================================================================== After pressing [G]o to start the Import, JEPRS checks for the Import file, starts reading from it, and then imports the references into your database. What you see on the screen depends on how you set the default called ``Edit references before adding to database?'': >> No editing/Import all at once. The messages window will clear, and then a horizontal bar graph will appear. As JEPRS reads in your Import File, the graph will show what percentage of the file has been read in. If at any point you decide you want to stop importing, just press [Esc]; once you do, a pop-up dialog box will ask you to confirm your decision. Press [Y] to terminate Import, or press any other key to continue. >> Edit references/Import one at a time. If this option is selected, then as each reference is read in from the Import File, you are presented with the >Edit Reference< screen. The cursor moves to the menu. If you just press [Enter] or [S]ave, then the reference is immediately saved into your database. You can instead press [A]bandon, in which case the current reference is discarded, or you can press [E]dit, in which case you can edit the reference before saving it. After you have chosen either [A]bandon or [S]ave, another menu appears at the top of the screen and a pop-up window appears. This window tells you the number of references read in from the Import File, as well as what percentage of the file has been read in. The menu then allows you to import the next reference by pressing [Enter] or [I]mport, or stop importing by pressing [E]xit. The two menus are set JEPRS User's Guide, page 74 up for simplicity: that is, if you want to save each reference, you can just press [Enter] twice (once at the first menu to [S]ave, and once at the second menu to continue to [I]mport). Whether or not you have chosen [E]dit references before importing, once 100% of the file is read in (or you [E]xit importing), the ``Messages'' window will display the total number of references read in as well as the total number of references saved into the database. You are then prompted to press any key to return to the >Import Menu<. ************** Exporting ********** JEPRS has a very rich and powerful Formatting capability, which is accessed by selecting [F]ormat from the >Main Menu<. However, there is one particular type of formatting that JEPRS' format commands cannot do: the MedLine format. So JEPRS has the ability to export in the MedLine format at the >Export Menu<. (Note that this feature is probably only important to biomedical researchers, students, and clinicians.) >>>>> Input <<<<< By default, JEPRS uses the keyboard for input. This means that when you press [G]o to start exporting, you have to use the keyboard to manually enter the number of each reference that you want exported. Sometimes this is not the best way to specify the references you wish to export. For example, you may want an entire subsection of your reference file exported, or you may want to use a Number File as input. Either of these is very easy to do. When at the >Export Menu<, press [I]nput. This will bring up a pull-down menu. Notice that when you make a selection, a yellow arrowhead appears next to that name on the right side of the screen. This is a reminder of your choice. Here is a rundown of your options: >> Keyboard input. After pressing [G]o, you will be prompted to enter the number of every reference that you want exported. >> Number file input. After pressing [G]o, JEPRS will look for the Number File, using the name specified on the >Global Defaults Menu<. This is just a text file containing numbers of references, with each number on a separate line. You can create this file yourself with a text editor or word processor (in the DOS Text or Non-document mode). In addition, JEPRS can create this file if you press [F9] when at the >List Menu< or the >Search Results< screen. For more information on the Number File, see the Appendix chapter on JEPRS' Files. >> Reference file input. If you select this item at the pull-down [I]nput menu, then you are asked at which references you wish to start and end. If you want to export the whole database, then just use the JEPRS User's Guide, page 75 default values (which are the first and last reference in the database). Otherwise, you can enter any two reference numbers at which to start and end exporting. >>>>> Output <<<<< When you select [O]utput from the >Export Menu<, a pull-down menu pops up to give you a choice of [S]creen, [P]rinter, or [T]ext File. You can mix and match any combination of outputs. Check the right side of the screen under ``Output:'' to see which of the outputs are currently selected. New with version 2.0 of JEPRS was the ability to send output to the screen and/or a printer. Nonetheless, the most useful output is still a Text file. >> Screen. Once you press [G]o to start, the exported references will be displayed on the screen, continuously scrolling from bottom to top. >> Printer. Your exported references will be directed to your printer. >> Text File. The references will be sent to the currently defined Text File (see the >Global Defaults Menu< to view the name of that file). >>>>> Defaults <<<<< There are two local defaults on the >Export Menu<. >> Remove printer codes from references. JEPRS is quite powerful in that in addition to printer codes (for example: underlining, italics, etc.) in the Format Styles, you can also have printer codes within your references. However, this can cause a problem during exporting, since no other program recognizes these codes. Therefore, if you set this default to [Y]es, then these codes will be removed before sending your references to the output device(s). >> Convert all keywords to uppercase. JEPRS itself doesn't really care if you keep your keywords in ALL UPPERCASE, all lowercase, or miXeD UpPeR ANd LoWerCaSE. However, the standard MedLine format has its keywords in ALL UPPERCASE. If you want all your keywords converted to uppercase during export, set this default to [Y]es (this doesn't affect your reference database itself; the keywords there remain unchanged). >>>>> Starting an Export <<<<< Just press [G]o to start, once you've decided all the defaults are to your liking. If Screen output is on, then the references will continuously scroll up the screen. If Screen output is off, a pop-up JEPRS User's Guide, page 76 box will appear, telling you which references are being sent to the output device(s). At any time, you can press [Esc] to stop exporting, and a pop-up dialog box will ask you for confirmation. Press [Y]es to stop exporting, or any other key to continue. ************** Compressing the Database ********** The file system JEPRS uses for storing your references is very efficient. It uses much less disk space (and many fewer files) than most database systems. Nonetheless, it does have one minor inefficiency: When you edit references, it marks the old version as invalid, and then adds a new version to the end of your database. This results in some wasted space in your database file. If this ever becomes a problem (for example if you are running out of disk space), you can easily correct it. On the >Main Menu< and the >Compress Database< screen, there is a listing for ``Number of moved references'' or ``Number of relocated references''. This number tells you how many of your references are (partially) duplicated in your database. You can use the >Compress Database< function to get rid of these extra references. The upper left quadrant of the screen displays some useful information. ``Reference file'' and ``Ref Key file'' refer to the names of your database files currently in use. The total number of references in your database, as well as the number of moved (relocated) references is also listed. If the number of moved references is zero, there is no point in compressing your database (but it won't hurt if you do). >> Insufficient Disk Space. JEPRS will tell you whether there is sufficient disk space to compress your database. That's because JEPRS needs to create a temporary file that is as big as your current database. JEPRS is smart enough to check for disk space before starting the compression. If there is not enough space on the current default drive, JEPRS will ask you to insert a new disk and/or specify a new drive name. If you have a two-floppy drive system, you can replace your JEPRS program disk with a new floppy; just don't replace your data disk, because obviously JEPRS will need access to it! For example, if you have the JEPRS.Exe on drive A: and your database (Ref1.JPR & Ref1.JPK) on drive B:, then when JEPRS tells you there's insufficient space, replace your A: disk with a fresh floppy, then enter [A] when JEPRS asks you for a new disk drive name. Warning!: If you are using floppy disks, do not replace your disk until JEPRS tells you to. Just enter the one letter drive name and press [Enter] after replacing your disk. If you do not have sufficient disk space anywhere, just press [Esc]. (Once the compression is over, replace your floppy in drive A: with your JEPRS.Exe disk.) JEPRS User's Guide, page 77 >>>>> Starting File Compression <<<<< Just press [G]o to start the database compression. As JEPRS is doing its stuff, you'll see ``Number of references processed'' being incremented for each reference that JEPRS is copying to the fresh database. You will also see a warning in the ``Messages'' window. You must obey that message. That is, do not attempt to turn off your computer while JEPRS is compressing your database. Just like everywhere else in JEPRS, if you need to abandon program execution, just press the [Esc] key. If you do press [Esc], then you will be asked to confirm your decision: press [Y]es to stop compression, or any other key to continue. When JEPRS is done with the first part of compression, it will display a message saying that it is copying the new database to your current database's directory. When everything has been completed successfully, JEPRS will display the following message: Compression successful. Press any key to continue. JEPRS User's Guide, page 78 C H A P T E R T W E L V E _________ Format Styles: A Tutorial #################################### One of JEPRS' most powerful features is its ability to let you define 30 Format styles and use these to format the output from your database. Recall that you can define different output styles for Journal, Book, and Abstract citation types: JEPRS automatically checks each reference to see whether it was defined by you to be a journal, book, or abstract, before choosing which format to output. ##################################### To modify a Format style, start up JEPRS and go to the >Main Menu<. Press [F2] to go to the >Global Defaults Menu<, then choose [D]efaults/[J]ournal definitions. This will bring up a selection menu for the Format styles; use the arrow keys and [PgUp] and [PgDn] to highlight the style you wish to edit, then press [Enter] to make your selection. You should now be at the >Global Defaults: Journal Definition< screen. Here is where you can enter the codes for formatting references. Review the chapter on Global Defaults to remind yourself what each of the codes means. A summary of each code's meaning is displayed at the bottom of the screen. Modifying Format Styles is very straightforward, once you get the hang of it. So let me first give you an example of a typical entry. Note: If you are reading this as the laser-printed documentation provided to registered users, then the underlining, italics, etc., will appear on paper just as they would with JEPRS output. However, if you are reading this from the JEPRS.Doc file supplied with the program, then all of the text in the examples will appear normal and it won't be of much help. As an alternative, you can try printing out some examples using the Format styles provided in the program, or you can register with the author and be provided with the original laser- printed documents. The best way to enter a new Format Style is to first find an example of a reference with the most information. For example, for a book format, find out what is required for formatting the book title, chapter title, publisher, editor, volume, pages, and year. Let's say you are entering a new formatting style that when printed out should JEPRS User's Guide, page 79 look like this: =================================================================== Sample Reference: 1. Miranda, LM, Lin, VK, and Wright, WE. (1989) Cloning and expression of Myogenin: A gene that can direct vertebrate myogenesis. In: Proceedings of the Southwestern Developmental Biology Symposium. (John Jones, Ed.) Alan R. Liss, Inc., 7:34. =================================================================== We'll do this step by step. 1. The first thing that JEPRS expects in the formatting instructions is the text that connects the last two authors; in this case it's ``and '' (don't forget the space), so that so far your format is: and 2. Once the `connector word' is specified, everything else is sequential; that is, you start at the beginning of the citation and specify, character by character, the text and fields/codes to be printed. In our example, the first item printed is a number; each reference will be numbered sequentially (regardless of their original numbers in the database). This requires the use of JEPRS' \# code, so now your definition looks like this: and \# 3. As I said, you build up your Format Style character by charcter and code by code. Therefore, since in our example the number is followed by a period and a space, that is what your format should look like: and \#. 4. After those spaces comes the authors. But here you have to make a choice among four possible codes: \F, \L, \1, and \A. Since in this case every author is listed last name first, the code is \L. Since the authors are not italicized or underlined or anything else, then just add this author code to the end of the current definition: and \#. \L 5. The authors are followed by a period, two spaces, and then the year in parentheses. Since the year code is \Y, your definition now looks like this: and \#. \L. (\Y) 6. Next comes two spaces and the title, which is in italics. The title code is \T and the italics code is \~. Since italics codes are toggles, you must put one code before the title, and one after: and \#. \L. (\Y) \~\T\~ JEPRS User's Guide, page 80 7. Following that comes the text ``In:'' and the journal/book name (and a period) which is underlined. The journal code is \J and the underline toggle code is \_, so now you have: and \#. \L. (\Y) \~\T\~ In: \_\J.\_ 8. Now comes the editor, in parentheses with ``, Ed.'' appended to it. This would look like: and \#. \L. (\Y) \~\T\~ In: \_\J.\_ (\E, Ed.) 9. After the editor comes the publisher (\Pu): and \#. \L. (\Y) \~\T\~ In: \_\J.\_ (\E, Ed.) \Pu 10. Soon to follow is a comma, a space, and the volume which is in bold face. The volume code is \V and the boldface toggle is \B, yielding: and \#. \L. (\Y) \~\T\~ In: \_\J.\_ (\E, Ed.) \Pu, \B\V\B 11. Immediately following the volume is a colon, the page number, and a period to end it. Since the page code is \Pa, you now have: and \#. \L. (\Y) \~\T\~ In: \_\J.\_ (\E, Ed.) \Pu, \B\V\B:\Pa. 12. Of course you always want to end each reference citation with a carriage return so the next one starts on the following line. To do this, add a new-line code \/ (that's a backslash followed by a forward slash, not a capital `V'). If you want a blank line between citations, add another new-line, so now it looks like this: and \#. \L. (\Y) \~\T\~ In: \_\J.\_ (\E, Ed.) \Pu, \B\V\B:\Pa.\/\/ So now you're done, right? Well, not quite. There is one other thing you might want to consider. Some books might not have chapter titles or an editor or a volume number. If JEPRS tried to format these books with the format style given above, it would look like Figure 2. =================================================================== Sample Reference #2: 2. Miranda, LM, and Wright, WE. (1999) In: Muscle differentiation and you! (,Ed.) Smith Books, Inc., :234. =================================================================== That looks quite unprofessional. But JEPRS can get around this with its ``optional inclusion'' codes. Anything within these codes is not printed if the field also within these codes is empty. Since the Title, Editor, and Volume fields above are empty, you could specify optional inclusion codes around their text to prevent it from printing out (of course, if those fields do have text in them, they will print out normally). Here is how I would modify our sample format using optional inclusion codes (\< and \>): JEPRS User's Guide, page 81 and \#. \L. (\Y)\< \~\T\~ In:\> \_\J.\_\< (\E, Ed.)\> \Pu, \<\B\V\B:\>\Pa. As I've modified it, those codes tell JEPRS not to print `` \~\T\~ In:'' if there is no Title; not to print `` (\E, Ed.)'' if there is no Editor; and not to print ``\B\V\B:'' if there is no volume. Therefore, our sample would be printed like Figure 3. =================================================================== Sample Reference #3: 2. Miranda, LM, and Wright, WE. (1999) Muscle differentiation and you! Smith Books, Inc., 234. =================================================================== Now that's much better. There are some things you should consider when using optional inclusion codes: Only one field can be included in the optional inclusion; in other words, ``\< In: \J \>'' is legal, but then ``\< \T In: \J \>'' is illegal because it includes both the Title and Journal fields. You won't need them around every field, since I doubt you'll ever come across a reference with no authors or no title. The total number of characters within an optional inclusion cannot exceed 40 characters. That's it for the Format Style codes. If you have a format that you can't seem to get to work, send me a copy and I'll see if I can help you. The one major journal that is not amenable to this kind of formatting is Science, which has both footnotes and multiple references in its bibliography. My recommendation for that case is to use JEPRS to send the formatted references to an Output Word Processor File, then retrieve this into your word processor and modify it there. =================================================================== ***** ADVANCED TOPIC: ***** Printer Codes in References Here's something to keep in mind regarding formatting codes: Because JEPRS evaluates these codes as it runs (rather like a language interpreter) there is nothing preventing you from entering these codes into your references. For example, if some of your references discuss something about the ``c-myc oncogene'' then instead of having just ``c-myc oncogene'' as a keyword, you can have ``c- \~myc\~ oncogene'' as a keyword. Then it will print out like this: JEPRS User's Guide, page 82 ``c-myc oncogene''. There is a definite advantage to this: in addition to esthetics, it can make your searches more specific. For example, if you search for ``myc'' you will find references both to ``c-myc'' as well as ``myco- plasma'', whereas if you search for ``\~myc\~'', you will only find what you want: ``c-\~myc\~''. =================================================================== See the Advanced Topic for information on using formatting codes in your references. ************** Comma-Delimited Output ********** JEPRS has the ability to format your output in `comma-delimited' form. This format can be used by many standard database systems (such as dBase, Excel, and Paradox) as a method of input. This feature thus allows you to output to a comma-delimited file so that you can import it into your favorite database. This is useful if a colleague of yours doesn't use JEPRS: it provides compatibility between the two systems. It also gives you an ``escape hatch'': if, in the future, you decide to use a reference management program other than JEPRS, then all your work isn't put to waste-you can just use comma-delimited output to convert your JEPRS database into the new database program's system. =================================================================== Sample Comma-Delimited File: "1","Wright WE","Myogenesis","Cell","44:1","1997" "2","Jones RR","Anatomy","Science","2345:33","1996" "3","Doe J","The Cell","Nature","9932:423","1997" =================================================================== Comma-delimited is generally defined as the following: Each text field is surround by double quote marks and separated by commas. Each record (that is, each reference) is on one separate but adjacent lines. A very simple example can be seen in Figure 4. JEPRS User's Guide, page 83 >>>>> Requirements for Comma-delimited Output <<<<< Making a comma-delimited output file requires two major steps: 1. Creating a printer definition in which all the text fields are empty, and all the numeric fields are zero (0). Note: By setting the ``Characters per line'' field in the Printer Definition to zero, you are really telling JEPRS to set it to infinity. 2. Creating a Format style in which you enter the codes for how you want your fields output. As just described, your Format style definition must have each field enclosed in double quotes and separated by commas. >>>>> A Sample Format Style <<<<< Here is a sample Format style for comma-delimited output (note that there is just a space as the `connector word' at the beginning of the definition): "\#","\A","\T","\J","\V","\Pa","\Y", "\Pu","\E","\K"\/ (Don't forget the \/ at the end of the definition, so that each record is placed on a different line.) This is just a sample of a Format style for comma-delimited output. You can arrange the fields in any order you like, and you can even exclude specific fields if you like. JEPRS provides you with 4 options for outputting the authors: \A, \F, \L, and \1. However, \F, \L, and \1 all add extraneous commas that are great for bibliographies, but wreak havoc on programs trying to import references in comma-delimited form. Therefore, I recommend you use only \A to specify the authors field in formatted output for comma-delimited. There is a [D]efault on the >Format Menu< that allows you to specify a replacement character for the double quote character if it appears in your references. This will avoid a problem such as a reference that contains the keyword Open reading frame/"ORF". If you tried outputting this as comma delimited, then JEPRS would produce output as follows: "Open reading frame/"ORF"" which, I can assure you, will mess up your database program's importing. That's because it will look at that line and think the keyword is "Open reading frame/" and it will probably just discard the "ORF"". Therefore, if you use the Replace " with... Default on the >Format Menu<, then you can substitute a single quote character for the double quote character. JEPRS User's Guide, page 84 C H A P T E R T H I R T E E N _________ Printer Definitions: A Tutorial #################################### This tutorial will give you instructions on how to create or modify a printer definition for your printer. This is a topic that many novices find intimidating, but I'll try to show you that it can be very easy to do. Just have a copy of your printer manual handy, and follow the step by step instructions here. If you plan on sending all your output to a WordPerfect 5.x or PC-Write 3.0 file, you do not need to define a printer definition. ##################################### Keep in mind that JEPRS allows you to define up to 5 printer definitions in your Config file. Why would anyone have five printers? There are in fact several scenarios where more than one printer definition would be useful: You have one type of printer at home, and another type of printer at work. For example, you might have a laser printer at work, and a dot matrix at home. Your printer supports several fonts. Many dot matrix printers can support 10 characters per inch (cpi), 12 cpi, and 16.66 cpi. Many laser printers support fonts of different sizes and typestyles. You can use a separate JEPRS printer definition for each font. ************** Sample Laser Printer Definition ********** Before continuing with a sample definition, first review the chapter in the User's Guide on Global Defaults, especially the section on Printer Definitions. That section of the chapter will explain to you what kinds of information JEPRS is expecting when you define a printer. If you read that section before continuing here, you will have a much better understanding of how to modify the printer definitions to suit your particular needs. Edit the printer definition at the screen entitled ``>JEPRS Global Defaults: Modify Printer Formats<''. You get there from the >Main Menu< by pressing [F2] to go to the >Global Defaults Menu<; then select [D]efaults/[P]rinter Definitions. Then select one of the JEPRS User's Guide, page 85 printer definitions to modify. The sample we will create is a printer definition for a Hewlett- Packard LaserJet IIP printer. Of course, for your own printer, you would substitute the names and commands present in your printer manual for the commands we're entering here. This tutorial will provide you with the basis for understanding which codes to enter, and how to enter them. When you first get to this menu, the cursor is placed after ``Printer Name:''. At this point, enter the name you want to appear on the JEPRS menu for selecting printers. In other words, enter a short descriptive name, such as your printer and font. In this example, I will be creating a definition for an HP LaserJet IIP with a 12 pitch (that is, 12 characters per inch) Courier font; therefore, enter: HP LaserJet IIP, 12 pitch Courier Now press [Tab] to get to the next fields. The information JEPRS wants here is the ``Printer Initialization Code.'' This is the sequence of codes JEPRS sends to your printer at the beginning of printer output from the >Format Menu<. What kinds of codes would you want here? This is where you would tell your printer the font you want to use, specifying the point size, typestyle, and/or pitch. For example, on a dot matrix printer, you might want to specify printing at 16 characters per inch (compressed type). In my example, I'm going to tell the LaserJet to print in a Courier typestyle, 10 point (size), 12 pitch (12 char/inch), 8 lines of text per vertical inch, and 88 lines per page. To do that, now get out the printer's reference manual. In the back it probably lists all the codes for everything you want it to do. For example, the LaserJet IIP manual says this is the code to enter for 12 pitch spacing: <Esc>(s12.00H where <Esc> refers to the <Esc> character (ASCII char #27). Likewise, the HP manual shows that the following codes are for 10 point size, Courier typeface, 8 lines per vertical inch spacing, and 88 lines per page, respectively: <Esc>(s10.0V <Esc>(s3T <Esc>&l8D <Esc>&l88P OK, it was easy enough finding the printer codes, but now how do you enter them into JEPRS? Don't worry-that's also very easy. >>>>> Entering Special Codes <<<<< For most of the codes, you just type in the code at your keyboard. But some special codes require an extra step. For example, if you tried entering the <Esc> code by pressing the [Esc] key at your JEPRS User's Guide, page 86 keyboard, JEPRS would interpret this as you asking to go to the menu at the top of screen (notice that at the bottom of JEPRS' screen it says ``[Esc]=Menu''). So how do you enter a special code like <Esc>? Easy: just press [^P] before pressing the [Esc] key. That is, hold down the key marked [Ctrl] and tap the [P] key once. You won't see anything on the screen, but then you can press the [Esc] key, and JEPRS will now interpret that as an <Esc> character, rather than the JEPRS command to return to the menu. (IBM-compatible computers show an <Esc> on the screen as an arrow pointing left.) =================================================================== ***** ADVANCED TOPIC: ***** Entering ASCII Codes There is another way to enter special codes, if you know their ASCII value. ASCII (pronounced ``As-key'') is the American Standard Code for Information Interchange. It is simply a standard code so that different computers can talk to each other. In this code, every letter and digit has a code. For example the code for the letter `A' is 65, the code for `B' is 66, and so on. In a similar manner, the <Esc> character has a code of 27. Most printer manuals have an ASCII table at the back. You can use this information to enter the <Esc> character without pressing the [Esc] key. Just as before, press [^P] before entering the code for <Esc>, but this time instead of pressing the [Esc] key, hold down the [Alt] key and enter the ASCII code on the number pad on the right side of your keyboard. That is, to enter the code for <Esc> (which is 27), hold down the [Alt] key and press [2] and then [7], and then let go of the [Alt] key. =================================================================== >>>>> Back to the Example . . . <<<<< Now that you know how to enter special codes, entering the printer codes for the LaserJet IIP is easy. Since I want to have 12 pitch, 10 point, Courier type at 8 lines per inch, 88 lines per page, I need to enter the code <Esc>(s12.00H<Esc>(s10.0V<Esc>(s3T<Esc>&l8D<Esc>&l88P into JEPRS' ``Printer Initialization Code''. So press [^P] and then [Esc] to enter the <Esc> character, then type in ``(s12.00H'', then [^P] and [Esc] and type ``(s10.0V'', then [^P] and [Esc] and type ``(s3T'', then [^P] and [Esc] and type ``&l8D'', then [^P] and [Esc] and type ``&l88P'', and press [Enter]. The next field JEPRS asks for is the ``Printer Reset Code''. This code is sent by JEPRS to your printer whenever you have finished printing from the >Format Menu<. What kind of codes would you want to send? Probably the only thing you want to send is a ``reset'' code JEPRS User's Guide, page 87 which will return your printer to its default settings. For the HP LaserJet series, this code is <Esc>E so I would enter that as [^P] then [Esc] and then type ``E'' and press [Enter]. The next field is ``Title''. This is where you enter text that JEPRS will print on the top of the first page of output from the >Format Menu<. You might want to enter something like ``Bibliography'' here. JEPRS does not automatically center this text. So you might want to add a few <Tab>s to get the text centered. But-Ooops!-you can't enter a <Tab> directly, because JEPRS considers it a special code, just like the <Esc> character. To enter a <Tab>, you must first press [^P] to enter a special character, and then press the [Tab] key. Repeat this for as many <Tab>s as necessary. On an IBM or compatible PC, the <Tab> character looks like a small circle. The next field is the ``Header''. Here is where you enter text that you want printed on the top of each page that JEPRS sends to the printer at the >Format Menu<. You might want to enter something like ``JEPRS Output from Ref1.JPR on 15 Dec 1990, page \P''. Remember, if you include the `\P' page code here, then JEPRS will automatically insert page numbers in the Header. ``Left margin'' is the next field. You can enter how many spaces you want JEPRS to skip before printing text on a line. In my example, I'm using a 12-pitch font so to get a 1-inch left margin, I will enter ``12'' in this field. Next comes ``Characters per line''. Again, using the example of a 12-pitch font, I want 78 characters per line (that's because the paper width is 8.5 inches, there are 12 characters per inch, and I want 1- inch left and right margins, so that's: 8.5 - 1 - 1 = 6.5 x 12 cpi = 78). So I will enter ``78'' here. ``Pause after each page'' is usually [N]o. The only time you want to set this to [Y]es is if you have to feed each sheet of paper to the printer by hand. If [Y]es, then after JEPRS prints each page, it pauses and asks you to press any key to continue. I will enter [N]o here. The next thing JEPRS wants you to enter is ``Top Margin''. This tells JEPRS how many lines to skip at the top of each page. I will enter ``5'' here to give a 1-inch top margin (that's because JEPRS adds 3 lines to the top margin for the Header and the Title, so the total is really 8 lines; and remember that I have previously set the vertical line spacing to 8 lines/inch, so this will give me a 1-inch top margin). ``Lines per page'' tells JEPRS how many lines to send to the printer before sending a <Form-Feed> character (the <Form-Feed> character tells the printer to eject the current page). I'm using 11- JEPRS User's Guide, page 88 inch long paper, and (remember) using 8 lines of characters per vertical inch, so that gives me a total of 88 lines. But I'm also leaving a 1-inch top margin, and I want to leave a 1-inch bottom margin, so the number I'll enter is ``72''. (This Lines Per Page is not the same as the printer's own Lines Per Page; that is, in the initialization codes I entered 88 Lines Per Page for the printer [for letter size paper], but I entered only 72 Lines per page here, so that JEPRS will actually print 72 lines per page.) The last of the short-answer questions is ``Form feed last page''. When JEPRS is done printing, and fewer than the ``Lines per page'' number of lines has been sent to the printer, JEPRS doesn't automatically send a <Form-Feed> to the printer. This is OK with dot- matrix printers, since you can just pull out the last page yourself. But if you have a laser printer, the last page will be stored in the printer's memory, but won't actually be printed until it gets a <Form- Feed> character (that's why if you use the [PrtScr] key with a laser printer, it doesn't seem to print right away). Therefore, I recommend you set this to [Y]es if you have a laser printer. In that case I'll set the example printer definition to [Y]es since it's a LaserJet IIP. The next group of fields is the character attribute fields. These fields allow you to enter codes for boldfacing, underlining, italicizing, superscripting, and subscripting portions of your references. Just enter the codes your printer requires for each of these attributes. For our example, the LaserJet IIP printer, the codes are as follows: [Attribute] [On Code] [Off Code] Underline <Esc>&d3D <Esc>&d@ Boldface <Esc>(s3B <Esc>(s0B Italic <Esc>(s1S <Esc>(s0S Two things to note: First, the <Esc> character above is entered by pressing [^P] before pressing [Esc]. And, second, the LaserJets have no built-in ability to handle super- and sub-scripts, so I have left those fields blank on purpose. The last field entry is for ``Comments''. JEPRS ignores what you enter here; it is for your use only. You would probably just enter a short description of all your commands. In the example, I will enter: Courier: 12 pitch, 10 point font at 8 lines per vertical inch, 88 lines per page. JEPRS User's Guide, page 89 ************** Dot Matrix Example ********** Now let me give you some examples from a dot matrix printer manual. One very popular series of printers is Panasonic's KXP . . . series. In the back of the KXP-1080 printer manual, I looked up the code for `Font Selection: Selects NLQ or Draft Font'. The manual states that NLQ (Near Letter Quality) text is selected by using the command: ESC+x+n where n=1,49,129, or 177 The way that I have been representing codes, that would look like this in JEPRS: <Esc>x[1] where <Esc> is entered by first pressing [^P] and then pressing [Esc], `x' is entered just by pressing the [x] key on your keyboard, and [1] is entered by first pressing [^P] and then holding down [Alt], pressing [1] on the numeric keypad (not the [1] on the top row of the keyboard), and then letting go of the [Alt] key. (The [1] is the ASCII code 1, which appears as a `smiley face' on IBM compatibles.) Likewise, the Panasonic manual states that to turn on Draft Printing Mode, use the command: ESC+x+m where m=0,48,128, or 176 In my own nomenclature, that code would look like this in JEPRS: <Esc>x[48] where <Esc> is entered as a special code, and [48] is entered as an ASCII code. Warning! Panasonic gives you the option of entering the ASCII codes [0], [48], [128], or [176] in the Draft Printing Mode example above; however, I entered [48] instead of [0]. That's because JEPRS can't send the ASCII code for [0] to your printer. So if your printer manual gives you an option of sending something instead of ASCII [0], use any of the other choices, but don't use [0]. JEPRS User's Guide, page 90 A P P E N D I X O N E _________ JEPRS' Files #################################### All of the major file types that JEPRS uses are listed on the top left portion of the >Main Menu< screen. If you've read through the tutorial chapter in the User's Guide, then you should be at least vaguely familiar with the names of each of these files. You can change the names of any of these files at the >Global Defaults Menu<. Here is a complete description of their functions and uses. ##################################### >>>>> Reference File <<<<< The reference file is the main database file that JEPRS uses to store the references you enter using the program. This file (which has a default name of ``Ref1.JPR'') is maintained completely by JEPRS. Never modify the Reference file with any program other than JEPRS! There is currently no other program in the world that can properly read or write a JEPRS database file; it is a proprietary format. For anyone who is interested, the file specification is available from the author by sending a self-addressed stamped envelope to the address on the order form. To provide compatibility with other programs, JEPRS offers MedLine and comma-delimited export capabilities. >>>>> Ref Key File <<<<< This is a matching file for the main database (Reference) file. JEPRS uses it to keep track of where the references are in the main file. You cannot access the main Reference file without this Key file. The Key file's default name is ``Ref1.JPK''. Do not try to modify this file with any program other than JEPRS-otherwise you may lose all your data. >>>>> Help File <<<<< This file contains all the information displayed in the Help screen whenever you press [F1] for help in JEPRS. The name of this file is ``JEPRS.Hlp''. Each Help File is specific for each version of JEPRS. JEPRS User's Guide, page 91 If you try to use the Help File from JEPRS Version 2.0 with Version 2.5 of JEPRS.Exe, you will often get incorrect information. >>>>> Text File <<<<< This is a file that can be created by JEPRS. If you press the [F10] key when you are displaying the results of a search, or when you are on the >List Reference< screen, or if you specify [O]utput=[T]ext File on the >Search Menu<, then the text of the reference(s) will be sent to this Text file (default name is ``JEPRS.Txt''). Text will also be sent to this file if you specify [O]utput=[T]ext File on the >Format Menu<. Once you create this file with JEPRS, you are free to edit it in a word processor, or send it to your printer for printing. JEPRS will never have to get information from this file; it only sends text to it, so you are free to change it any way you wish. Printer codes for underlining, boldface, etc. are sent to this file only under the following conditions: 1) When you are at the >Format Menu< and 2) When [D]efaults/[T]ext file formatting=[Y]es (see the >Global Defaults Menu< to set this value). >>>>> Number File <<<<< This file (default name is ``JEPRS.Num'') can be created by JEPRS. If you press the [F8] key when you are displaying the results of a search or when you are on the >List Reference< screen, or if you specify [O]utput=[N]umber File on the >Search Menu<, the numbers of the reference(s) will be sent to this file. The Number File is a normal DOS text file, just like the Text File above, but instead of containing the text of the entire reference, it only contains the number of the reference, with each number being on a different line. You can create a number file yourself with a text editor (or word processor in DOS Text file or Non-document mode). There are a few simple requirements for a Number File that you must adhere to: It must be a normal ASCII text file. You can verify this by using the Type command at the DOS prompt: C:\JEPRS> Type JEPRS.Num If you see any foreign or graphics characters, or if the numbers aren't lined up on the left side, then it's probably not an ASCII file. Each number must be on its own line. If more than one number is JEPRS User's Guide, page 92 present on a line, only the first one is used. If characters other than a space or Tab appear before a number, that line is treated as a comment. Comments can appear by themselves on a line, or after a number. Empty lines are treated as comments. Invalid numbers (negative numbers or numbers larger than the database) are ignored. An example of a legal Number File would be: =================================================================== 34 This line is a comment 55 3;This is a comment (the "3" is valid) 99 This is a comment. This is ignored: 12 =================================================================== Keep in mind that Number files can be quite useful: They can be used as input on both the >Format Menu< and the >Export Menu<. A chapter in the Appendix explains some of the advantages of using a Number file. >>>>> Config File <<<<< The Config file (short for ``configuration file'') contains the Format Styles, Global (and some local) Defaults, default directory and file names, and Printer Definitions for JEPRS. Its default name is ``JEPRS.Cfg''. >> Format Styles. You can define up to 30 of your own Format Styles (also called journal definitions) and keep them in the Config file. To edit the Format Styles, go to the >Global Defaults Menu<, choose [D]efaults, and then [J]ournal definitions. For more information on editing the Format Styles, see the chapters in the User's Guide called Global Defaults and Format Styles: A Tutorial. >> Printer Definitions. Up to 5 Printer Definitions can also be stored in the Config file. Follow the instructions above for editing the Format Styles, except choose [P]rinter definitions. Multiple printer definitions are useful if, for example, you have a laser printer at work, and a dot matrix at home. Also, you can define each printer definition to use different fonts (see your printer JEPRS User's Guide, page 93 documentation for the codes). See the chapters on Global Defaults as well as Printer Definitions: A Tutorial for information on Printer definitions. >> File/Directory Defaults. The file names on the >Main Menu< and the >Global Defaults Menu< can be stored in your Config file. For information on saving your filenames, see the chapter on Global Defaults. >> Global & Local Defaults. To customize JEPRS, you can save a number of defaults in the Config file: [ [Menu] Global/Local Default Name] Error Beep Global Defaults Text File Formatting Global Defaults Printer # Global Defaults Format Style # Global Defaults Color Mode Global Defaults Colors for Formatting Global Defaults Blinking on Formatting Global Defaults WordProcessor Type Global Defaults Sort References Search Menu Case Sensitivity Search Menu Format Style Format Menu Replace " With . . . Format Menu Remove Subheadings Import Menu Edit During Import Import Menu Import Format Type Import Menu Remove Printer Codes Export Menu Uppercase Keywords Export Menu Whenever you modify any of the above defaults, and then go to the >Global Defaults Menu< and choose [D]efaults/[S]ave defaults+files, all of the defaults listed above are saved into your Config file. >>>>> Word Processor Input File <<<<< This is a new file type that can be used with version 2.5 of JEPRS. It can be used as input on the >Format Menu<. You create this file with either WordPerfect 5.x or PC-Write 3.0, and it includes codes that JEPRS can read in order to automatically generate a bibliography. See the Advanced Topic in the chapter Formatting References for more JEPRS User's Guide, page 94 information on using the JEPRS codes. See the chapter Global Defaults for specifying which word processor you are using. >>>>> Output Word Processor File <<<<< This is a new file type that can be created with version 2.5 of JEPRS. On the >Format Menu<, you can specify [O]utput=[W]ordProcessor File, in which case JEPRS will send your output to this file, which will be compatible with either WordPerfect 5.x or PC-Write 3.0; you specify your word processor type on the >Global Defaults Menu<. JEPRS User's Guide, page 95 A P P E N D I X T W O _________ Upgrading Version 1.x to 2.x #################################### Version 1.00, 1.10, and 1.11 of JEPRS used files called Format files to store configuration and format style information. Starting with version 2.0, these files are called Config files and are incompatible with the version 1 files. However, a file called JConvert.Exe is included for registered users that will automatically convert your Format files to a Config file. ##################################### ************** Converting Format Files to a Config File ********** Before starting the conversion of Format files to a Config file, you should do some preparation. That's because JConvert.Exe can use up to nine of your Format files to create one all-encompassing Config file. The number of Format files used, as well as their conversion results, are listed here: [ # of Format Files] [Destination in Config File] 1 Directory & Filename Defaults 5 Printer Definitions 3 Format Styles/Journal Definitions Thus, JConvert can use up to 9 of your Format files. Of course, if you have fewer than nine Format files, that's OK too, since you can just use duplicates of your pre-existing Format files. The rest of this chapter assumes you will be creating only one Config file; if you wish to create several, you can do that by either repeating the steps in this chapter or by using DOS's Copy command to create duplicate Config files, and then use JEPRS to directly edit those Config files. Get a pen and a piece of paper. Look through your Format file(s) to JEPRS User's Guide, page 96 see which one contains the directory and filename information you want in your Config file. Write down the name and current directory of this file. Now write down the names of up to 5 Format files containing your various printer definitions. Since JEPRS version 2.0 and above can support up to 5 printer definitions in one Config file, you no longer will need several Format files for this purpose. (If you have fewer than 5 files, don't worry, we'll deal with this later.) Now write down the names of up to 3 Format files that contain your Format style/Journal definitions. JEPRS version 2.0 and above supports up to 30 Format styles per Config file. (Again, if you have fewer than 3 files, we'll deal with this later.) Now you're all set to start converting. ************** Running JConvert ********** You should have a file called JConvert.Exe in your JEPRS directory. If you don't, go back to your distribution disk(s) and look for it there; then copy it to your JEPRS directory or working disk. This file is the program that will actually convert your Format files to a Config file. JConvert.Exe is only provided to registered users. Enter the program name at the DOS command line (you don't need to add the `.Exe'): C:\JEPRS> JConvert A full-screen message will appear, describing the function of the program, as well as a warning to be sure you know the names of your Format files before continuing any further with the program. You can press [Esc] now to stop the program. However, if you don't want to stop, press any other key to continue. Near the top of the screen is a reminder that pressing [Esc] at any time will abandon creation of the Config file; if you press [Esc], the Config file will be deleted but the Format files will remain intact (in fact, JConvert will never modify or delete your Format files). Realize that, unlike JEPRS, JConvert will not ask for confirmation before terminating the program if you press [Esc]. The first prompt asks you for the name of the Config file. The default name is ``JEPRS.Cfg'', but you can specify any file name (and a DOS Path, if desired). You can also use JEPRS' standard editing keys: [Ins], [Del], [Home], [End], [left arrow], and [right arrow]. Just remember that if you want to edit the filename rather than replace it, press one of the editing keys before pressing any letters or numbers, otherwise JConvert will replace the old filename. If the filename you specified already exists, JConvert will warn you with the message: <Filename> JEPRS User's Guide, page 97 ...already exists. Overwrite it? (y/n) Press [Y] to delete the old Config file and replace it with the one you are about to create. If you press [N], then JConvert will leave the old file alone, and will terminate the program. JConvert will then ask you for the name of the Format file containing the DIRECTORY/FILENAME information. The default name is ``Format.JPR'', but you can enter any filename. Type in the name of the file you wrote down earlier, and press [Enter]. JConvert then displays a message that it is reading in the Format file and then writing to the Config file. The next prompt is for the FIRST Format file containing PRINTER information. The default name is the filename you entered for directory/filename information. Again, you can use that name or enter any other name. Enter the name of one of the files you wrote down before. The program will then display a message stating that it's reading in the FIRST printer format, and then writing it to the Config file. In a like manner, JConvert then asks you for the SECOND, THIRD, FOURTH, and FIFTH Format files containing PRINTER information. Just enter the names of the files you wrote down in the previous section of this chapter. If you had fewer than 5 Format files with printer information, just press [Enter] every time you are prompted for a new filename. In this case, you'll just have duplicate printer definitions in your Config file. Of course, you will be able to modify these later on from within JEPRS. When you are finished converting your files, and you finally start JEPRS with your new Config file, the printer selection menu at the Global Defaults Menu will show the title of each printer definition as the Format file from which it originated. The last section of the program starts off by asking you for the FIRST Format file containing FORMATTING CODES. Enter one of the three names you wrote down on your list. Then JConvert displays a number corresponding to each of the Format styles as it reads them in and writes them to the Config file. It then proceeds to ask you for the SECOND and THIRD Format files containing FORMATTING CODES. Enter the two remaining Format filenames on your list. If you don't have 3 Format files, just press [Enter] when JConvert asks you for the filenames, and it will automatically use the first filename you entered for formatting codes (and you'll just end up with duplicate or triplicate codes which you can then modify at the >Global Defaults Menu< in JEPRS). When JConvert has successfully completed the conversion, the following message will appear: JConvert finished. and your computer will beep. You will then be returned to DOS. JEPRS User's Guide, page 98 A P P E N D I X T H R E E _________ Practical Uses for Number Files #################################### One of JEPRS' most underutilized features is the Number file. This is a situation I hope to change with the addition of this chapter to the Appendix. ##################################### One of the features I required JEPRS to have was a way to keep track of a specific set of references. This set would be one that could be created by you, the user; for example during a search. Many other programs will allow you to send the results of your search to a file or the printer, but once you exit the program, that grouping of references is lost until you perform another search. But what if you're writing a paper and you need a group of references for the bibliography, which are not obtainable by a simple search? Most programs don't deal with this very well. You can enter reference numbers at the keyboard, but what if you made a mistake in a long list? The keyboard doesn't really sound like such a good idea. So I came up with the idea of a Number file; this has the advantage of both specificity (you can set up a group of references that wouldn't necessarily be found together in a search) and modifiability (you can use JEPRS to add references to a previous list, or use any standard text editor to remove or change references in a previous list). >>>>> An Example <<<<< Recall that JEPRS can use Number files as input not only on the >Format Menu<, but also on the >Export Menu<. Let's say you've just finished a discussion with a colleague. You tell her that you have five great papers that discuss a new Syrinx 2A vector you can use for cloning genes, and those references are in JEPRS. Your colleague may have JEPRS or some other reference management program that can read in MedLine formatted files. (Or your colleague may even keep her references in a generic database system that can read in comma- delimited files.) Needless to say, your colleague does not relish the idea of getting a printout from you and then typing your references into her database. With the number file, there's an easier way. JEPRS User's Guide, page 99 All you have to do is start up JEPRS, go to the >Search Menu< and then: press [T]erms and specify `[K]' (for [K]eywords) and then enter ``Syrinx 2A''; press [G]o to start your search. Then press [F5] at the >Search Results< screen to Mark all the references, then press [F8] to send all the Marked references to the Number file. Then press [Esc] twice to return to the >Main Menu<, select [U]tilities, then select [E]xport. At the >Export Menu<, choose [I]nput/[N]umber file, and choose [O]utput/[T]ext file. Then press [G]o to start exporting. JEPRS will read in the numbers of the five papers on the Syrinx 2A vector from the Number file, look up those numbers in the database, format them according to the MedLine format, and send them out to the Export File. Voil ! Then you just copy the Export File to a floppy disk, hand it to your colleague, and she can read it into her program (because any biomedical reference database program worth its salt can read in a MedLine formatted file). This procedure may sound complex at first, but once you try it, you'll see how easy it really is. >>>>> Why Numbered References? <<<<< Let me explain why I instituted numbered references, and how I find them useful in everyday experiences. I initially tried keeping my article reprints in folders, based on subject keywords. However, I quickly ran into the problem of one paper with two primary keywords (say, Myogenesis and Transfection) and not being able to decide which folder to put it in. So the very first requirement for JEPRS was that it have a numbering system-one that the user couldn't change, accidentally or otherwise. That way, I now keep my photocopies in numerical order; if I need to find papers based on subject, I can now just use JEPRS' >Search Menu<: this gives me the reference number, which I then use to look in my filing cabinet of numerically arranged references. If a reference becomes outdated, I just recycle the paper it's printed on, and mark one of its keywords as Deleted; before adding new references, I do a search for Deleted in keywords to see if I can Edit an old reference rather than Add a new one. JEPRS User's Guide, page 100 JEPRS Version 2.5 Order Form Printed Manual Please send this form with payment to*: Louis M. Miranda 400 Selby Avenue #301 St. Paul, MN 55102 Name:______________________________________________________ CompuServe ID number (optional):___________________________ Address:___________________________________________________ ___________________________________________________ ___________________________________________________ Please specify the disk size you want JEPRS on: ()--3.5-inch disk ()--5.25-inch disks REGISTRATION. Registration is $49.95 per copy ordered (see the file called Site_Lic.Doc for information on bulk pricing and site licenses). Please register me for the latest version of JEPRS. Also send me printed documentation and update notices. I understand that six months of user support is included in the registration price..............$__________ Postage and Handling: $4.00 ($10 outside USA/Canada)$__________ Total enclosed......................................$__________ Please send check or money order in US $ addressed to "Louis M. Miranda". Purchase orders are also accepted. *--If you cannot reach the author at that address, please try to contact me through CompuServe (73567,471) or the ASP: Association of Shareware Professionals 545 Grover Road Muskegon, MI 49442-9427 JEPRS User's Guide, page 101 Index 4DOS Program 35 Help File 90 Add new references, samples Number File 91 54 Ref Key File 90 Adding references 22 Reference File 90 ASCII Codes, entering 86 Text File 91 ASP, Association of Shareware Files on disk 9 Professionals 7 Format screen colors 25 Author+Year 41 Format Style Codes Automatic Bibliography aka Printer Codes 42 Generation 26 Format Styles Beep, error/warning 32 Default 58 Bibliography, Automatic Editing 39 Generation 26 Selecting 57 BRS/Colleague files Formatting codes 42 Importing 72 Go To DOS 24, 34 CHR$ 36 Help key 19 Citation type 52 Importing files 71 CL-MedLine Importing references Importing 71 Editing 72 Command line options 11 Indent Length 40 COMMAND.COM (DOS) 35 Installation 10 Compressing the Database 76 Journal definitions COMSPEC (DOS) 35 Editing 39 Config file name 11 Journal Name 40 CONFIG.SYS (DOS) 35 Journal Number 40 Connector word 79, 83 Journal/Abstract/Book Context-sensitive help 19 definitions 41 Current Contents on Diskette Listing References 21 Importing 71 Main Menu 17 Current Contents on Diskette Marking references 70 (CCOD) 28 MedLine files Customer Support 8 Exporting 74 Database Importing 71 Creating 13 Memory Defaults Available 17 Global 31 Total RAM 17 saving 33 Menu Delete reference 46 Line 14 Directory, default 32 Title 14 DR-DOS Program 35 Messages window 14 Entering ASCII Codes 86 Modify Search Menu 69 Entering Special Codes 85 New Features 4 Exiting the program 16 Number File 29, 98 Exporting references 74 Optional inclusion 42 File names, changing 32 Ordering information 34 Filenames 31 Page number (\P) 37 Files 31 Page numbers 87 Config File 92 PaperChase 28, 72 Help 20 Importing 71 JEPRS User's Guide, page 102 PC-Write 24, 34 67 Printer Starting JEPRS 11 form-feed 34 System information 17 initialization code 37 System Requirements 5 name 37 Text file formatting 32 number 37 Time and date 18 reset code 37 TSR (Terminate & Stay Resident) selecting 33 program 35 Printer codes 36, 81 Unregistered Version 6, 18 Printer definition 84 Use Printer # 24 Printer definitions Vendor.Doc file 7 editing 35 Version number, DOS 18 Saving 38 Version number, JEPRS 18 Printing Welcome Screen 11 attributes (underlining, Why Numbered References? 99 etc.) 38 Word Processor Type 24, 34 characters per line 37 WordPerfect 24, 34 form feed last page 38 WordPerfect Text Boxes 26 header 37 left margin 37 lines per page 38 pause after each page 38 title 37 top margin 38 Printing attributes codes 43 Prompts vs. Menus 14 Reference type 52 References Number of in reference file 18 Number of relocated 18 Registering 6 Replacing citations Author+Year 26 Sequential Numbers 26 Save Defaults+Files 24 Screen color options 12 Screen colors 33 Screen design 14 Search Results Screen 68 Search terms 63 Searchable fields 63 Searching Case sensitivity 67 Sorting 68 Searching references 23 Sequential Numbers 41 Shareware 6 Sort references during format 40 Sorting using Matches to free memory