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JEPRS (TM) Tutorial JEPRS version 1.10 March, 1989 by Louis M. Miranda 6033 East Northwest Highway, #1106 Dallas, TX 75231-7463 USA JEPRS is a trademark of Louis M. Miranda; Copyright 1985-1989 Louis M. Miranda. Disclaimer of Warranty This software and documentation are sold "as is" and without warranties as to performance of merchantability or any other warranties expressed or implied. Because of the various hardware and software environments into which this program may be put, no warranty of fitness for a particular purpose is offered. Good data processing procedure dictates that any program be thoroughly tested with non-critical data before relying on it. The user must assume the entire risk of using this program. Any liability of the seller will be limited exclusively to product replacement or refund of purchase price. I. Introduction. JEPRS (pronounced "Jeepers!") is a program that maintains a database of references to articles published in scientific journals and books. It allows you to add, update, list, search, and format references in the format required for practically any journal. It is made to run under PC/MS-DOS (version 2.0 or higher) on IBM PCs and 100% compatibles. JEPRS itself requires only 128k of RAM, so any computer with 256k or more can run the program. A hard disk is not required, but searches are considerably faster on a hard disk compared to floppies. Since JEPRS is distributed as "shareware", you are free to give copies to others, but if they decide to use it, they are obligated to pay a fee (see Options choice on the Main Menu). You may be wondering to yourself, "Why should I bother to use JEPRS?". There are two very good answers to that question: 1. JEPRS is inexpensive! 2. It's very easy to use. Sure, every program in the world is going to claim that it's very easy to use. But have you every tried a command-line driven program that requires you to perform a search with some awkward, hard-to-remember command like "S -Au -or -Ti Wright/Myogenin -t+" (you get the idea)? JEPRS doesn't do that to you. It is a menu-driven program that lists every single option on the screenyou don't have to memorize anything. (Defining new formats can get a little complex, but once you define them the first time, you never have to bother with them again.) JEPRS prevents you from entering wrong answers whenever possible. It's very difficult to make a mistakeyou really have to try. Other questions you may be asking yourself are: "What if it becomes outdated? Will I then have 1000 references that I will have to type all over again if I switch to another program? Then it really hasn't saved me any time!" These are very reasonable questions. Much as I hate to admit it, yes, sometime in the future you may want to switch to a program other than JEPRS. It would be a complete waste of time to have to manually re- enter every reference in the database into that new program. One feature JEPRS has is the ability to output references formatted according to the National Library of Medicine's MedLine format. This is a common format used by most biomedical reference management systems. For example, PaperChase (an on-line program that allows you to search the MedLine database) lets you down-load references in the MedLine format. JEPRS can both read and write files with this format; any program worth its salt should be able to do this also. Therefore, switching between programs should involve no more work than taking the time to tell JEPRS to format all the references in the database according to the MedLine standard. Then just read this text file into the other program. It's that simple. Therefore, you will get the benefit of JEPRS now, and be able to switch to other programs in the future, painlessly. New Features of version 1.10 Many enhancements to JEPRS 1.00 have occurred with this new version. First and foremost, the Search option has been extensively rewritten with a very modern user interface (note that the next version of JEPRS will sport a rewritten Format option user interface). In addition to being easier to use and more forgiving of mistakes, the Search option has a number of new features. This includes the ability to: start and stop the search at specific reference numbers; limit your search to only a specific number of matches; more easily define the output of your search (and mix and match various outputs); sort your search by first author; and specify up to 10 search terms (instead of just 2), allowing the use of parentheses to determine how the search is interpreted. Also new for search terms is a special feature for searching in the YEAR field: You can now enter a range of years (e.g., 1984-1988) instead of just one year. In addition, the Modify Search option now allows you to modify your search up to 3 times (instead of just once) and gives you on-screen help for your first modification. Of course, a number of minor bugs in the program have also been corrected. Files on Disk You should find a total of 17 files on this disk. Below is a list of those files and a short description of their use: ReadMe.JPR: This file contains the most basic information for starting JEPRS. JEPRS.Exe: This is the JEPRS program itself; entering "JEPRS" at the DOS prompt ("C:>") starts the program. JPRTutor.JPR: The file you are reading now: A tutorial text file that you should read before doing any extensive work with JEPRS. JPRGuide.JPR: The User's Guide to JEPRS. This contains the most extensive information on JEPRS. It is not meant to be read sequentially; you should refer to it whenever you have specific questions about a specific aspect of the program. Order.JPR: Printing this file on your printer produces a form you can use to register your copy of JEPRS. Help.JPR: Contains the text for JEPRS's context-sensitive help screens. If JEPRS can't find this file when it is running, you will not be able to get 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! Format.JPR: A sample format file that contains the formatting instructions, printer control codes (in this case for an IBM Graphics printer and most Epson-compatible printers), and default directory and file name information. FormStar.JPR: Similar to Format.JPR, except this file has control codes for a Star SG-10 printer. FormPana.JPR: Similar to Format.JPR, except this file has control codes for a Panasonic KXP-1080i printer. FormLsr1.JPR: Similar to Format.JPR, except this file has control codes for a Hewlett-Packard LaserJet printer with a 10-point Times Roman regular, bold, and italic font loaded (note that JEPRS doesn't supply you with the actual fonts, but rather it assumes you have them and have already downloaded them to the printer or have them in a cartridge already plugged in). FormLsr2.JPR: Similar to Format.JPR, except this file has control codes for a Hewlett-Packard LaserJet printer using the condensed (16.5 characters per inch) font. FormLsr3.JPR: Similar to Format.JPR, except this file has control codes for a Hewlett-Packard LaserJet printer using the standard 10 characters per inch Courier font. Text.JPR: Sample text file. Since you cannot directly access the database using the DOS Type command, JEPRS allows you to enter selected references into an ASCII/DOS text file. You can use DOS's Type and Print commands on these text files. Number.JPR: This is a sample "number" file. It is really a normal ASCII/DOS text file, but consists of nothing but numbers of references. JEPRS can create this file (for example, in a Search) and then use its contents during formatting (on the Format Screen). Procomm.Log: A sample MedLine-formatted file. This can be used in the Options:MedLine command to add a MedLine-formatted file to the database. (This is probably only of interest to biomedical researchers who use MedLine-formatted files.) Installation Before installing JEPRS, make a copy of all the files on this disk! Never use your original disk to run the program. This is especially true with a Shareware program like JEPRS, since in order for the documentation to be correct (and prevent major hassles for other users) you must distribute the software exactly as you received it. One- and Two-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 your version 1.10 disk onto your present working disk: JEPRS.Exe Help.JPR ReadMe.JPR JPRTutor.JPR JPRGuide.JPR Note that 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 Help.JPR to your work disk. (If you use the version 1.10 JEPRS.Exe file with the version 1.00 Help.JPR file, the Help screens will give you wrong information!) The last 3 files listed above are the documentation files (you're reading JPRTutor.JPR right now) and once you print them out, there's no need to keep them on your working disk. Of course, no files should ever be deleted from your original 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): cd \ md JEPRS cd \JEPRS copy a:*.* (this assumes that your disk is in floppy drive A:. Substitute the "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. II. Starting JEPRS. In order to get the most out of this JEPRS tutorial (and to avoid getting any error messages), the following files must be in the current directory: JEPRS.Exe Ref1.JPR Ref1.JPK Format.JPR Help.JPR You will see later that you can easily specify alternative names and locations for these files. Now enter the command "JEPRS" at the DOS prompt. If all goes well, the screen will momentarily clear, some introductory messages will appear, and finally the Welcome Screen will appear (which includes the copyright notice, and to whom the program was provided). Type any key to continue to the Main Menu. III. The Main Menu. You are now presented with the Main Menu, from which you can enter any of JEPRS's commands. For now, ignore the information on the right side of the screen ("Current System Information"). The box on the left side of the screen contains the Main Menu. Before continuing, let's use the Help facility as a demonstration of the ways available to invoke a command. Every command listed (Add, Update, List, Format, Search, Options, Help, and Exit) can be invoked by at least two methods: (1) Use the up and down arrow keys to highlight the command you want to use, then press Enter to start that command; (2) Press the key corresponding to the first letter of the command's name (for example, press H for Help, or O for Options). Two of the commands have one additional way to invoke them; Help and Exit can be performed by pressing the function key listed to the right of the command name (that is, press F1 for Help or Esc for Exit). Now press F1 so you can see the built-in Help facility in JEPRS. IV. Help. After pressing F1 you should see the Help Screen on the right portion of the display. The Help facility provides context-sensitive help no matter where you are in the program. If more than one screen of information is available, the bottom of the screen will display "Continue or Exit?"; press E to exit and return to what you were doing before, or press any other key to continue with Help. Now press E to return to the Main Menu. Help is generally available throughout the JEPRS program; you will always know if it is available, because "F1=Help" will be displayed on the bottom of the screen. General help is obtained, as you have just done, 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. V. List References. The next thing you probably want to do is List the references so you can see what kinds of information JEPRS is capable of storing. Press L to get to the List References screen. (If you wish, you can now press F1 to get Help.) JEPRS now asks for the number of the reference you wish to display. Press 5 and then Enter; the fifth reference in the database is subsequently displayed. Note that JEPRS allows 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. Again, JEPRS asks you to enter the number of the next reference to be displayed. Note, however, that there are several keys that perform special functionsthese are described on the bottom of the screen. Press the key marked PgDn (or Page Down on newer keyboards). You'll see that the next reference (#6) will be displayed. In a similar manner, pressing PgUp will display the previous reference. Pressing F9 will cause the currently displayed reference to be sent to the printer in a standard compact form. Pressing F10 will send the reference to a DOS Text File (again, in a standard format), while F8 will only send the number (e.g. "6") to a Number File. These special files will be discussed in greater detail in the sections on Main Menu Options and Format References. Menus vs. Prompts. This brings us to a distinction that JEPRS makes with respect to what you enter into the program: a Menu versus a Prompt. A Menu is what you saw on the Main Menu: A highlight bar is present, and when you press the arrow keys you can move the bar to various commands. To invoke a command, you just press Enter after highlighting the command you want. Or, you can just press the first letter of the command instead (don't press Enter this time). A Menu can appear down the side of the screen (as in the Main Menu and Options Menu) or across the top of the screen (as in the Search Menu). You can always tell a Menu by your ability to use the arrow keys to move the highlight bar around. A Prompt on the other hand is when a question or statement is displayed on the screen and you are asked to respond. For example on the List screen, you are prompted for the number of the reference you wish to display. Generally a default value is given for a Prompt. For example, when you first enter the List screen, the number "1" is displayed next to the prompt. This means you can just press Enter and that will be the value accepted by JEPRS. In order to provide a value different from the default value, just enter the new value and press Enter; there is no need to press Del or BackSpace to delete the old value, JEPRS simply replaces it with the new one. But what if you want to modify the old value? For example, if the default value is listed as "1", but you want to display reference #10. Just move the cursor to the right of the "1", press 0 (so it should display "10" now) and press Enter. Why didn't JEPRS erase the old value this time? Because you pressed a non-character key (the right arrow key, this time) before you pressed a character key. In other words, if you pressed 0 before you pressed the right arrow key, then the "1" that was displayed would have been replaced by the "0" that you entered. This editing ability of JEPRS for the Prompts can be very useful, so keep it in mind (especially when entering a lot of text, like file names and directories). See the User's Guide for more information on which non-character keys you can use to edit the text. Now press Esc to return to the Main Menu. VI. Add New References. Press A to get to the Add References screen. You'll notice this looks very similar to the List screen, except there are more keys listed on the bottom of the screen. In order to make the formatted output as consistent as possible, JEPRS has some very specific expectations in terms of how you add reference citations: 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: Authors are entered last name first, followed by a space and then the initial(s). There is no space or periods between initals (but dashes are OK for hyphenated names). Spaces and dashes are OK between long last names (e.g., da Vinci or Weaver-Jones). For multiple authors, place a comma and a space after each author, except the last author (details and examples are in the User's Guide). Do not place an "and" or "&" before the last authorJEPRS can do this for you when formatting. Journal: It is generally easier and takes less typing to enter the standard abbreviations for journals, rather than the full name, but this is not required (e.g. Mol Cell Biol instead of Molecular and Cellular Biology). 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. Pages: No requirements. 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's 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: You can only enter an A (for abstract), B (for book), or J (for journal) here. No other input is acceptable. The reference type is useful for 2 reasons: (1) it allows you to limit your search to, for example, only books or only journal articles; and (2) it is also required for proper formatting during the Format function, since JEPRS can format references differently, depending on whether they are an abstract, book, or journal. Number (#): This is automatically assigned by JEPRS. You cannot change it, and JEPRS will never change it either. Editor: No requirements (but don't end it with a period) Publisher: No requirements (but don't end it with a period). Keywords: Keywords must be separated by a semicolon (";") and a space. Notice that a variety of special function keys are displayed on the bottom of the screen. Many of these perform the same function they would in a word processor or text editor. The arrow keys move the cursor in the direction pointed by the arrow. When you go to the end or beginning or a line, the cursor will wrap around to the other side. The Enter key is the same as pressing the down arrow key. PgUp will move you to the first line of the Title; PgDn will move you to the first line of Keywords. Home moves you to the first character of the line your are on; End moves you to the end. BackSpace deletes the previous character, while Del deletes the current one. Ins toggles the Insert/Overwrite mode. Check the box in the lower right portion of the screen to see which mode you are in. In Insert mode, characters to the right of the cursor are pushed ahead when new charcters are typed; in Overwrite mode, characters to the right of the cursor are overwritten when new characters are typed. F1 will give you help (just like it always does). When you are finished, press Esc to bring you to the one-line menu at the top of the screen. Since it's a menu, you can use the arrow keys and press Enter, or just press the first letter of the command. Choose Abandon if you made a mistake or changed your mind and decide not to save this reference citation; choose Return if you wish to go back and edit this reference; or choose Save if you are ready to save it. For now, choose Abandon. On the next menu, choose Main Menu (Continue allows you to add more references if you wish). VII. Update References. After returning to the Main Menu, press U to go to the Update References screen. You are now prompted for the number of the reference to be updated (you can also press F1 at this point to get help). Enter 5. You will now see basically the same screen you saw with Add References. Likewise, the function keys are identical to those in Add References. Edit the reference any way you wish, then press Esc to get to the menu at the top of the screen. As before, choose Save or Abandon; then choose Continue or Main Menu and press Enter. If you decide to continue, you will again be prompted for the number of the reference to be edited. You now have the choice of entering a number or pressing PgUp to update the previous reference or PgDn to edit the next reference. Pressing Esc will return you to the Main Menu. Note that since JEPRS does not have a Delete Reference option, the Update Reference option can be used to remove an old reference citation and replace it with a new one. VIII. Format References. JEPRS's most powerful utility is its ability to format references in the style of almost any journal. When at the Main Menu, press F to go to the Format References screen. Your first choice will be where you want the output generated by this part of the program to be sent: printer, screen, text file, or various combinations thereof. Note that an "s" appears at the cursor; this means that if you just press Enter here, the screen is the default output, so press Enter now. The next screen asks you what format you want to use. Note that you have the ability to define any 10 formats you wish (format number 11 [MedLine format] is predefined by JEPRS). If the Format file wasn't found by JEPRS when it started up, then no titles will be listed; otherwise, the titles present in the Format file are listed from 1-10. Enter "3". JEPRS then informs you that it is reading data from the Format file; these are the actual formatting instructions used. You will learn later how to program JEPRS yourself with your own formats, but for now let's just use the ones sent with the program. The final question is to determine what will be the source of the numbers of the references to be formatted. Again, a letter appears at the cursor position (this time "k") to signal a default value will be chosen if you just press Enter. If you press K, then you will be queried to enter the reference numbers at the keyboard. If you press N, then JEPRS will look for a Number File (again, you'll see more about this later) which is a text file that contains just numbers of references in the order you want them formatted. If you press R, then all the references in the data base will be formatted automatically (note that if you have a large data base, this may take a long time). Press K to list the references specified by keyboard input. You are then prompted for the number of the reference to be formatted. Enter any valid number of a reference in the data base file. If you enter an invalid number, it will be ignored (don't worry, the system won't crash). After pressing Enter, the program will read in the reference for the number you specified, and then display it according to the formatting instructions in the format file corresponding to the choice you made previously. Here is a quick rundown of what the special codes in the format file are for: \F, \L, \1 : Each of these is specifying that the authors be displayed: First name first; last name first; or last name first for the first author and first name first for each additional author; respectively. \T : Place title in output. \J : Place journal in output. \N : Place reference number in output. \C : Place citation type in output. \Pa : Place pages 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. \/ : Start new line. \<, \> : Start and end (respectively) optional inclusion. \S : Toggle subscripts. \^ : Toggle superscripts. \~ : Toggle italics. \B : Toggle boldface. \_ : Toggle underline. All of these are explained in more detail in the User's Guide. In addition, examples are given there so that you can get a better idea of how to program them. Note that you'll need your own text editor or word processor to edit the Format file; JEPRS cannot currently edit it. When finished, press Esc to return to the Main Menu. IX. Options. When at the Main Menu, press O to get to the Main Menu Options screen. On your right, you will see information reminiscent of that on the Main Menuit's system information that, again, you don't have to worry about now. On the left of your screen, you will see a list of file names and commands. This menu allows you to change any of the files that you are using in JEPRS, so you don't have to exit the program just to use a different data base file, for example. 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 Help file), it will first look in the directory specified in the Help file name; if none were specified, then it 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. Further down on the list are a few additional commands: Error/warning beep, Ordering information, MedLine format file, and Go to DOS. To invoke any command, do the same thing you did on the Main Menu: either use the arrow keys to highlight the command you want and then press Enter, or just type the first letter of the command (e.g., O for Ordering information). Error/warning beep allows you to turn JEPRS's 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 type "off" after invoking this command, and JEPRS will never beep at you. Ordering information will present you with details of how to order the latest version of JEPRS from the author (that's me). JEPRS is an absolute bargain at $25! MedLine format file allows you to add references formatted according to the National Library of Medicine's standard MedLine format. Most reference management programs can format files this way (including such things as PaperChase, an online access system to MedLine, and Current Contents on Diskette), so it's an easy way to interchange files between programs. For example, if you use PaperChase to search for any papers published on a particular subject, PaperChase allows you to save them in the National Library of Medicine (NLM) format. You can then download those references to a file on your computer. Then start up JEPRS and invoke the MedLine format file command, specify the name of that file when it asks you for the name of the MedLine format file, and JEPRS will automatically add those references to your database! Isn't that easy? Go to DOS allows you to temporarily exit JEPRS and return to the PC/MS- DOS 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 press Enter to return to JEPRS! If you use this command, forget to enter "exit", and then run JEPRS again, you may permanently mess up your data files! As long as you enter "exit" to return to JEPRS, your data will be completely safe. X. Search. When at the Main Menu, press S to get to the Search Menu. The menu itself is displayed across the top of the screen. At the right is a list of the default settings for all the options. Note that you can start and stop the search at any point in the database; stop after you've found a particular number of matches; direct the output to the screen, printer, files, or any combination thereof; have case-sensitive or case-insensitive searches; and sort the output by the first author. First we'll start off with a simple search: we'll look for one author, and leave all the options at their default values. To specify your search terms (that is, what field(s) you wish to search through and what text you wish to find), press T for Terms. A prompt appears asking "Enter Search Terms:" (note also that a message appears in the bottom left of the screen, in the Messages window, giving you instructions). Press A and then Enter. Now enter the text you wish to search: "Wright", and press Enter. Note that the text was converted to uppercase because the default is case-insensitive search. You are now returned to the Search Menu. Just press G for the Go command, and the search will begin. Notice that the Message window changes to let you know how many references have been searched and how many matches have been found. If you're using a hard disk you'll notice that JEPRS searches quite rapidly. You can press Esc at any time to stop the search. When the search is completed, the first matching reference is displayed on the screen in a compact format. The effects of the function keys are displayed on the bottom of the screen. To continue to the next matching reference, just press the space bar. However, you also have the option of outputting the reference currently displayed to the printer or a file. Press F9 and it will be sent to your printer (make sure JEPRS is set up for your printer by defining codes for underlining, boldface, etc., in the Format.JPR file). Press F10 and the current reference will be sent to a text file. If you press F9 then only the number of the reference will be sent to a file called a "number file". The use of this file is explained in the tutorial section called JEPRS's Files. Pressing F3 will take you back to the Search Menu, and Esc will take you back to the Main Menu. If your search resulted in more than one match, you also have the option of pressing F5 to modify your search. This is especially useful if your search came up with too many matches and you want to further restrict the search. It is a very useful feature. Now press F3 to return to the Search Menu. Let's try one fairly complicated search. Let's say we're interested in muscle cell differentiation and we want to find papers authored by (Wright and Lin) or (Lassar and Weintraub) that also have keywords (Myogen or MyoD) that appeared between 1985-1989 and that were published in (Cell or Science) but not (J Cell Science). Complex, eh? Just press T for Terms, then enter the following: (A+A)/(A+A)+(K/K)+Y+((J/J)-J) Recalling that "A" stands for author, "K" for keywords, "Y" for years, and "J" for journal, now look back at what we were originally searching for so that you understand the usage of the operators ("+", "/", and "-") and parentheses. After you pressed Enter, the first "A" will blink and the cursor will move to an empty line. Enter "Wright". Now the second "A" will blink and the cursor's on the next line; enter "Lin" here. Continue with the rest until you've entered all the items in the search. Notice that the corresponding letter will blink to tell you which term you are entering. After entering the last term, you are returned to the Search Menu. Press S to go to Sort. Now type "On" and press Enter; this turns sorting on. Now press G for Go, and the search begins. After completing the search, the matching references are displayed just like before in the simple search, except they will be in alphabetical order (by first author). Now press Esc to return to the Main Menu. XI. JEPRS's Files. When you're at the Main Menu, you'll notice several file names listed on the right side of the screen. By the time you get this far in the tutorial, you should have heard the names of most of these files mentioned. Now I'll go into a little detail as to what each file is used for, and whether you can modify any of these files. 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. You should never try to modify this file using any other program! For example, if you tried to look at this file using a word processor, you would probably only see 3 words on the screen: JEPRS Reference File (the same is true if you try to use MS-DOS's "type" command to view the file), but all the data is still there. However, if you then saved this file with your word processor, you would delete all the references that JEPRS had saved! Therefore, let me repeat: Never modify the Reference file with any program other than JEPRS!!!! Ref Key File: This is a matching file for the main database (Reference file) that JEPRS uses for keeping 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. Again, do not try to modify this file with any program other than JEPRS otherwise you will lose all your data! Help File: This file contains all the information displayed in the Help screens whenever you press F1 for help in JEPRS. Again, do not modify this file! If you do, the help screens will not display the proper help, and will become worthless. The default name for this file is Help.JPR. 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 if you press the F10 key when you are on the List Reference screen, the text will be sent to this Text file (default name is Text.JPR). Text will also be sent to this file if you specify File Output on the Format References Menu or on the Search 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. Number File: This file (default name is Number.JPR) can be created by JEPRS. If you press the F8 key when you are displaying the results of a search, or if you press the F8 key when you are on the List Reference Screen, the text will be sent to this file. It 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. Why would you want a file like this? JEPRS can use this file on the Format References Menu: The last question JEPRS asks you on that menu is "What will be the source of the references to format?". You have the choice of "Reference file" (in which case all the references in the Reference file will be formatted), the "Keyboard" (in which case you can specify, one by one, the references at the keyboard), or "Number file", in which case JEPRS will read in the numbers in the Number file, find only those references in the database, and format them. How can something like this be useful? Let's say you've just finished a discussion with a colleague. You tell him/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. But let's say s/he has a program that's different from JEPRS, but s/he doesn't want to have get a printout from you and then hand-type all those references back into his/her program. With the number file, there's an easier way! All you have to do is start up JEPRS, go to the Search Menu and then: go to Terms and specify "K" (for Keywords) and then enter "Syrinx 2A", go to Output and turn the Screen "Off" and the Number File "On", then press Go to start your search. When the five papers are found, their numbers are automatically sent into the Number file. Then press Esc to return to the Main Menu, and press F to get to the Format References Menu. When asked for where the output should go, just press Enter. When asked for the formatting style, enter "11" for the MedLine format. Then, when prompted for the source of the references, press N for Number file. JEPRS will then read in the numbers of those five papers on the Syrinx 2A vector, look up those numbers in the database, format them according to the MedLine format, and send them out to the Text File. Voila! Then you just copy the Text File to a floppy disk, hand it to your colleague, and s/he can read it into his 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. Format File: This file contains the formatting instructions and printer definition instructions for JEPRS. It's default name is Format.JPR. Creating or modifying this file is undoubtedly the most complex feature of JEPRS, but it is also its most powerful feature. This is the only file that JEPRS cannot create itself (that will probably change in future versions of JEPRS; register now to keep up-to-date on the latest release!). You must use an external word processor or editor (like Borland's SideKick program) to create and edit it. The best way to understand what I'm about to describe is to start your word processor or editor and load the Format.JPR file that's included with JEPRS, so you can look at it while I'm explaining what everything does. Note that if you use a word processor to look at this file, you must load and save the file in a text file mode (i.e., in WordStar you must use the Non-Document mode; in WordPerfect you must use Ctrl-F5 "Text In/Out" key to save and retrieve a DOS Text file). You will immediately notice that many lines begin with a minus sign "-". This tells JEPRS to ignore those lines, so you can enter any comments you like on those lines. The only place you cannot place a comment line is between a descriptor (such as "Left Margin") and its value ("8") which must appear on the very next line. Other than that, you will see it divided into several sections: "Printer Commands", "Page Formatting Commands", "Directory and Filename Defaults", "Journal Titles", and "Journal Formats". Note that the order of these is not necessary, but be aware that if you change the order around, it may take quite a bit longer for JEPRS to read this file in; it's best just to leave it in its present order. The first section is "Printer Commands". This contains all the printer- specific commands for things like underlining, boldface, italics, etc., that JEPRS uses for formatting output. If none of the Format files supplied with the program are for your specific printer, you must use the manual that came with your printer to enter the correct information in this section. "Printer Initialization Setting" is the command sent to your printer the first time JEPRS prints something. Most of the time this will be empty, but you may want to specify near letter quality mode on a dot matrix printer, or a specific font on a laser printer, for example. On a Star Micronics SG-10 printer, for example, the command for near-letter-quality mode is "<Esc>4". If you wanted to enter that using SideKick, you would go to the first line in the file following "Printer Initialization Setting" and enter Ctrl-P (to enter a control character) then Esc then the number 4. In a similar fashion, enter your printer's special commands for each of the descriptors listed: Underline on/off, Bold on/off, italic on/off, subscript on/off, and superscript on/off. If your printer does not support any of these features, just leave the line blank (by blank, I mean make sure there are no characters on that line, not even spaces! If you leave spaces, they will printed in the formatted output, which would be very undesirable!). The second section is "Page Formatting Commands". This allows you to specify how your page should be formatted when references are output using the Format References Menu. "Left Margin" refers to how many spaces JEPRS prints at the left margin before printing text. "Line Length" refers to the maximum number of characters that fit on a line (not including the left margin). "Header" refers to text that will be printed at the very top of every page of the output. "Heading" refers to text that will be printed at the top of the first page of the output. "Top Margin" is the number of spaces that should be skipped at the top of each page before printing. (If "Indent Length" is shown, just ignore it; it is a feature that is not yet implemented; JEPRS will just ignore it.) "Page Length" is the number of printed lines per page, not including the top margin or header. The third section is "Directory and Filename Defaults". Here you can change the default names of any file that JEPRS uses. Note that when you start JEPRS it immediately looks for the format file on the current directory with the name Format.JPR. If it doesn't find it, it uses all the default names for all the files JEPRS normally uses (e.g., "Ref1.JPR" for the Reference File). If you want to call the format file by a different name, or have it on a different directory or drive, then you can specify this when you first start up JEPRS. Let's say that you created 2 format files: one with commands for your dot matrix printer (called "FormDot.JPR") and one for your laser jet printer (called "FormLasr.JPR" that is in a directory called "C:\Laser\"). To start JEPRS with the first file, enter: C:\JEPRS\> JEPRS Formdot.jpr where "C:\JEPRS\>" is just the DOS prompt, and "JEPRS Formdot.jpr" is what you actually entered. On the other hand, if you want to use your laser printer with JEPRS, start JEPRS this way: C:\JEPRS\> JEPRS C:\Laser\FormLasr.JPR where, again, "C:\JEPRS\>" is just the DOS prompt, and "JEPRS C:\Laser\FormLasr.JPR" is what you actually entered. Once JEPRS reads in those format files, it automatically assigns the names you specify in this section to the files it uses. The next section is "Journal Titles" where you just enter the names of the journals, from one to ten, that you create formats for in the "Journal Formats" section. The last section is "Journal Formats"; this is where you get down to business. Here you enter the special formatting instructions JEPRS uses to format output in the Format References Menu. All the special characters are explained in the Format References section of this tutorial. Some things you must know: 1. These can be no longer than 100 characters; if they are, output will be messed up and JEPRS is not (yet) smart enough to detect this kind of problem. 2. 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". 3. 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 a new line twice; 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 References Menu, and compare the output to the codes in the format file. After comparing them carefully, you'll get a better feel for how the system works. Once you've spent the time to modify the Format File to your specific needs, using JEPRS is an absolute breeze! XII. 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. Highlight Exit, then press Enter. When you do this, JEPRS will beep (unless you turned off the Error/Warning Beep on the Options Menu) and then ask you if you really want to exit the program; if you do, press Y; it you don't, press N. If you press Y, you will be returned to the PC/MS-DOS operating system. If, however, you turn off your computer without exiting JEPRS, then you may lose data from your data files. So remember, always exit JEPRS before turning off your computer! XIII. Concluding Comments. Well, that's it for your guided tour of JEPRS. I sincerely hope you find it to be an easy-to-use, convenient system for maintaining a database of references to the scientific literatureand a bargain at $25. If you have any comments, questions, or complaints about JEPRS or its documentation, I would love to hear from you. Send comments to the address listed at the beginning of this document. Thank you. Lou Miranda.