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JEPRS (TM) User's Guide 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. 1. 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 is distributed as "shareware"; this means that you may make copies to give to others (at no charge) for test purposes. If JEPRS is used, then the user is obligated to pay a shareware fee to the author (me), just like any software you purchase in a store. It is not public domain! Please see the Options choice on the Main Menu for ordering information. Registration has several advantages: ■ I only provide support (i.e., answers to questions) to users who have registered. If you register, you may write to me and I will respond as quickly as possible to your question. (If you haven't registered, you have a much lower priority for answers.) ■ Free update! The next major update is sent free of charge to registered users. Later updates may be purchased for a nominal fee (probably $10). Major updates are planned about every six months, but that is not set in stone. ■ Laser-Printed documentation. The Tutorial and User Guide are sent to registered users as offset-printed versions of laser-printed originals. ■ Update Notices. Registered users are always kept up-to-date with reports of minor updates (to fix bugs or add small numbers of features). In addition, I anticipate these notices will also include useful tips for getting the most out of JEPRS. Before continuing with this documentation, you should have read the file called ReadMe.JPR and the Tutorial (JPRTutor.JPR). These two files contain basic information for installing JEPRS and starting the program up for the first time. The User Guide you are reading now is meant to provide more in-depth information and is not really meant to be read from beginning to end in one sitting. Refer to this document only when you have specific questions or if you want more detailed information on how JEPRS works. Creating Your Own Database When you used the tutorial, JEPRS automatically used the sample Ref1.JPR and Ref1.JPK database files. Now you probably want to create your own database. Since JEPRS automatically uses files named Ref1.JPR and Ref1.JPK, it is easiest to have your database files use these names. Therefore, before starting up JEPRS the next time, use the MS-DOS Rename command to rename the sample database files as follows: C:\JEPRS> Ren Ref1.JP* Sample.JP* The command above will rename the sample files to Sample.JPR and Sample.JPK. If you then start JEPRS as you normally do, that is: C:\JEPRS> JEPRS you will get an error message saying that it can't find the database files. You have the option of quitting the program or creating the files. Press F6 to create a new database. JEPRS will then create two new files, called Ref1.JPR and Ref1.JPK, that will be your database. These files will initially contain no reference citations; however, they will both be 100 bytes in size because JEPRS keeps some instructions in them regardless of how many references they contain. Of course, you have the option of calling your database files anything you want: you're not limited to Ref1.JPR and Ref1.JPK. In order to do this, though, you must edit the Format.JPR file. There is a section where you can specify the names of the Reference File and the Ref Key File. Just enter the names of your files there. In addition, you can call the format file something other than Format.JPR. See the next section to see how to specify its name on the command line. 2. Starting JEPRS. 2.1. The Basics. You start the program by simply entering the command "JEPRS" at the DOS prompt, like this: C:\JEPRS> JEPRS 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. If you are starting JEPRS without a database (for example, when you are creating a new one, as explained in the previous section), 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, F4 to specify a new name, or F10 to exit the program. 2.2. Advanced Features. There is one command line option that you may use when starting JEPRS. If for some reason you wish to use a different name for the format file (in other words, you're not calling it Format.JPR or it's not in the current directory), then you can specify its name on the command line, like this: C:\JEPRS> JEPRS FormLsr1.JPR This tells JEPRS to use FormLsr1.JPR as the format file, which must be in the current directory. If you wish, you may also specify the directory it is in, if this is not the current one. For example, if you keep FormLsr1.JPR in a directory called C:\PRINTER, then start JEPRS like this: C:\JEPRS> JEPRS C:\PRINTER\FormLsr1.JPR This tells JEPRS not only the name of the file, but also in which subdirectory it is located. 3. The Main Menu. 3.1. The Basics. 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's commands. The box on the left side of the screen contains the Main Menu. Every command listed (Add, Update, List, Format, Search, Options, Help, and Exit) can be invoked by at least two methods: ■ Use the up and down arrow keys to highlight the command you want to use, then press Enter to start that command, or ■ 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). 3.2. Advanced Features. Notice the information on the right side of the screen labelled "Current System Information." This provides some useful information to you regarding the environment that JEPRS is working in. It also is useful to me if you discover any problems with the program. If there are any problems, it is very helpful to me if you copy down the information here (or press <Shift><PrtScr> to print it on your printer) and send it to me along with your problem. Each line is described briefly here: ■ Version number and date released. For version 1.10, JEPRS was released to the public in March 1989. Sometimes users don't have the most current version of JEPRS and a bug you may have discovered may already have been fixed in a newer release. If you discover a problem, always let me know what version you are using. ■ MS-DOS version. This tells you which version of PC/-MS-DOS you are using (e.g., 2.11 or 3.21) to run JEPRS. [My understanding is that when you run the DOS Compatibility Box in the OS/2 operating system, the version number will read "10.0"; but I don't have OS/2, so I don't know for certain that this is true.] ■ Error/Warning Beep. This tells you whether the error beep is turned on or off. You can change its setting on the Options Menu. ■ System Memory Available. This tells you how much extra space JEPRS has available to it. The bigger your database, the smaller this number. Note that this number remains constant no matter how much memory you have installed in your computer. In future versions, I may allow JEPRS to take advantage of whatever memory you have available. ■ Total Computer Memory. This just informs you how much memory you have installed in your computer. For reasons not evident to me, some IBM computers display one kilobyte less than they actually have (e.g., 639kb is displayed even if your computer really has 640kb installed). JEPRS cannot detect `extended' or `expanded' memory, so if you have this kind of memory, this program doesn't know it's there and will not report it. ■ 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. ■ Directory and File Names. These are the names specified in the format file or, if you haven't specified one, the default names JEPRS uses. Note that if you specify a different name on the Options Menu, it will be reflected properly here. A note about the directory name: this is not necessarily the currently active directory! JEPRS first searches for files exactly as they are listed; if it can't find them in the current directory, only then does it look in the directory specified in Directory Name. See the section of this manual on JEPRS Files for more information regarding what these files are used for. ■ The current time and date are displayed on the bottom of the screen. Of course, if your computer's internal clock has the wrong time and/or date, then this will not be correct. 4. Prompts vs. Menus. 4.1. The Basics. Note that on the Main Menu you can move the highlight bar around 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. 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 "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. 4.2. Advanced Features. 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 character you press must be a non-printing key which must be one of: LeftArrow RightArrow Delete If you press one of those keys before pressing a 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 Options 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 RightArrow 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. 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. 5. Help. 5.1. The Basics. At most points within JEPRS, you have the option of pressing F1 to get 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. Help is generally available throughout the JEPRS program. You will always know if Help is available, because "F1=Help" will be displayed on the bottom of the screen if it is. 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. 5.2. Advanced Features. In order for Help to work, JEPRS must be able to find the file called "Help.JPR". If JEPRS can't find this file, it displays an error message: "<filename> not found. Press any key to continue." when you try to get Help. If the help file is not in the current directory, and it is not in the directory specified on the Options Menu, then you should specify its name in the "Help File name" on the Options Menu. Each Help file is specific for each version of JEPRS. Therefore, if you get an update (for example, you switch from JEPRS version 1.10 to version 2.00) you must replace the old Help file with the new one supplied with the update. Otherwise, Help will provide incorrect information. 6. List References. 6.1. The Basics. JEPRS asks for the number of the reference you wish to display. Enter any number; the corresponding reference in the database is subsequently displayed. 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. 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. Pressing the key marked PgDn (or Page Down on newer keyboards) will cause the next reference 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. 6.2. Advanced Features. JEPRS is smart enough to know whether you've entered a valid reference number or not. If you enter a number that's too large, an error message will be displayed which will tell you both the number you entered as well as the total number of references in the current database. 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 #77 then "77" will be displayed as the default value for the next reference; just press Delete once and then press 2 and #27 will be displayed. 7. Add New References. 7.1. The Basics. This part of the program allows you to enter new references at the keyboard (you can load references in the MedLine format [e.g. those from PaperChase or Current Contents on Diskette] automatically using the MedLine File command on the Options Menu). 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. Do not place an "and" or "&" before the last authorJEPRS can do this for you when formatting. Here are some examples of correct and incorrect entries [and the reason why]: Correct: Incorrect: Wright WE Wright, W.E. [punctuation] Lin VK-I Lin V K-I [extra space] Wright WE, Lin V Wright WE & Lin V [&] da Vinci L da Vinci, L [comma] 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"). When formatting bibliographies/reference lists, some journals 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 the journal'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)) but this is not required. See note regarding "L"s and "1"s under Year, below. 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 option 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. It is also required for proper formatting during the Format option, since JEPRS can format references differently, depending on whether they are an abstract, book, or journal. Number (#): This is automatically assigned by JEPRS. Neither you nor JEPRS can ever change it. 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. There are two reasons for this. First, the space is necessary so that, when performing formatted output, JEPRS can find a space in which to `break' a line if the line is too long. Second, if you want to output your references in the MedLine format, JEPRS needs to find the semicolon so that it can place each keyword on its own line. Keywords can be entered either in all capitals or mixed upper- and lower-case; there is no particular advantage doing it either way, since during a Search you can convert them to uppercase for comparison. The only disadvantage to using all upper-case is printing formatted output using a proportionally-spaced font (there is no problem with a fixed-spacing font). 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: MAMMALIAN MAMMARY GLAND Mammalian mammary gland With a fixed-spacing font, both lines take the same amount of space; but with a proportional font, the top 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 upper-case and lower-case) with a very wide right margin. Of course, if you plan on importing MedLine files, these have their keywords in all upper- case 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). 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 he 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). Pressing Esc will bring you to the one-line menu at the top of the screen. Since this is a menu, use the arrow keys to highlight a command and then press enter, or just press the first character of the command. Use Save to save this reference; use Abandon if you made a mistake or change your mind and decide not to save this reference citation; use Return to Edit to go back to this reference and continue editing it; use Help (or F1) to get Help. At the next menu, use Continue to add another reference or use Main Menu (or press Esc) to return to the Main Menu. 8. Update References. 8.1. The Basics. Updating references is essentially identical to adding references. The only difference is that you are specifically asked which reference you wish to edit. Since this is a prompt, you can enter a new number or edit the default value; you also have the option of pressing PgDn to edit the next reference or PgUp to edit the previous one. 8.2. Advanced Features. 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. 9. Format References. 9.1. The Basics. JEPRS's most powerful utility is its ability to format references in the style of almost any journal. 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. 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 any number from 1 to 11. JEPRS then informs you that it is reading data from the Format file (unless it is using the pre-defined MedLine format); these are the actual formatting instructions used. 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 which is a text file that contains just numbers of references in the order you want them formatted. If JEPRS can't find the number file, it will let you know, and then ask for a new name. At this point you can either enter a new file name or press F9 to go back to the Main Menu. If you press R, then all the references in the data file will be formatted automatically (note that if you have a large data file, this may take a long time). In the case of file input (either reference or number files), you are additionally asked: "Do you wish to pause after ever 20 lines?". If you press Y, the screen will display 20 lines of text, then pause and wait for you to press any key to continue. Then it will display the next 20 lines of text and pause again; in this manner, text will not scroll off the screen before you get a chance to look at it. If you press N, the screen will to continue to scroll without stopping (you can press Ctrl-NumLock to pause the screen display). In either case, pressing Esc will bring you back to the Main Menu after the next full reference has been displayed. If you press K to list the references specified by keyboard input, you are then prompted for the number of the reference to be formatted. After pressing Enter, the program will read in the number you specified, and then display it according to the formatting instructions in the format file corresponding to the choice you made previously. If you enter an invalid number, it will be ignored (don't worry, the system won't crash). Pressing Esc will bring you back to the Main Menu. 9.2. Advanced Features. The Format References section is by far the oldest module of JEPRS, and this is reflected in its rather antiquated user interface. I am very well aware of this limitation and, in fact, the next major update (due out probably in September 1989 or so) will sport a completely rewritten user interface here; I plan on making it look very much like the Search Menu (which is the newest module). I would also like to provide the user (you) with the ability to modify the Format File from within JEPRS (without having to exit the program and use your own editor) but this is a large undertaking and may not make it into the next version, but should be done by the version after that (March 1990?). If you have any suggestions on how to improve JEPRS's user interface, please let me know and I'll see if I can incorporate them into the next release. 10. Options. 10.1. The Basics. This menu allows you to change the names of 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 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. Changing a file name. To change a file name, press the first letter of the file type, or just highlight the file type and name using the up and down arrow keys and press Enter. At the bottom of the screen, you will be prompted for the new name of the file. Note that the old name is displayed there so that you can edit it (see the section in this manual on Prompts vs. Menus to see how). Edit the old name or just type in a completely new name, then press Enter when finished. Note that if you are changing the name of the reference file or reference key file, you will be prompted for both file names, since they are specific for each other. 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 (or Current Contents on Diskette) 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, but forget to enter "exit" and then run JEPRS again, you will permanently mess up your datafiles! As long as you enter "exit" to return to JEPRS, your data will be completely safe. 10.2. Advanced Features. On your right, you will see "Additional System Information." The first four pieces of information (MS-DOS and JEPRS version numbers, Disk #, and Licensee) are more for my use in case you are having a problem with the program. "Number of references in reference file" tells you how big your database is; it should say zero when you first create a new database, and should grow as you add more reference citations. "Number of relocated references" isn't much use to you now, but it will be in the future. In order for JEPRS to make the database as compact as possible, it stores references exactly as you enter themthey are in "variable length" fields. The only problem a programmer (that's me) runs into is if the user (that's you) decides to modify one of the references and make it longer than it used to be. In order to cope with this possiblity (so you, the user, do not have to worry about it) JEPRS marks the old (shorter) reference as invalid and then adds the modified one to the end of the file: this is a "relocated" reference. If a significant number of references are "relocated" then a lot of disk space is wasted. What I plan on doing in the future is to create a command to get rid of these garbage references. In the meantime, they are harmlessly sitting in your database. "Available space on default drive" tells you how many bytes of space are left to use. 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. 11. Search. 11.1. The Basics. All you need to do in order to perform a simple search is to specify one search term and then press Go to start. 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 Terms. ■ Enter "A" to search the author field. ■ Enter "Wright" to search for this text. Once you press Terms, you are asked to "Enter search:"; this is where you enter the letter(s) corresponding to the fields to be searched. JEPRS lists the letters and fields at the bottom of the screen; they are reprinted here for your convenience: Authors Editor Keywords Citation type Title Year Publisher Journal You can perform mulitple searches by connecting the field names with operators. An operator is one of: + = 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 Author +[and] Title, then enter "Wright", then enter "Myogenin". [When you're entering the text, you must enter it in the same order as the field names; 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 letter blink while you are entering the search text for it.] Because the 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". ■ "A/T" is logically identical to "T/A". ■ "A-T" is very different from "T-A". ■ 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 enter the name of the author you don't want to find. This will accomplish the same thing as "-A". Once you press Go to start the search, the Messages window on the bottom of the screen will show you the number of the references being searched as well as how many matches have been found. You can press Esc at any time to stop the search and display the results found at that point. If Text File, Number File, or Printer Output is on, then when searching is done the Messages window will show which references are being sent to the designated output. If Screen Output is on, then the screen will clear and the Search Display will be shown. The first reference found (or the first one alphabetically, if Sort in on) is displayed and function key assignments are shown on the bottom of the screen. These are described here: ■ Esc: You will be returned to the Main Menu. ■ F3: You will be returned to the Search Menu. At this point you may then 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. ■ F1: As always, this will give you help. ■ F5: This allows you to modify your search by bringing you to the Modify Search Menu. The first time you modify your search, two or three lines of instructions are provided (with "Instructions" in red letters on color monitors). Your previous search terms are displayed on the top right of the screen. The number of matches JEPRS has found for the current search is displayed in the upper left 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 databaseit 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. ■ F8: Sends the number of the most-recently displayed reference to the Number File (see description of files near the end of this guide). ■ F9: Sends the entire text of the most-recently displayed reference to your printer. It uses a compact format pre-defined by JEPRS which includes boldfacing and underlining. However, if you have not properly defined those attributes in the Format File then it will not print correctly on your printer. ■ F10: Sends the entire text of the most-recently displayed reference to a Text File. Note that it includes printer formatting codes (underlining and boldface) so that you can still print it on your printer. However, if you import it into a word processor, you will see all of those weird codes mixed in with your text. If you want to create a Text File without codes, then create a Format File without codes for a printer and use that one in JEPRS before creating a Text File. 11.2. Advanced Features. One important thing you should realize about searches is that 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) Turn Case Sensitivity on and search for "Stein"; then "Frankenstein" would not be a match; (2) Use a space or other delimiter such as "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 F5 (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 one of your references didn't contain both Stein and Steinberg as authors! There are a number of options (displayed on the right side of the Search Screen) that can modify your basic search strategy: ■ Begin. When at the Search Menu, pressing Begin will allow you to specify 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; then you would specify Begin at #600. This would cut down your search time significantly. The default value is 1. ■ 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 number of matches have been found. Let's say that you know that a certain search, like keywords for "DNA" will yield a lot of matches, but you only want to see the first 15 of them. Press Matches 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 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. Normally when JEPRS does a search this option is Off. That means that both your search text and the references in the database are both 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". If you wish to make the comparisons directly without converting to uppercase, then turn Case Sensitivity "On". The default is "off". ■ Output. JEPRS lets you specify any combination of output to Screen, Printer, Text File, and/or Number File. When you press Output, the cursor moves next to Screen and lets you enter "on" or "off"; then press Enter and "on" or "off" for the printer; and so on until you specify values for each output. Any combination is allowed except turning them all off; if you do so, JEPRS will beep and then turn on the Screen for you. The default is Screen on, everything else off. ■ Sort. By default, JEPRS displays the references in the order they were found in the database. Optionally, you can turn Sort On, in which case they will be displayed alphabetically by the first author's last name. If there is more than one paper by the first author, they will be displayed together, but in no particular order. I am thinking about adding the ability to sort first by author and then by year if the first author is the same. If you think this is a good idea, or if you have any better ideas, let me know. 12. JEPRS's Files. 12.1. The Basics. All of the major file types that JEPRS uses are listed on the right side of the screen of the Main Menu. If you've read through the tutorial, then you should be vaguely familiar with the names of each of these files. 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. 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; it is provided to you on the original disk that you received JEPRS.Exe on. 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". Note that each Help File is specific for each version of JEPRS. If you try to use the Help File from JEPRS Version 1.00 with Version 1.10 of JEPRS.Exe, you will get nonsense help most of the time. ■ 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 "Output: Text File -----> On" on the Search Menu, then the text of the reference(s) 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. 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, just as if it were being sent to your printer (it uses the codes present in the Format File). If you don't want to have any codes embedded in the Text File then you can create a new Format File that has no printer codes, then load this Format File into JEPRS before sending output to the Text File. ■ 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, or if you specify "Output: Number File --- --> On" on the Search Menu, the number(s) of the reference(s) 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. You can create a number file yourself with a text editor (or word processor in DOS Text file/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 MS-DOS Type command at the DOS prompt (e.g., "C:\JEPRS> Type Number.JPR"). If you see any weird characters, or if the numbers aren't lined up on the left side, then it's not an ASCII file. ■ Each number must be on its own line. If more than one number is present, only the first one is used. ■ Spaces and/or Tabs are OK before a number, but no other characters are allowed. If any other characters 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 (they're ignored). ■ 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 another comment (and the "3" is valid) 99 This is another comment line. This is ignored: 12 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, default directory and file names, and printer definition instructions for JEPRS. Its 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 or PC/MS-DOS's Edlin) 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 the file 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. ■ 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). Note to users with printers that have very long codes (for example, laser printers): JEPRS allows a maximum of 40 characters for the printer initialization code and 20 characters for each of the other codes; if more than this number of characters are present, only the first 40 (or 20) will be used and rest will be discarded. ■ 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. So if your printer prints 10 characters per inch and you want to leave a 1-inch margin, make the left margin 10. "Line Length" refers to the maximum number of characters that fit on a line (not including the left margin). So if you want to leave a 1-inch right margin and, using the example above, your printer prints 10 characters per inch, then your line length would be 65 ( = 8.5 inches - 1 inch left margin - 1 inch right margin = 6.5 inches x 10 characters per inch = 65 characters). Things get a little tricky if your printer prints a proportionally spaced font (like a LaserPrinter's Times Roman font). 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 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 font or that you send the format to a Text File (instead of to the printer) and then import it into a word processor. "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. Each of these can be up to 100 characters of text (a Tab counts as 1 character). "Top Margin" is the number of spaces that should be skipped at the top of each page before printing. For example, if your printer is set for printing 6 lines per vertical inch and you want to leave a 1-inch top margin, then enter 6 here. (If "Indent Length" is shown, just ignore it; it is a feature that is not yet implemented; JEPRS will just ignore it if it is there.) "Page Length" is 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 your 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 "Page Length". ■ 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" (unless you specify a different name on the command line; see the section entitle "Starting JEPRS: Advanced Features"). If it doesn't find it, it uses all the default names for all the files JEPRS normally uses. The default names are listed below: Reference File: "Ref1.JPR" Ref Key File: "Ref1.JPK" Format File: "Format.JPR" (or whatever you entered on the command line) Help File: "Help.JPR" Text File: "Text.JPR" NumberFile: "Number.JPR" 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 Formdot.jpr where "C:\>" 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 C:\Laser\FormLasr.JPR where, again, "C:\>" 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. ■ Journal Titles. Here you just enter the names of the journals, from one to ten, that you create formats for in the "Journal Formats" section. ■ 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. 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". 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. 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. Here is a complete rundown of what the special codes in the format file 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 and first name first for each additional author (e.g., "Miranda, LM, VK Lin and WE Wright"). \T : Place title in output. \J : Place journal name in output. \N : Place reference number in output. \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, for 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. \/ : 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 the fields being present. For example, let's say that the rules for a certain journal state that if you are referencing a book that 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 Development' in: Cell Development. But if you had a book that didn't have chapter titles that you could use, the output would look kind of funny, like the next line: WE Wright. `' in: Molecular Basis of Development. 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 defintion): 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 Development' in: Cell Development. WE Wright. Molecular Basis of Development. And that is much nicer output! More examples are given below for you to study (also look at the examples in the Format Files 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. See below for examples. \S : Toggle subscripts. \^ : Toggle superscripts. \~ : Toggle italics. \B : Toggle boldface. \_ : Toggle underline. Note that if you haven't entered the printer-specific sequences for these codes in your Format File, then they won't print on your printer. Once you've spent the time to modify the Format File to your specific needs, using JEPRS is an absolute breeze. Here are bunch of examples for you to look at and study. It may seem a little overwhelming at first, but you'll soon find you understand it in no time at all! Note: If you are reading this as the Laser-Printed documentation provided by the author then the underlining, italics, etc., will appear on the paper just as they would with JEPRS output. However, if you are reading this from the JPRGuide.JPR file supplied with the program, then all of the text will appear normal and it won't be of much help. As an alternative, you can try printing out some examples using the Format Files provided with the program, or you can register with the author and be provided with the original Laser-Printed documentation. The best way to enter a new formatting 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 look like this: 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 ", 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 number in the database). This requires the use of JEPRS's "\#" code, so now your definition looks like this: and # 3. As I said, you build up your format character by charcter and code by code. Therefore, since in our example the number is followed by a period and two spaces, 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 three possible codes: \F, \L, and \1. 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\~ 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? Wrong. There is one thing else 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 this: 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 this codes is not printed if the field also within this code 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 "\>"): 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 this: 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. ■ Since your definition cannot exceed 100 characters, you may want use optional inclusions carefully. And of course 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. It is hard to imagine anyone exceeding this limit, but if you find that you do, let me know and I'll try to extend it. That's it for the Format File 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 a Text File, then import this into your word processor and modify it there. Three things to keep in mind regarding formatting codes: ■ The maximum number of characters that you can use to specify formatting instructions in the Format File is 100 characters. ■ They must all be on one line: you can't have it split into two lines. If you do, JEPRS will ignore the second line. They are shown in this documentation as being on two lines simply because the column width of the text prevents them from being all on one line. ■ Because JEPRS evaluates these codes as it runs (kind of 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 when you print it out, it will look like: "c-myc oncogene". As I see it, there is one advantage to this and one disadvantage. The advantage is that it can make your searches more specific: if you search for "myc" you will find references both to "c-myc" as well as "mycoplasma", whereas if you search for "\~myc\~", you will only find what you want: "c-\~myc\~". The disadvantage is the lack of portability to other programs. For example, if you format your references according to MedLine to send them to another program, those codes will remain with your keywords. Of course, you could always just delete them in the other program. The choice is yours as to whether this is an advantage or disadvantage! 13. 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 to 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 (and your screen colors will return to what they were before JEPRS started). 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! 14. Ordering/Registering JEPRS. JEPRS is distributed on a "shareware" basis. This means that you are free to distribute copies to other people you think may be interested in using it. They are then free to try out the program at no cost. However, if you decide to use the program, then you are obligated to pay a fee. The fee is ridiculously small considering the amount of work JEPRS can do. I am currently charging only $25. That registration fee includes: ■ Unlimited use of the program. ■ The latest version of JEPRS will be sent to you (if you do not already have it). ■ Laser-printed documentation will be sent to you (this is a printed version of the JPRTutor.JPR and JPRGuide.JPR files). ■ The next major update will be sent free of charge! ■ I will answer any questions you have about the program. If you do not register, I will not answer any questions (unless that question has a bearing on whether you decide to purchase the program, such as questions about compatibility with other reference management programs). To order/register use of JEPRS, print out the "Order.JPR" file that's included on the disk, and fill out the information requested. Or just send $25 to: Louis M. Miranda 6033 East Northwest Highway #1106 Dallas, TX 75231-7463 Please specify whether you want it on a 5 1/4 inch floppy disk or a 3 1/2 inch disk. Also send me the name of the person (or organization) that's listed on the Welcome Screen (the first thing you see after starting JEPRS) as well as the version number and date (so I can send you a new version if you don't have the most recent one). 15. Distribution. JEPRS is distributed as shareware. This means that you are free to try the program on a trial basis at no cost, simply by copying the program from someone else. If, however, you decide to use the program, you are obligated to pay a fee (see the Order.JPR file on the distribution disk, or look at the Ordering Information screen on the Main Menu Options screen. 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 condition (that is, unmodified by you) at no charge. Likewise, JEPRS may be posted on bulletin boards as long as there is no fee for downloading the program. If you do so, I would appreciate a note from you specifying the phone number and name of the bulletin board you posted it on. If you charge any fee whatsoever for acquiring JEPRS (for example a commercial shareware distributor charging $5-10 per disk) you must receive an agreement in writing from me! I do not anticipate denying that right to anyone, but I would just like to be aware of the distribution channels that JEPRS is moving through to keep the most current version in distribution. 16. Further Help and Questions. If you have any comments or complaints about JEPRS, I would love to hear from you. Likewise, if there is a problem with the documentation or something that is not clear, feel free to write to me at the address above and I'll write back to you as soon as possible. Thank you for your interest and support of JEPRS!