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1. ae a 74 SEARCH IRESULTS sananne aeuoneasansens 24 Bibliography FORMAT 26 amp eanvaw gen E 77 HTML 77 e 78 OTHER LO DONS E 78 DIRECTORIES cost 40 FOR MORE INFORMATIONS ccceccecccccceccceccccceccceceecececesceeucenseececes 40 Acknowledgments I would like to acknowledge the help I have received from number of different people While I accept full responsibility for any errors you may find in this program the many bugs that you do not find are due to the efforts prodding encouragement of the people who have been willing to try out the latest versions even those that weren t done yet I d especially like to thank Karry Kazial and Jerry Hough for trying multiple different versions and pointing out numerous errors I would never have found on my own I would also like to thank Robert Lawson for giving me a reason to work on the comma delimited import and export functions In addition for helping coaxing me to work on previous versions of the software I would like to thank Adrian Werner and Adam Keeton I d also like to offer belated thanks to several people w
2. You can specify that any words that have these characters placed before them will receive extra formatting that won t be applied to other words around them This is useful for titles that contain words that must be displayed in bold or italic type such as species names To enter a field that uses one of these codes you type the text as normal but you add the code letter to the front of each word with no spaces you want modified For example if the code were set to indicate bold text then the following text entered in a record This is a test of the formatting characters Would be displayed as this in the bibliography This is a test of the formatting characters In previous versions of BioBase the formatting for fields containing a special code would be disrupted by the special code meaning that the specified words would only have the formatting indicated by the code 26 not that of the rest of the field This meant that if a particular field were specified as underlined while the character were a signal for bold formatting the bibliography would look like this This is a test of the formatting characters This bug has been fixed in the current version of BioBase so that the bibliography will now look like this This is a test of the formatting characters You need to be careful that you specify all the formatting that might be relevant The control codes are must useful for things like species names and p
3. The final four columns of check boxes are for text formatting The B check box tells the program to put this field in bold text while I and U produce italic and underlined text respectively The P check box tells BioBase that this field should go in parentheses Any combination of these four boxes may be checked for any field The final column of text boxes can contain one of two different sets of information either the punctuation for a particular field or the prefix for that field The label at the top of the column tells which of the two it is currently displaying either Punct or Prefix The punctuation is the string that you wish to be placed bibliography after a field This can consist of simple punctuation or short words the field is only 5 characters long For example if you set the Punct column for the Author fields to be a period and the author of a particular citation is Smith John then in the bibliography the citation would have Smith John added The punctuation is added to the bibliography according to the setting that you select from the Options window if you have the Never Add option selected then the punctuation is ignored If you select Add When Needed then the punctuation will be added to the bibliography if the last characters of the field do not match the characters in the punctuation column Selecting Always Add adds the punctuation regardless of the text in the field To specify the spaci
4. All records in one file X records One file per letter Add Links between pages For HTML files you can specify a variety of formatting options The first option is the font to use when making the bibliography and the font size between 1 and 7 While you can specify any font on your computer the font that a web browser will display will depend on the fonts on the computer with the browser and the settings for the web browser The three option buttons allow you to specify how the records put in the bibliography file The first option puts all the records 28 single file The second allows you to specify how many records should be put into the file before BioBase makes a new file The final option is to have all the records starting with the same letter for whatever field is the one being used to alphabetize the bibliography be in a file producing a file called A html B html etc In the event that you choose to use either of the last two options you can select to have BioBase automatically put links in the HTML for those files so that you can navigate between them more easily Text Bibliography Text Formatting Include Carriage Returns Maximum Line Length 75 If you choose the Text file option the bibliography will only contain the formatting option to put the text of the field in parentheses the P check box on the Edit Style dialog box The other options you spec
5. any records that matched the previous search will be checked for the new search string s You can only search the results of the last search since the program only stores the results of one previous search to conserve memory To search a specific range of records enter the first record you want to search and the last record you want to search in the appropriate text boxes If you type a minimum value below 1 it will be set to 1 automatically and if your maximum value is greater than the number of records in the database then it will be changed to the number of records in the database Unlike the search actions the search location functions are not stored between searches This means that if you repeatedly want to search a given range of records you must enter the search editor to tell it which range to search otherwise the default of all records will be searched Editing a Specific Record You may also choose a specific record number to display and edit To do this you can press Ctrl G or select Goto Record from the Search Menu A dialog box will be displayed where you can type the record number you want to see If there is no record with that number than you will receive an error dialog box Show and Search Result Displays When the results of a search are displayed on the edit screens or the Show All command is chosen from the record menu the program will show each matching record in order You can navigate through this by
6. pressing the OK button on each screen which will save any changes to the particular record and move to the next one You can also move through with the arrow keys Pressing either arrow key saves any changes to the current record and moves through the list of records If you press the Left Arrow then the program will display the previous record that matched the search if it is displaying search results or the previous record in the file if using the Show All command Pressing the right arrow causes the program to display either the next record that matched the search or the next record in the entire file again depending on whether the program is displaying search results or using the Show All command If you press the left arrow while on the first record or press the right arrow button while viewing the last record then you are returned to the main screen Pressing the Cancel button returns you to the main screen without saving any changes to the record you are currently viewing Pressing the delete button deletes the citation you were examining and displays the next record If no records remain then you return to the main screen When you delete a record from a database the information is not actually removed just marked as usable space By default the program will overwrite deleted records as new records are added You can change this behavior with the Options command see Configuration Options below This means that if a record is de
7. Copy Pressing this button copies the information for this record to the Windows clipboard using the report template to format the text This allows you to easily paste this information into word processing software without requiring you to re enter your citation Additionally this button also creates a duplicate of the record in memory which can then be put into different or the same SDB files by opening a record of the appropriate type and pressing the Paste button You can only copy a record into a citation of the same type so you cannot paste information from a journal article into a book reference for example The paste button will only be enabled when there is a reference of the appropriate type in memory This information is stored in memory until you exit BioBase and the information on the clipboard is stored until you copy another item to the clipboard or exit Windows Configuration Options BioBase allows the user to change several options that determine how the program will function The majority of these are accessed using the Options command from the Edit Menu This will present you with a dialog box that allows you to change these options Each of the different options is available by clicking on the appropriate tab to display the appropriate settings Punctuation Never Add to Bibliography Add to Bibliography When Missing Always Add to Bibliography The first set of options determines how the program
8. Eptesicus fuscus some consequences for echo processing J Acoust Soc Am 89 1402 1413 Darwin C 1964 On the Origin of Species A Facsimile of the First Edition Harvard University Press Cambridge The Underline Words Only option specifies that for any fields that have Underlining specified in the style only words will be underlined e g this is an example as opposed to underlining the spaces between the words as well e g this is full underlining This option only applies to the RTF bibliography The option to Update Repeated Years tells BioBase that when there are multiple references with the same author s and year that a lowercase letter should be added to the year of each citation following 21 the first in the bibliography For example if this option were on two references by J Smith from 1999 would appear in the bibliography as Smith J 1999 Smith J 1999a This allows you to refer to such references without confusion and it keeps you from having to manually add the extra letter in your bibliography The records are first ordered alphabetically before the letter is added to the year The extra letter is only added in the bibliography no changes are made to the actual data file Force Chronological Order in Bibliography refers to the ability of BioBase to use the year of publication to order references from the same author even when the year is not the field by which the references are being al
9. Internet or CD ROM databases such as Medline or Silver Platter The custom format is similar to the UNIX and OVID formats but you can specify which fields to include the order of those fields and the tags that identify the different fields The comma delimited format puts each citation on a single line in the text file with each field surrounded by quotation marks and commas separating the different fields A comma delimited text file can be imported in to just about any spreadsheet program allowing you to convert files between even more file formats by using the spreadsheet to save the file in a specific database format if your database can t read any of the other export formats directly For specific information about the different formats including the specific ordering of the fields in the files and the tags used to identify each field open the BioBase help file and search for EXPORT to access this information for each of the different formats Once the records have been exported you open the database to which you want to add the records and choose Import Ctrl I from the File menu if you are importing from a BioBase format file Otherwise you need to use the sub menu to tell BioBase which format you are expecting the import file to contain The program will display a file selection dialog box where you can choose the file that you want to import If you are importing a large number of records or if the file you are adding the records
10. only supports 32 bit windows there will no longer be updates to the Windows 3 x version of the program I will maintain the last version 2 3 1 of the 16 bit version of BioBase on the web site for people to download but there will not be any more changes made to it I am distributing this program as shareware the registration fee is 20 US For more information on registering the program start the program press 1 for help and search for Registering I would also like comments particularly bug reports requests for additions to future versions or criticism especially if it s constructive even if you do not want to register the program I am offering BioBase on an as is basis I do not make any warranties express or implied as to the suitability of this program for a particular use I have made every effort to eliminate any bugs and ensure that the program will perform as explained but I m unable to account for the millions of combinations of hardware and software that exist today I ll be more than happy to help anyone who has problems running the program but I cannot guarantee that the program will perform correctly for any particular individual I have to make the same warning about the documentation and help file for the program I have done everything I can to make them clear and comprehensive but I may missed some options or give unclear explanations Please feel free to contact me at the following address if you have
11. option buttons allow you to search for all the records that are marked for adding to the bibliography all the records that are not marked for the bibliography all the records that are marked for export and all the records that are not marked for export The case sensitive check box functions identically to the one on the Search All dialog box You can also specify to the program to report all the records that do NOT contain the text that you have typed By choosing the check box marked Find Records that Do Not Match Search you can enable this type of searching The AND and OR options function identically with the Not searching as they do with the normal searching For example searching for Smith OR John would report any records that contained one of those two strings After selecting the option to find records that do not match your search BioBase will report matches for records that contain neither Smith nor John Search Multiple Fields The final search allows you to search several different fields for different text Search Multiple Fields is selected with the F7 key Mult on the toolbar or from the Search Menu The dialog box displayed after selecting this choice allows you to put a check mark by each field to mark which ones you wish to search The text boxes next to them allow you to type the text to try and find If the check box next to a field is not selected then the text that is in its search text is ignored You may
12. or specify the format for output from BioBase The first button marked Report generates a report of the type you have specified from the current database The second button allows you to set the Style the formatting options for bibliographies produced by BioBase The final option uses the current Style and database to produce a bibliography See Making a Bibliography for more information The final button brings up the help file for BioBase where you can find more information on the program and its functioning When you start the program you will briefly see the opening graphic which shows among other things the version of the program Since Visual Basic does not automatically correct for variations caused by different screen resolutions I have programmed BioBase to detect the resolution of the screen and adjust the size of the different dialog boxes so that they fit on the screen However I have noticed that on some computers usually running at a resolution of 800x600 in Windows 95 that the program displays incorrectly so that the dialog boxes are so large that their edges are off the edge of the screen If you install the program and this problem occurs choose the command Change Display Resolution from the Edit Menu and in the dialog box that is displayed by choosing this command select the option to have BioBase Shrink Forms This should take care of the problem Entering Records Once the main window is displayed you ca
13. prevent this from causing the data file to expand and take up disk space you can use the Compact Database command on the Edit Menu Selecting this command removes all deleted records from the database decreasing its size Once you do this you will not be able to recover any records you did not wish to be deleted Recovering records simply marks them as active so that they will no longer be overwritten To access this function choose Recover Records from the Records menu This version of BioBase does not ask whether or not you want to recover a particular record it simply recovers all the deleted records in the current database If you have selected Overwrite Deleted Records from the Options dialog box then deleted records will be replaced by new records so you will want to recover a record as soon as it is deleted since it may be impossible to do so later Moving Records Between Databases Since BioBase only allows you to have one file open at a time you cannot move records from one database to another directly What you must do is edit those records you want to copy to another file and click the Export box on the edit screens for those records Then you choose the Export command from the File Menu Previous versions of BioBase could export records in BioBase format only BioBase can export in several other formats to facilitate exchanging files with other database programs Now clicking on Export under the File menu brings up a s
14. some consequences for echo processing J Acoust Soc Am 89 1402 1413 Book This reference type is for citations of entire books For that reason in addition to the standard fields it includes fields for the publisher city of publication and number of pages in the book A sample references is provided below Griffin D R 1958 Listening in the Dark Yale Univ Press New Haven Article Chapter in a Book Chapters from a collection of articles are placed in this citation type Along with the standard fields it has space for the title of the book the editors the publisher the city of publication and the starting and ending pages A sample reference from this type of citation is listed below Fenton M B 1988 Detecting recording and analyzing vocalizations of bats pp 91 104 In Ecological and Behavioral Methods for the Study of Bats Kunz T H ed Smithsonian Institution Press Washington DC Thesis This citation format is used to record bibliographic information on theses dissertations It contains fields to record the institution that granted the degree the type of degree earned e g MS PhD etc and the type of document e g thesis or dissertation etc and the number of pages A sample reference in this format is provided below Burnett S C 1999 A study of the use of computers for data storage Ph D Dissertation The Ohio State University Columbus OH 256 pages Meeting Abstract This re
15. specify with the word and used when there is more than one author By entering all your author editor fields in this format you make it possible for BioBase to make many changes that you would otherwise have to do by hand 22 2 In addition version 3 3 of BioBase supports automatic replacement of repeated author names with a string you specify I added this option because some journals require that multiple references with the same author s do not repeat the author s names instead replacing them with or something similar With this option on BioBase can automatically perform this conversion for you when making the bibliography However this will only work if the author fields are exactly the same including spacing and the initials For instance references with the author field of Burnett S C and Burnett S would not be recognized as matching Only if they are completely identical will BioBase replace them With the default setting two articles from one author would be listed in the bibliography as Lachenbruch P A 1967 An almost unbiased method of obtaining confidence intervals for the probability of misclassification in discriminant analysis Biometrics 23 639 645 1968 On expected probabilities of misclassification in discriminant analysis necessary sample size and a relation with the multiple correlation coefficient Biometrics 24 823 834 Alphabetizing Once the Style is customized
16. to is large gt 200 records then you may want to turn off the overwriting of deleted records so that the import procedure proceeds more quickly When you get files from an Internet database either by e mail or on a disk you can import that information directly into BioBase to save on retyping The specific formats for the different files are elaborated in the help file but the general format of such a file is to have a specific tag that identifies a particular field For example the author s of a citation are often indicated with AU or a similar tag followed by the text for that field The author from a citation might appear like this AU Smith J H The ordering of the fields is not important for the most part as long as the tags identify the fields correctly When importing anything 29 except the comma delimited formats see below BioBase doesn t care which field comes first and in fact the order of the fields in the file can vary between citations and BioBase will not complain However one area that BioBase is currently very strict when importing these types of records is when dealing with information on the source of the citation This information typically consists of one line that includes information such as the year of publication journal title and volume and the page numbers For BioBase to correctly deal with this information you should make sure the file you re importing conforms to the format specified in the hel
17. to your liking you tell the program to make a bibliography by choosing Make Bibliography under the Bibliography menu pressing Biblio on the toolbar or pressing Ctrl B All records that have been marked for adding to the bibliography will be extracted from the data file and put in to either a plain text listing or a file in RTF format depending on the type of output you have chosen from the Options window If you have chosen the Full Rules for Alphabetizing BioBase will alphabetize your records using all of the following rules If this option was not checked then only the first rule will be used 1 If the first fields for two citations are exactly the same then the second field will be used to alphabetize them For example if the authors are the first field and the journal title is the second field in the Journal Article Style then an article by Smith J published in Animal Behavior would be listed before one by Smith J published in Behaviour If a particular record does not have information entered for a field that is listed for adding to the bibliography then that field is ignored and the bibliography is generated using the fields containing at least one character If the field that is blank is the field 24 that is being used to alphabetize the records then the citation will be alphabetized on the first field that does contain text 2 All commas and periods are ignored while determining the correct order For exampl
18. BIOBASE 2 4 The Bibliographic Database for Windows 9x NT 1992 2000 Stephen C Burnett Documentation 11 July 2000 Table of Contents TN TROGUCTIO stad natch sede Cade 1 PROGRAM INSTALIATION cccccececececececeeeceeeeseeeesseseeecensesssseeeseeess 2 PROGRAM OVERV EW 2 How BioBase 4 GETT NG SIARIEC 4 vite conan eae ae eto 7 ne erie 7 ENTERING Records 6 Entering Authors NAMES ela 6 OTHER Fields 7 DEFAULTS 9 CITATION EE 10 JOURNAPARTICI 10 cs devs 10 IN ABOOK cin Ga 10 THESIS Sse E vs 10 MEETING ABSTRACT eles 11 WE Da PAG Bee E 11 QUITTING THE PROGRAM TI Searching for Records 12 SEAIC Ho T la A EAE AEE TEETE
19. EEEE 12 SEARCH ONE snio Skee Aas A a 12 Search Multiple Fieldsi va 12 CLI WOR Sean ANG wannabes SMe E 12 Editing Specific Record 17 Show All and Search Result Displays cccccecececeseseeeeeeeeeeeeeeess 17 FORMATTING eens ee 16 Making A 17 General FORMATTING 19 AUTHORS FORMATTING 22 2 hee 24 Special CHARACTER FORMATIING 2 OTHER Citation OPTIONS 0ccccccececececcececscecucsccucesesucecceceeeeusesesucsecueeaeees 26 BioBase File MANAGEMENT ccccccececececeeeeeeeeeeeseseseseseeuseseeeseeeeess 26 Moving Records Between 27 Custom FORMAT IMPORT EXPORT 2ccccecececcnceceececensececenseceseeeecensecesenteqens 29 Comma delimited IMPORT EXPORT cccccececececeseeceecececesucceeeeeeeeesesueeeeeeess l Copying and Pasting Records cceccecececececececceeecesuceceeeeeessceseseseeseseseses 73 Configuration oe 73 PUNCTUATION 77 MEMORY U SAGE
20. Therefore it wasn t usually necessary to save the changes because they were saved as you worked This is no longer the case because BioBase uses a temporary file to save your changes To be sure those changes get into your main file you should save your work either as you work or when you exit the program Searching for Records Once you have entered records you will often need to edit only those that match certain criteria All three search have some things in common They all allow you to use the Search Editor to specify where in the database to search as well as any actions you should take on any records that do match your search specifications You can tell the program to search all records search a range of records or to search only the records that were successfully matched in the previous search You can choose to have the program simply report matches mark matches for adding to the bibliography or export change matches so that they are not added to the bibliography or exported or you can delete matches BioBase allows three different types of searches to find records that meet your specifications Search All Fields The first type searches every field in every record for the text you enter The dialog box to type the search text is activated by pressing F5 Selecting All from the toolbar or selecting the Search All Fields command from the search menu You can enter two different search strings to find and you may select t
21. ake a bibliography complete with formatted text using an RTF or HTML file that you can import in to your word processor The format of the bibliography and the text formatting are very user customizable I have tried to make the program as flexible as possible but there are so many different official ways of formatting a bibliography in the sciences that I m certain that the program won t work with some styles If when you do find some format that you can t produce I would like to receive information about that format so that I can add it to a future version of the program A sample of the format sent to one of the above addresses would be greatly appreciated How BioBase Works The program currently allows six specific types of citations Journal Articles Books Articles in Books such as a compilation of articles on a common subject Thesis e g a Ph D dissertation Meeting Abstract and Web Pages Each type of citation has slightly different fields in it but all six have some fields in common such as the author title and year of publication Each database is limited to about 2 million records Once you have entered your data you can examine the information in several ways You can have a customized report printed on the main screen to a text file or directly to the printer you can search for specific records using a variety of methods and you can export specified records for importing into different databases Most important
22. any problems or questions about the program or documentation Internet mail will receive a quicker response Ground Mail Electronic Mail Stephen Burnett burnett 33 osu edu preferred Dept of EEOB Or Ohio State Univ stephen burnett alumni carleton edu 1735 Neil Avenue Columbus OH Web 43210 USA www geocities com efuscus biobase biobase html Program Installation BioBase comes with a Windows standard setup program Because this version of the program was written using Visual Basic 6 0 there are more files that must be installed in the correct directories for BioBase to run The setup program does this installation for you allowing you to specify the directory to install the actual application in to while other files such as the DLL s required for the program to run get installed in the WINDOWS SYSTEM directory The setup program also automatically creates a program group and places the icon for the program in that group along with an icon for this documentation file and the help file The program is distributed as a ZIP file with the name BBASE330 ZIP Once you have downloaded the ZIP file decompress the files it contains to a directory on your hard drive and then run the file named SETUP EXE which will be in the directory The program will guide you through the steps of installation asking for the directory to install the program in and copying files to the appropriate directory IMPORTANT NOTE The version of Visual B
23. asic 6 0 used to produce this version of BioBase can be a bit of a problem when installing a program Since it comes with some DLLs that are newer than those included with Win95 during the install you might be required to allow the installer program to update your system files reboot your computer and then run the installer again Be sure to perform all the steps to make sure that your computer gets the updated files As I cannot test even a fraction of the different combinations of hardware and software there is no way for me to promise that this process will not damage your operating system or data files While no one has ever had a complete failure of Windows when not following ALL the steps for the install of BioBase some programs that required the same DLLs as BioBase installs were disabled Make sure you run the installer twice to update all the files on your system Program Overview Once the program has been installed you can start it from the Start menu by using the icon placed there by the setup program BioBase works with six different types of citations journal articles books articles in books thesis dissertations meeting abstracts and web pages Search for help on Citation to find more information on the different types The format of each record is slightly different each containing information that is only relevant to that type of citation The program will use the information you enter about your citations to m
24. ce is extremely large Some dialog boxes cannot be stored in memory most notably the Edit Style and Edit Template dialog boxes so there will be a delay each time one of these windows is shown This delay is unavoidable due to the way that the program has to work with these screens Search Results 75 Edit Screens for Matching Records Display Matching Records Spreadsheet Make Report of Matching Records in Main Window The next options concern the display of search results If the default Goto Edit Screens is chosen then as soon as a search is finished a report will be displayed on the main screen and then the edit screens for the records that matched the search will be shown sequentially so that you can edit the information If you select Display in Spreadsheet as shown above the program will display search results in the spreadsheet window where you can see all the matching records listed and edit only those you wish If this option is chosen the only information displayed on the main screen will be the text searched for and the number of records that matched your search If Display in Main Window is chosen instead then the program will not show the edit screens but it will still generate a report in the main window 6 Bibliography Format Text File unformatted HTML File formatted Full Alphabetizing RTF Formatting Font Arial Font Size 12 MS Word RTF File WP RTF Fil
25. deleted records in the database and report that number in the main window To do this you select the Count command from the Records menu Formatting Output BioBase allows you to freely modify the way that the program displays information This is done two ways modifying the report Template and editing the bibliography Style A report is displayed on the main window whenever the results of a search are conducted or the Make Report function is selected A report can also be sent to a text file or directly to the printer The Template is the information indicating which fields should be included in each report It is usually a waste of time to produce a report using every field especially for long databases as this would become rather time consuming The main screen is also limited to the amount of text that it can actually display about 64 000 characters will fit on the main screen These limitations are imposed by Visual Basic so there is no easy way around them When the screen is full it will not be able to display any more information but the program will still run This means that displaying a Report for even a medium sized file 200 300 records can use up all the text that the main screen can display If this happens you should remove the text from the main screen using the Cut command and have your reports put in a file or sent to the printer You can also display your reports on the spreadsheet window which is capable of disp
26. e The Bibliography section of the window contains three option buttons and a check box The option buttons determine the file format of the bibliographies produced by BioBase An RTF Rich Text Format file is in a format that many popular word processors DOS Windows and Macintosh can read Files in this format can have formatted text such as bold or italic type When this option is chosen the box below the Bibliography section will allow you to choose the options that apply to this type of file HTML is the file format used by web pages and any web browser can view HTML files HTML files will contain the majority of the formatting that the RTF files can Depending on the bibliography format you have chosen the options available to you will differ The check box marked Full Rules for Alphabetizing determines how the program alphabetizes the records while making a bibliography If this option is checked then all three rules listed in the Formatting Output section are followed If this option is not checked then only the first rule is used Selecting this option results in bibliographies with a slightly modified order for the citations but this comes at the result of slower operation Unchecking this box will speed up the bibliography option This option only improves the alphabetizing of records if the citations are being alphabetized by a field such as the Authors or Editors fields that contain people s names Otherwise choosing t
27. e Smith J and Smith J are considered equivalent 3 The word and is ignored when determining the correct order For example Smith J and Jones J is the same as Smith J Jones J This is to prevent the word and which is present in many author listings from affecting the order of the citations in the bibliography This may result in some citations being out of order if the bibliography is being alphabetized by title Using all three rules results in the order of citations being slightly different from the order determined without using these rules but the procedure is slower These rules were designed primarily for use when the Authors or Editors were the first item in the citation If this is not the case then these extra rules will not serve much purpose If you are not alphabetizing by one of those fields or if your are just making a rough draft I would recommend turning this option off since the order of citations may be different then you expect and the speed increase is very noticeable on even moderate 100 records databases For the final draft when the Authors Editors are the first field I turn this option on Extra Fields Keywords Comments Abstract Location Owner Language un Formatting Formatting Formatting Formatting ee au Expand Jo
28. e database and find the records that are marked for deletion it is generally rather small However the advantage to not overwriting is that you can undelete records without having to worry that the record you want to recover has been overwritten The disadvantage is that in this version of BioBase there is no way to specify if a particular record should be recovered so all the records you have deleted will be recovered I recommend keeping this box checked until there is a noticeable slowing in program speed then uncheck this box to speed it back up If working with overwriting off you should choose Compact Database any time you delete a large number of records from the database The third option is to ask for a bibliography name as opposed to giving the bibliography the name of the current file with a new extension for example the file mydata sdb produced a bibliography called mydata rtf If this option is selected you ll be able to specify the name to use for the bibliography file If this option is not selected or if you press cancel when asked for a file name BioBase will assign the file name using the old system The last choice allows you to tell BioBase whether or not it should take information from a file being imported and add that to the 219 author field This option also selects whether or not the default author information is put in the 2 author field as well This is for convenience in importing records without having
29. each screen The first is labeled Add to Bibliography All records with this box checked will be put into a bibliography when you create one The second check box is labeled Export If the Export box is checked when you choose the Export command from the file menu this record will be copied into an external file that you can use to merge the contents of different databases see Moving Records Between Databases below Currently BioBase supports the import export of files in the native SDB file format comma delimited text and several different formats used by CDROM databases commonly available including OVID UNIX SPIRS and a user customizable format that can work with various other CDROM formats Both of these check boxes can be changed any time you are viewing the record or you can have the program change these fields for you based on different search criteria see the section on Searching Pressing the OK button saves the information in the current record to the temp file and returns to the main screen Pressing the Cancel button returns to the main screen without saving the current information Pressing the Left arrow button is equivalent to pressing OK while pressing the Right Arrow will save the current information and bring up a new blank record form of the same type This is useful if you need to add several records of the same type but you don t want to go through the dialog box to choose the record type each time Finally the d
30. elect to use an AND search which only reports matches for records that contain all the text you specify or you may use an OR search that counts a record that matches any of the text you typed as a match The case sensitive check box functions identically to the same box on the other two search dialog boxes The check box labeled Find Records that Do Not Match Search functions identically to the same check box on the Search One Field dialog box Search Editor Each of the three search types allow you to invoke the Search Editor by clicking on the button on the bottom of the search screen The search editor allows you to specify any actions that you would like the program to perform on the records that match your search criteria There are 6 different actions that the program can perform on your matching records 1 Nothing the default 2 Add Matches to the Bibliography 3 Remove Matches from the Bibliography 4 Mark Matches for export 5 Do Not Export Matches 6 Delete Matches The first option specifies that the program report on any matches it finds without changing them in any way Option 2 tells BioBase that every record that matches your search criteria should be marked for adding to the bibliography After performing a search with this option every record that matched the search will now have the check box for Add to Bibliography selected Option 3 performs the opposite function changing all matching records so that th
31. elete button deletes the current record this button is only available if you are viewing a record that has already been saved Defaults If one or more of these fields contain information that is the same for a set of records that you are entering you can save yourself time by having the program automatically enter these common values called Defaults to each new record you create To set up the Defaults select Set Defaults from the Records menu or press Ctrl D A dialog box will be displayed that allows you to modify the defaults You can type text in for each field that you want to have a default value The defaults store the same number of characters in each field as a record You can also choose to have your new records automatically marked for adding to the bibliography or exporting by selecting those check boxes To tell BioBase to use the defaults you have typed in you must select the Use Defaults check box otherwise the defaults will be ignored BioBase creates a default file called BIOBASE DEF as soon as it starts the first time To make changes to the defaults you simply type the new text and press the OK button This will save all your changes Pressing Cancel will return the defaults to their previous values You can also save different sets of defaults so that you don t have to constantly re type the information To save a set of defaults make the changes you want it to have and then click the button labeled Make N
32. ew Default File This will present you with a screen where you can type a 12 character descriptive name for the defaults and an eight letter file name the 32 bit version still requires that the filename be in the old DOS 8 3 format The extension on a default file is DEF automatically so you should not type an extension in this box otherwise your DEF file will not be created Once you have made list of DEF files you may select one of from the list box in the bottom left corner of the Set Defaults screen This list will show the filename and the descriptive name of each DEF file in the directory specified on the Options screen see Configuration Options for more information The status bar will indicate the name of the default file currently selected or None if use defaults is not selected Citation Types BioBase has six built in citation formats for your use The first three have been available since the first version while the remaining three were added in version 3 0 Each citation type has some shared and some unique fields Journal Article This reference type is for citations from scholarly journals and magazines The citation contains all the standard fields along with the journal title journal volume number and starting and ending pages A sample citation in this format is given below Masters W M Jacobs S C and Simmons J A 1990 The structure of echolocation sounds used by the big brown bat Eptesicus fuscus
33. ey are not marked for adding to the bibliography Options 4 and 5 function identically except that they change the status of the Export value for each record The final record allows you to remove any matching records from your database without having to manually delete them This option should be used very carefully One important thing to note the settings you select in the search editor will apply to any further searches you make until you change them This means that if you select option 6 and then conduct a series of different searches on your database every record that matches your search strings will be deleted To prevent such mistakes each search dialog box has a text box above the search editor button that indicates what action will be performed on any matching records If the box is blank option 1 is selected If any other option is chosen then you will be able to tell without having to go to the Search Editor The search editor also allows you to specify the range of record that you want to search You can search all records in the database the default you can search only those records that matched the previous search or you can search a specific range of records where you supply the first and last record number to search Searching within the results of the last search will allow you to narrow your search results down based on a new set of search conditions It doesn t matter which type of search you used for the previous search
34. ference type is intended for abstracts presented at professional meetings As such it has fields for the date of the meeting and the city in which the meeting took place A sample reference of this type is Burnett S C 1998 Differentiating sonar calls of handheld and flying big brown bats Eptesicus fuscus 28 Annual North American Symposium on Bat Research 27 31 October 1998 Hot Springs AK Web Page This citation is intended to store information on the World Wide Web It includes fields for the URL the online format eg www gopher etc and the date that it was last accessed This last field is useful given the rather volatile nature of the Internet and many citation guides indicate that it should be included when making references to web sites A sample reference in this format Smith J 1999 This is my web page Online http www anonymous com j_ smith Last accessed on May 6 1999 Quitting the Program When you have finished working with your database you can exit the program by pressing Ctrl Q or Alt F4 or selecting Exit from the File Menu If your database has never been saved or has been modified since you opened it you will be asked if you want to save the file If the file has never been saved then a file save dialog box will be displayed where you can select the directory and filename for your saved file NOTE Previous versions of BioBase did not use a temporary file to store changes as you worked
35. hat the program can identify where to add remove spaces Finally BioBase can replace the word and with a different character for example changing Smith J and Jones R to Smith J amp Jones R For BioBase to replace and with some other character you must be sure to type the word and in the author field in the first place If the only changes you require in the author fields are of these types then you can enter your author information and have BioBase make any changes You should be sure to include the information BioBase needs to make those changes however BioBase will be able to make changes to a citation with authors listed as Smith J J and Jones R A because this contains periods between initials and it contains the word and so that BioBase knows where to make any changes requested by the user Authors entered as Smith JJ amp Jones RA will not be suitable for modification by the program If you periodically must submit citations with the authors a format that BioBase cannot convert your information to then you will have to enter the records in that modified format For this reason there are 2 author fields for each record One of the most problematic situations concerns the order of the authors names some citation formats require citations in the format of Smith J J and Jones R A while others require Smith J J and R A Jones Unfortunately BioBase cannot change the order of the authors names
36. he import file If the file doesn t follow this format then when trying to read it in BioBase will crash or produce records with incorrect data in them To prevent this from corrupting data I recommend that you test import a few records into an empty database to prevent any data loss At this time there is no way to change the order of records if they all fall on the same line You can save your settings for the CD databases in the same way as saving Style and Default files This allows you to have a variety of different import filters without having to constantly re enter the data for them NOTE When importing from any of these text formats BioBase requires that there be at least two 2 blank lines at the end of the file If these blank lines aren t there then the program will get stuck in endless loop and you will have to close the program Comma delimited Import Export Since the previous versions of BioBase the procedures for working with comma delimited files have been improved in an effort to make them more useful In earlier versions the comma delimited import didn t allow you to specify the order of the citations as BioBase assumed that they were in a specific order This meant that to import these type of records you had to be able to make their order match the one BioBase assumed Now you are able to specify the order of citations in the comma delimited file in the same way as when you specify the order of citat
37. his option may cause the citations to be slightly out of order in the bibliography Generally for rough drafts turning this option off will be correct enough and speed the program up considerably When producing a final draft 77 where the citation order depends alphabetizing names I would recommend turning this option on For a final draft where people s names are not the main factor leaving this option off results in a better ordered bibliography RTF Bibliography The box for an RTF file contains four items a listbox where the user can choose the name of the font to use in the bibliography a text box where the user chooses the size of the font and 2 option buttons to specify the format of the RTF file Versions 1 0 1 5 produced RTF files in a format that had the unfortunate side effect of causing WordPerfect for Windows to crash while trying to open those files I was finally able to fix this problem with no help from the tech support for Word Perfect not that I m bitter for wasting 3 years trying to get their help The program defaults to producing a WordPerfect or WP format RTF file since every program that could open the old format RTF file seems to be able to read the WP format RTF The Word RTF option button tells BioBase to make RTF files in the old format in the event that you have a program that cannot read the WP format RTF file HTML Bibliography HTML Formatting Font Verdana Font Size
38. ho helped with suggestions and bug reports for earlier versions of BioBase Eric Arsenault Florent Bourgeois Andrew Millard Andreas Sprenger and Ric Troyer Hopefully everything that they ve reported to me has been fixed by now I apologize if I ve missed anyone who has provided me with help or comments I m afraid that I don t keep as accurate a record of the email I receive if it s more than a few months old so I may have deleted some messages If that is the case I apologize and hopefully you ll forgive my oversight Finally I would really like to thank everyone who has actually registered BioBase since it s gratifying to know that people actually find my work to be worthwhile Introduction BioBase is a database designed primarily for recording bibliographic data for scientific or other types of references The program allows you to enter different citations and output a bibliography complete with text formatting I wrote BioBase using Microsoft Visual Basic for Windows 6 0 and so it requires the appropriate run time files from VB6 I have included all the appropriate files in the distribution for the program since there are so many different ones I decided it was more important to have all the files in one place even if that made the download a little slower Previous versions of BioBase were available for both 16 and 32 bit versions of Microsoft Windows but because I began to use some 32 bit only tools and because VB6
39. hrases in different languages that are supposed to be displayed in a different font usually italics than the rest of the text in a given citation Other Citation Options Date Format mmm yyyy For web page citations many journals require that the date the page was accessed be included in the bibliography However they often have different specifications for how the date should be formatted in the bibliography You can specify a wide variety of different date formats in the Style screen for the web page bibliography Simply specify the format including any required punctuations such as or etc and BioBase will use that format when adding the record to the bibliography The example shown above would use the three letter abbreviation for the month mmm the day with no leading zero and the full four digit year yyyy To display the date as x x xx you could specify the string as m d yy BioBase File Management BioBase tries to maintain as small a file size as possible by using records that have been marked for deletion as the space for new records This way the file will not increase in size until new records have overwritten all the current deleted records If you do not choose to have the program overwrite the deleted records see Configuration Options 27 below then new records are added to the end of the file automatically This means that any records that are deleted will continue to take up space To
40. ify in the Style are ignored in a text bibliography but you can set such options as line length and whether carriage returns should be added to the file Other Options Make Imported Fields Lower Case Overwrite Deleted Records Ask for bibliography name Add Import Default to 2nd Author You can select to have a few other options for BioBase The three check boxes at the bottom of the options screen allow you to set how the program behaves in certain situations The first option applies to importing records from other databases This option tells BioBase to automatically make all imported fields have only their first letter capitalized This is especially useful when importing records from CDROM and Internet databases where fields are often given as all capital letters This saves you from having to go in and manually edit each field The second option labeled Overwrite Deleted Records determines how BioBase adds new records to the data file If this box is checked then new records are first placed in spots where a record had been deleted before adding them to the end of the file If this box is not checked then new records are added to the end of the file automatically Overwriting deleted records generally results in smaller files because the only way to remove a deleted record is by choosing Compact Database from the Records menu While there is some speed decrease when overwriting is enabled the program must scan through th
41. in this manner For this reason the second author field was added so that you could type the authors in a format that BioBase could not produce automatically If you only use one ordering system for your authors then you do not need to access the second author field at all To access the second author field click the mouse on the option button labeled Second Author in the lower right corner of the record entry screen The Author field will now serve to enter and display the text that is in the Second Author field for that particular record To return to viewing the First Author field click on the option button labeled First Author The setting you choose when you specify the formatting for the bibliography will tell BioBase which author field you want to use when making a bibliography see Formatting the Bibliography for more information Other Fields After the author s there are fields for the Year of publication Month of publication and the Title of the article book The fields that come after those depend on the record type that you are adding The Journal citation has fields for the Journal Title Volume Number Starting Page and Ending Page while the Book citation has fields for Publisher and City of Publication The Article in a book has fields for the Book Title Starting and Ending Pages Volume number Editors City of publication and Publisher Each of the three other types of citations has fields that also apply only to
42. ions in a custom import format F Record Type _ Degree Authort Document Type Author r Number of Pages Year F Meeting Title a Month F Meeting Dates na Journal Title Z Date Accessed Book Title Online Format Publisher hz F Keywords is City Comments m F Editors ho Abstract F Volume Location is Volume Number Owner F Start Page Language End Page Format Comma Delimited Cancel Export All fields The figure above shows a sample of settings to import a comma delimited text file from another application Each field is selected for inclusion with a checkmark and a number is entered to indicate the order that the fields are placed in the file BioBase requires that the numbers be sequential so that if there is number 10 and 12 there has to be a field numbered 11 If this is not the case you will receive an 22 error message and you will have to correct the numbering Additionally only one field can exist within each set of quotes in the text file For example if the start and end page are included as a single field in the file 1 10 for example there is no way for BioBase to separate those and they would have to be placed in one field and separated manually This means that there can be no more than one field with a given number otherwise the import and export procedures can crash For the record ty
43. it See below and in the help file for more information on the other citation types The bottom of the screen for each of the six citation types contains six fields that are not generally included in the bibliography Keywords Comments Abstract Location Owner and Language These are fields for you to enter extra information about the citation that will make it easier for the program to perform a search as well as letting you store more data The Keywords field is 255 characters long it is intended for a list of individual words that relate to this record The Comments field is also 1000 characters long this field can be used to store a short note or description of the citation The Abstract field is the longest 2500 characters it can be used to save relevant parts of the citation s abstract or to add more comments or keywords The location is intended to store a string that indicates where this particular citation may be found such as library call numbers or the name of the folder that the copy is filed in The owner field is designed to hold a short string that identifies who is working with possesses this citation this is useful if several people are using the same database and need to know who has a particular book etc The language field is simply intended as a place to indicate the language of the citation again this is most useful in a database that is accessed by several people There are also two check boxes at the bottom of
44. laying about 16 000 records avoiding the much smaller limitation of the main window However the template settings do not affect the fields shown on the spreadsheet currently all fields except for the abstract are shown in the spreadsheet You can choose to view a record by double clicking on that record on the spreadsheet When you select Edit Template from the Record menu or the Options screen you will see a dialog box with a list of all the possible fields Putting an X in the box next to a particular field will tell BioBase to put that field in the next report fields that do not exist in a specific record will be ignored when making a report e g a journal does not have a city field The format of the final report will be based on the template Currently each field in a record is placed on a separate line with a blank line between records and if a field is longer than the screen is wide then the text continues off the edge of the screen Making a Bibliography The bibliography is even more customizable than the report When you choose to edit the style you are presented with the Style editing screen There are several separate sets of check boxes divided up by the purpose they serve Each of the different sets of boxes is selected by choosing the appropriate tab for the citation type you are editing Because of Visual Basic s limitation on how many items can appear on a single dialog box clicking on the tab labeled Other Cita
45. leted you should recover it immediately to prevent it being used to store new data see the section on recovering records to see how You may also want to see information about every record that you have entered into your database so far You have two options to achieve this The first is to select Show from the Records menu This will present you with an edit screen for each record so that you can modify any aspect of each record The second option is to choose Make Report from the Report menu or by pressing CtrIl M What this does depends on the state of the menu items on the report menu cine Bibliography Help Edit Template Make Report Ctrl M Report on Screen Reportto Spreadsheet Reportto File Reportto Printer If Report to Screen is checked then the information is displayed on the main window Choosing Report to Spreadsheet tells the program to display all the records in the spreadsheet window If Report to File is marked then the report is sent to a file with the same name as the current file with an extension of RPT If the file is not saved then the report if named UNTITLED RPT If there is already a file with the same name in the directory then the extension is changed to RO1 RO2 etc Report to printer sends the information to the print spooler The format of the report is determined by the settings in the Template see Formatting Output below You can also have BioBase simply count all the non
46. ls each of which provide information about the current SDB file or the settings for BioBase The first cell indicates the number of records present in the current file This number is based on the size of the file indicated in the second cell so if you have any deleted records in the file this number will include those records The third and fourth cells list the currently selected STL file and DEF file names respectively The final cell indicates the format for the bibliography either RTF HTML or Text Toolbar Gl Aline Pe New Open Save Options Add All One Mult Report Style Biblio Help The Tool bar consists of a series of buttons that allow you to access common commands without having to use the program menus The first three are for creating opening and saving SDB files The fourth button Options accesses the options dialog box where you can specify how BioBase should function see Configuration Options for more information The fifth button allows you to add a new record to the current database The next three are used for the three different types of searches The first of these searches every field of every record to see if it matches your search criterion The second search type searches a single field that you specify and the final search type searches for matches in multiple different fields See Searching for Records for more information The next group of three allows you to obtain
47. ly the program will produce a bibliography of the citations you select using the bibliography format that you define yourself Getting Started The program consists of one main window with a toolbar and status bar and several auxiliary dialog boxes The main window is a place for the program to report on its progress such as indicating how many records were exported Checking the Log Screen option on the File Menu can save the information on this screen If this option is selected indicated by there being a check mark next to the menu item then the program will save all the information in the main window when the program exits The information will be saved to a text file with the same name as the database you were working on when the program was terminated with an extension of LOG If there is already a file in the directory with that name then the extension will be changed to 101 102 etc For example the database TESTING SDB will produce a log file named TESTING LOG Note that the log file is only created when the program is terminated so any text that you remove from the main window will not be in the log You can edit the text using the commands from the Edit menu The program functions with the clipboard in the same way that other programs do however only text can be pasted on to the main window Status Bar 71 records 364 92 STL RNCSE DEF Default Bib RIF The status bar contains five different cel
48. n open a database Ctrl O or Open on the toolbar or begin adding records to a new one You can add a record by pressing Ctrl R on the keyboard selecting Add from the toolbar or choosing Add Record from the Record menu This will present a dialog box allowing you to choose the type of record journal article book article in a book thesis meeting abstract or web page that you wish to add You will then see a data entry screen a slightly different one for each type of record where you can enter all the relevant information about the citation You should make sure to type the information in each field as you want it to be displayed in the bibliography with some exceptions noted below For example if you want the authors names to be displayed in the format Smith J H then you have to type it that way in the Author s text box The first exception applies to all fields you do not have to specifically type the punctuation that you want applied to the end of each field BioBase has the ability to add punctuation you specify to the end of fields when it creates the bibliography Entering Authors Names The second exception applies to the author fields BioBase can automatically perform several conversions on your authors when making a bibliography For example it can remove periods from the authors names It can also add or remove spaces between the authors initials although to do this the initials must have periods after them so t
49. ng after a particular punctuation you need to indicate to BioBase by using a special character The character is the pipe character and for every pipe in the punctuation box BioBase will add space For example to have the punctuation consist of a period and two spaces you would type without the quotes This allows you to simply type for example a comma in one box and that is the only punctuation that will be added to the field the other blank spaces in the box will be ignored Punctuation is added outside any parentheses that you have added using the P formatting option The Prefix column contains the string of characters that you want the program to place before the field in the bibliography This is useful for such things as designating the abbreviation to go before a particular field Such as no or num for the number field Prefixes are always added to the bibliography unless the Prefix column for a field is empty The spacing for prefixes is specified in the same way as the punctuation using the character to indicate how many spaces should be put in the file The prefix field can be up to 20 characters long instead of the shorter length allowed for the punctuation As with the punctuation trailing or leading spaces are ignored The Edit Style screen only displays one set of characters at a time so to switch between punctuation and prefixes you click on the option button for the type of information yo
50. o have only records that contain both strings using the AND search option or records that contain either string using the OR option Checking the case sensitive will only report a match if the record contains a string that contains a substring that exactly letter for letter matches the string you typed For example if you type John and select case sensitive then Smith John would produce a match but Smith john would not Once the search is completed the output will depend on your selections in the Options screen If you chose report to screen the main window will display a report If you have chosen report to spreadsheet you will be presented with a spreadsheet showing all the matching records You can edit individual records by double clicking on the row containing them Any changes you make to the records won t show up in the spreadsheet until you click the Update button If you have chosen to have the edit screens shown then you will be able to move through all the edit screens for each matching record Search One Field The second search type only checks one particular field in each record The Search One Field is chosen from the Search Menu or with the F6 key or by selecting One from the toolbar The dialog box you see will allow you to type in text to search for and the field that you want to be searched As with the Search All Dialog you can type in two strings and select either AND or OR logic The final four
51. ose two fields are on the same line of the import file or that they should go on the same line of the export file While the order doesn t matter for importing it is vital that all fields that are present on their own lines have a separate number from other fields in that reference type or that apply to all fields It is however acceptable to have two fields in two different citation types with the same number such as the starting page in the Journal and Article in a Book citation formats The checkbox next to each of the fields indicates whether or not that field should be included when exporting records and whether or not that field is present in a given import file The last field box labeled Field Tag indicates the tag that is used to identify each of the fields Each field needs to have a unique tag although the fields that apply to only one type of record may use the same tag for different fields Because this version of BioBase allows importing and exporting multiple citation formats as opposed to only journal articles as earlier version were limited you need to specify a tag to indicate which type of record is being imported The tab labeled Citation Tags allows you to specify a tag for the reference type field along with the text that identifies each of the citation types On that screen you also specify the default import citation type the type of citation that BioBase will assume if the citation type is not indicated by t
52. p file If your file is different you can try using the custom format to import the files Custom Format Import Export Select Fields to Use Field Order Author 2 Title Year Keywords sS Comments je Abstract 7 Language fo BIOBASE CD Defa Save Settings The custom format allows you to specify which fields are going to be imported for each record and it also lets you specify the tags that the text file contains that identify the different fields Since there are multiple citations types with some overlap between fields the first of the pages on the dialog box to specify the user format is for fields that are contained in all the reference types This means that any changes made to this first section labeled For All Records will apply to every citation 50 In contrast there are separate tabs for each citation type that allow you to specify fields that apply only to that type of citation or that it shares with some but not all of the other citation types This means that you have to be certain that none of the fields on the specific reference type screens have the same number as the fields for all records unless those fields are on the same line The number next to each field is currently used by BioBase to determine the order of fields when exporting records and if two fields have the same number BioBase interprets this to mean that th
53. pe field there are additional options that have to be set to correctly import your records When you click on the additional options button labeled next to the record type field check box BioBase displays a second dialog box Citation Codes OF x Enter Citation Codes Default Citation Code Journal Article Book Article in Book Thesis Meeting Abstract Web Page Cancel As with the custom import formats this window lets you select the code that determines which type of citation is being read in You can also specify a default to use if there is no citation code present in the file If there is no citation code BioBase can only read in files containing the default citation type When you have finished setting your settings for the file pressing the OK button saves the format information in the BIOBASE CM file and opens a file dialog box to choose the file to import or automatically exports all marked records to an export file depending on which option you have chosen If you decide you don t want to import export the a file pressing the cancel button at any time stops the operation but may cause you to lose any changes you made to the import format 75 Copying and Pasting Records If you are only moving one record between files or if you wish to make multiple copies of the same reference in a single file there is an additional option available Each data entry screen has a button marked
54. phabetized This was usually only a problem if the year of publication was very late in the bibliography Turning this option on means that BioBase will order citations by year if they have the same information in the first field you ve specified to alphabetize them BioBase allows you to save different style information in STL files so that you can select from several different options depending on the format you need for a particular bibliography To save a different style make any changes you wish and click the Save Style button This will display a dialog box that allows you to enter a 12 character description for the style as well as an 8 character filename the Win95 version only allows the old DOS format 8 3 filenames The extension to style files is always STL so do not type this extension or any other in the filename box it will be added automatically If you do type one your STL file will not be created You should also be certain that you do not enter a filename that already exists or the old STL file will be erased BioBase does not check to prevent any filename conflicts You may choose from the list of available STL files by selecting one from the list box in the bottom left corner of the dialog box Each file will be listed in the listbox alphabetized by filename The listbox also displays the description of the file The status bar at the bottom of the main screen will display the description of the style file currently selec
55. ted for use Author Formatting Conjunction Use as Typed Replace And with Remove Spacing Use as Typed No Spaces Smith Use Spaces Smith Remove periods from Authors Repeated Authors should be replaced with This is also the location that you select any changes that you want applied to the authors and editors fields such as removing periods changing spacing of authors initials or replacing with some other character phrase It is important to note that BioBase can only make some of these changes if you have entered author editor information in the expected format Specifically for removing periods or changing the spacing of the authors initials BioBase assumes that the authors initials are indicated by the presence of periods If you do not have periods after your author initials BioBase will not be able to change their spacing The same applies to replacing the word and with a different phrase if the word and is not included in your author information then BioBase cannot change those records In general BioBase assumes that you enter author editor information in roughly this format Smith J A and Jones M B or J A Smith and M B Jones or some similar format Basically there should be a period after each initial in an author s name the spacing of the initials doesn t matter as BioBase can change that to whatever format you
56. tion Types accesses the Style information for the Thesis Meeting Abstract and Web Page citations Below is a sample from the section for formatting the style of the journal article bibliography I B U P Punct Author Year h2 2 Month Title Journal Title 6 1 Volume e E Number M Pages Checking the box next to a certain field tells the program to include that field when making a bibliography However if a field exists in more than one record type and you want it to be included for any record with that field then you have to check the box for each citation type For example checking the author box in the Journal section will not cause the author to be added for the other record types unless you check those boxes as well The column of boxes labeled Place is simply to keep a list of numbers indicating the order that the different fields will be added to the bibliography A place value of 1 means that a particular field will be the first one used for the bibliography If you are not adding a particular field to the bibliography as indicated by the fact that the first check box with the name of the field is unselected then you do not have to change the numbers in the place column BioBase will simply use the next highest numbered field that you have selected to include in the bibliography
57. to manually enter the author information in the second author field 29 40 Directories Data Files g data files sdb files Bibliography g data files sdb files STL Files g winuti DEF Files g winutil CD Files g winuti JNL Files jg winutil Starting with version 3 3 of BioBase you can specify the directories where the program should store your data bibliography and configuration files You can specify different locations for each of the file types When the program first starts these values are all set to the same directory in which the biobase exe file resides Finally this screen contains three extra buttons labeled Template Style and Defaults Selecting one of these buttons will allow you to edit these options without having to go through the menu commands For More Information If you need more information on how to use the program check the help provided with the program for the subject If the information is not there then feel free to contact me at the addresses located at the beginning of this document and I ll try to work through any difficulties you may be having
58. u wish to modify These option buttons labeled Show Punctuation and Show Prefixes are in the bottom right corner of the Edit Style screen General Formatting BioBase allows you to choose which of the two author fields should be used to make the bibliography and lets you set whether the bibliography should have any indentation or if it should be double spaced These options are chosen by selecting the General Formatting tab of the Edit Style Screen to show the options below 20 Use First Author Field Use both Start and End Page DoubleSpace Underline words only Indent Citations Indent First Line Indent after First Line Update Repeated Years Force chronological order in bibliography These options apply to both the RTF and text bibliographies but not the HTML files In the text bibliography the file will be double spaced using hard returns and the indentation will be done with tabs When the Indent Citation checkbox is not marked the two option buttons below it are inactive and they are ignored when the bibliography is made Choosing indent first line causes the first line of each citation to be moved in 5 spaces while choosing indent after first line causes all lines after the first to be indented A bibliography produced using the settings in the picture shown above would look like this Masters W M Jacobs S C and Simmons J A 1990 The structure of echolocation sounds used by the big brown bat
59. ub menu with several different choices The first choice is to export in BioBase format this is the same as exporting in previous versions and is accessed by pressing Ctrl E on the keyboard This tells BioBase to make a new file with the same name as the current data file and an extension of XPT If there is already a file with that name in the current directory then the extension is changed to X01 X02 etc For example the file TESTING SDB will produce an export file named There also UNIX SPIRS OVID Comma Delimited Custom user defined export formats When exporting in one of these other formats the name of the XPT file produced by BioBase is different to indicate which file format is being used The filename of the exported file is the same as the SDB file name and if the file is exported in a non BioBase format then a comment is added to the file name to identify the format of the file For UNIX SPIRS files the comment Unix format is added to the filename Similar comments are added for each of the 28 other file names The extension is still XPT and the same rules apply if the file name would conflict with a file that already exists in the directory Each of the other export formats produces a text file with specific formatting that applies is used by BioBase or other programs to identify which fields are being listed The UNIX SPIRS and OVID formats are two types of files produced by
60. urnal Titles Remove Periods from Journals 27 You can also choose to have other fields added to the bibliography Clicking on the Extra Fields tab displays a box that allows you to pick any of the extra fields Keywords Comments Abstract Location Owner and Language that you would like added to the bibliography and the formatting that you would like applied to them Selecting one of these fields adds it to every record type not just one These extra fields are added at the end of the bibliography in the order that they are listed above and this order cannot be changed You are not required however to add all of the fields any combination of them may be put in the bibliography BioBase also allows you to specify whether the journal titles should be entered into the bibliography as you typed them or whether they should be expanded In this case BioBase will query you for each new journal title as to the name that is typed into the file and the name you want put into the bibliography For example if you type Anim Behav you could specify that BioBase should put Animal Behaviour in the bibliography Similarly you can tell BioBase to remove any periods from the journal titles before adding them to the bibliography Special Character Formatting This form allows you to select special formatting be applied to words with special code characters placed in front of them BioBase allows four control characters
61. will add punctuation to the bibliography If Never Add is selected then no 24 punctuation will be added all the citations will appear exactly as you typed them in If Add When Needed is selected then if there is punctuation defined for a certain field punctuation is set on the Edit Style screen see Formatting Output below it will be added if the field does not already have that punctuation For example if the punctuation for the Journal Author field is set to a period and the text in one citation is Smith J then BioBase will put Smith J in the bibliography If the text is Smith J then BioBase will not add any punctuation Note that all the punctuation is added to the end of the field Memory Usage Remove Dialog Boxes from Memory Keep Dialogs in Memory faster The tab labeled Memory Usage allows you to change the amount of memory and resources that the program uses Selecting Remove Dialog Boxes from Memory will significantly decrease the memory and resources used by the program This will however slow the program down since the dialog boxes must be loaded from disk each time they are displayed If you choose instead to have the dialog boxes stored in memory the program will run faster at the cost of a larger memory usage In general I don t store the boxes in memory unless I m machine with a lot of free memory i e no other programs running or else a lot of RAM or if the speed differen

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