BioBase - The Bibliographic Database for Windows

BioBase 3.4 - The Bibliographic Database for Windows Win9x/NT

View User Manual (PDF file - requires Adobe Acrobat Reader 4)

The newest version is 3.4.5, which can only be downloaded as a full install. I've tried to make the changes useful along with fixing some bugs that people have pointed out to me. As always, if you have any comments, feel free to e-mail me...

New Version Notes

This is a copy of the text file that comes with the program...

BioBase v3.4.5
11 July 2000

This is version 3.4.5 of BioBase - the Bibliographic Database for Windows 9x/NT. This file replaces version 3.3.X of BioBase which has been available for the last five months.

The program was written with Visual Basic 6.0, and it requires the Visual Basic runtime files to run. The appropriate DLL files are all included with the archive, so you don't need to download any extra files.

There have been some issues with installing programs written with VB 6 on machines running older versions of Windows 95. Check the documentation that came with the program (bbase34.pdf) for more information BEFORE YOU TRY TO INSTALL THIS VERSION

To install the program, unzip the files to a temporary directory and then run the file called "Setup.exe" in the temporary directory. The setup program will ask you to choose a directory for installation and then it will copy the files to their appropriate places on the hard drive. It will
also set up an icon on the Start menu.

Changes made to version 3.4.5:

BUG FIXES:

1) The routines to save user CD files was incorrectly reading and saving files, sometimes leading to a crash because of a bad file name. Fixed.

2) The routine that adds the letter to the year of multiple citations from the same author(s) in the same year wasn't always detecting the first citation it should have marked. Fixed.

3) The tab order on the screens for import and export of the custom format were not correct. Fixed.

4) For Articles in Books, the report was ignoring several fields from the template, so that they were never displayed. Fixed.

5) When creating a new style, BioBase wasn't setting the date information for Web citations. Fixed.

OTHER CHANGES AND NEW FEATURES

1) The comma-delimited import and export now allow you specify the order that the fields should be in.

2) I've changed the custom import procedure to allow them to read more types of import tags (such as the tags with "%" used by the Refer format).

3) I added the ability to copy a citation from the data entry screen. The copy button copies the the reference to the clipboard (using the template format) for pasting into word processing programs etc. Additionally, the reference can be pasted into BioBase, allowing you to overwrite or repeat references without having to manually re-enter the information multiple times. See the help file and documentation for more details.

4) The defaults can now be added to the second author field as well as the first. This setting can be selected from the options menu.

Changes in version 3.3.1:

Bug Fixes:

1) When trying to export a custom format, the initial procedure that loaded the dialog box was erasing the CD file by accident.

2) When making an RTF bibliography, if there was formatting for the special characters (@ etc) and on the field that contained a special character, the field was ok, but the words with the special character had only the formatting for that character, ignoring the formatting for the field in general (for example if the field was underlined and the special character was italics, the field would be underlined but the words with the special character would only be in italics).

3) The alphabetize procedure was only going to the first two fields in the stl to alphabetize the references.

4) The expand journal title option wasn't working because I was setting the expanded journal title incorrectly, so that the bibliography ignored it.

5) The choice of whether or not to use the first author field in the bibliography was not being saved correctly in the STL file.

6) The HTML bibliography now actually uses the font selected by the user.

7) I fixed it so that the RTF and HTML bibliographies don't add extra punctuation to the fields that already have it, including recognizing that ? and ! are valid replacements for a ".".

8) I fixed the punctuation procedure that was incorrectly counting the number of tags on HTML fields that had them so that it wasn't punctuating them correctly when the field ended with a tagged character.

9) I fixed the HTML bibliography so that it included the extra fields (comments etc.)

10) When importing using the custom format, some fields might not be read correctly if they had the "wrong" type of characters. For example, the year field might be ignored if it contained letters in addition to numbers. This problem should no longer arise when importing fields that are on their own line, but in files where multiple fields are on one line, there may still be problems (which are inherent in trying to have BioBase import the correct information, and
is not a bug in my program per se).

11) Style files were sometimes being saved without the information needed for BioBase to read the version used to create them. This means that the automatic conversion routines may not work with STL files because of the missing information.

Other Changes:

1) BioBase now asks for a name for the bibliography before it makes it. This option can be changed by using the Option button on the tool bar, and turning of the option to "Ask for
Bibliography Name". If this option is turned off, the name of the bibliography file will be the name of the SDB file with the appropriate extension (.RTF, .HTML or .TXT). You can
also hit "Escape" or the Cancel button on the file dialog box, and BioBase will assign the name in the same way.

2) BioBase now makes a temporary file when ever you open a file or create a new one. This means that if you make changes to the file and don't save those changes, then you will lose them. This also means that when opening a large file, there can be a noticeable delay as Windows copies the file to the temporary file.

3) On the option screen, under "Directories" you have the option to specify the directory where your data files and the various files used by BioBase will be saved. These default to
the same directory as the main program file.

4) I added the new fields (and those that were missing) to the custom import/export functions. I modified the form to allow you to specify each of the fields that apply to a specific citation type using a tag strip, with one tab for each citation type. In addition, there is now a tag to identify which type of citation each of the imported records is. You can also specify the default type of record that BioBase should assume if that citation type tag is missing.

5) I added the new fields to the Comma-Delimited export and import functions so that you can export those fields. The fields that you choose to have added to the comma-delimited export file are saved in a file called BIOBASE.CM. This file is saved in the same directory
as you have specified for the CD files.

6) I added functions that check to see if the fields being exported to a comma-delimited file have any quotation marks in them. Since this is the character that indicates the end of a field, it cannot be anywhere except between the fields. Any double quotation marks are replaced with a single quotation mark (') so that the punctuation is at least similar.

7) You can now have BioBase automatically replace repeated authors with a string of your choice. This is due to the fact that some journals do not print the author(s) names if they are repeated more than once (usually replacing them with "------" or something similar). See the documentation for more information.

8) You can have BioBase automatically add a lower case letter to the year field of a citation that is from the same year and has the same author(s). For example, Smith, J. 1999 would become Smith, J. 1999a if there was another citation by the same author in 1999. The references are ordered alphabetically before adding any letter to the year. This change only applies to the bibliography, the data in the SDB file isn't changed. This information is specified in the Style.

9) You now can specify that in the bibliography, underlining should only underline words, as opposed to underlining the words and the spaces between them as well.

10) I added the ability to specify the format for the date field (in web page citations) to be added to the bibliography. You can specify this in the Style for the online citation format.

11) Added more options for the HTML bibliography. The bibliography can now be a single file with all the references, a user-specified number of references per file, or one file for each letter of the alphabet. For the last two cases, you can choose to have BioBase can also automatically add links between each of the different pages to allow for easier navigation. All of these options are controlled from the options screen

12) The prefix fields were increased so that they are 20 characters long for each of the fields.

13) The prefix and punctuation now use spacing specified by the user. In each of the fields, each space is indicated by the character "|". To specify punctuation of a period and two spaces, you would enter ".||" in the punctuation box for that field on the Style screen.

14) You can now force chronological ordering of your bibliography. This means that even though you may be putting the year field at the end of the bibliography, you can have BioBase order the records in the bibliography based on their year of publication. This maintains the correct ordering when the year is not in the first few fields for alphabetizing.

15) The Style now gives you the option to add only the starting page of a reference.

16) When using the "Expand Journal Titles" option, once you began making the bibliography, there was no way to cancel it. Now you can cancel it and tell BioBase to stop expanding the journal titles by hitting the cancel key or "Escape" whenever it presents you with a dialog box.

17) Changes to the STL file format mean that once you open an old format STL file in the new version of BioBase, it will be converted to the new format and will no longer work with old versions of the program. See important notes section above for issues with converting the older format STL files.

18) I added the ability to specify the font size in HTML bibliographies. The acceptable range is between 1 and 7.

19) Added a button for editing the bibliography style to the toolbar.

20) The bibliography format is specified on the StatusBar (as either RTF, HTML or TXT).

Changes made to version 3.0.3

1) The SDB file format has CHANGED. This means that once you open a database with this version of BioBase, you won't be able to open it with older versions! If there is enough demand for it, I could add the ability to have the program save in older file formats, but at this point, that doesn't exist.

2) The style format has also changed. The program automatically updates your STL files if you were using the last versions of BioBase (v2.3 or later). If your STL files are
from an older version, they will need to be deleted and then recreated.

3) The format of the default files (.DEF files) has changed. BioBase does NOT convert these files, so you have to DELETE them before running BioBase, otherwise, when you go to add a file, the program will crash because it reads the information incorrectly.

4) I added three different citation types. See the help file or documentation for details.

5) I added a tab strip control to the Config Screen to make it easier to use.

6) I found an error in the procedure used to make the report on the spreadsheet. FIXED

7) I changed over to VB 6.0. Since I'm no longer making a 16-bit version, I changed the name of the program to biobase.exe instead of biobase32.exe.

8) Pressing the update button on the spreadsheet when only one record was displayed caused the program to crash. FIXED.

9) Changed the punctuation procedures so that any punctuation is added after the use of parentheses for a given field.

10) I added animations to the search/bib making dialog just for eye candy. I included the search.avi and filemove.avi files with the program, but it they aren't there, then the program just doesn't try to load them up.

11) Added three new citation types (thesis, meeting abstract, and web page). Updated all the search procedures to search the new fields associated with these new citations.

12) For the web page citation, you can enter "today" in the date accessed field, and BioBase will automatically update the field with the current day's date when the record is saved.

13) In the web page citation, when the user double-clicks on the URL in the form, it opens the appropriate browser and pulls up that page (however, this doesn't seem to work under Windows NT, and it doesn't even always work on Win 9x machines for some reason).

14) I made it so that if the user is looking at the edit screens for a search result, and deletes one of the records, they can scroll back past that record and see the ones before and after it. Previous versions of BioBase wouldn't let you get past a record that you deleted while viewing
search results.

15) If the program had created a temporary file and the user ran the Compact Database command, BioBase would crash due to an error in the procedure. FIXED

16) I changed the procedures to automatically resize the forms at different resolutions so that the fonts are changed from bold to normal when the forms are being made smaller, since this makes it easier to read those forms.

17) I added the Number of Pages field to the book citation.

18) Made it so that the user can specify the amount of space to put after a field's punctuation. The character to indicate a space is '|'. See the help file and documentation for more info.

19) I added a tab strip control to the edit style screen. Since there are now six different citation types, I wasn't able to get all the controls on one form (VB limits the number of
controls a form can have). You have to click on the tab labeled "Other Citation Types" to get the screens to let you edit the three new citation style information.

20) I touched up the documentation and converted it to an Adobe PDF file to make it more portable. The file is now called bbase30.pdf.

Changes made in version 2.3.1

1) I added a tool bar and and a status bar. Both of these are specific to Win95 only, so they can't be used by 3.x users. The status bar displays the number of records in the file, the size of the file in KB, the name of the Style selected for
the bibliography, and the name of the defaults file.

2) Bibliographies can now be produced in HTML. They have access to the majority of the formatting available to RTF files and they can be directly viewed in a web browser or placed on the Web. A new section has been added to the options screen to allow you to specify the font for this type of bibliography.

3) I modified the behavior of the gauge when making the bibliography. Instead of having it display the current record number (which caused it to jump around in an irritating manner, it now increments once for each letter as it moves through the file. It doesn't move as quickly, but it gives more indication of how much progress has been made.
It still moves through the number of records when searching through the database.

4) When displaying records on the grid, if there were any newline's added (by pressing CTRL-ENTER)in any of the fields, the fields behind those for that particular record
wouldn't be displayed. I added a function to remove the newline's from the keywords and comments fields since those are the most likely to have them.

5) I fixed the problem with using the spreadsheet to view the report. If you were viewing the report, edited a record and hit the update button, the spreadsheet was cleared and no records were displayed. Now this works correctly.

6) When searching only a range of records, selecting either of the boxes to enter the range of records automatically switches to searching within a range. This way you can't
enter a min and max search value and then forget to select range.

Changes in version 2.2.3

1) BUG FIX: When running under Windows NT, the program would crash on exit due to a bad hWnd value. Fixed.

2) BUG FIX: If the user did a search on a file with no records (or a new file created when the program started) the program crashes with an invalid property value error. Fixed.

3) BUG FIX: The saveas function wasn't always saving the file. Win95 wasn't always properly releasing control of the file, so it couldn't be closed. Fixed

Changes in version 2.2.0

1 - progress bar now displays the progress of searches and bibliographies.

2 - user-defined import formats can now be saved in ".CD" files.

3 - BUG FIX - fixed a bug in the user-defined import that ignored any text that should have been put in the journal field.

4 - BUG FIX - fixed a bug in the report function. Certain fields were being ignored in the report to screen, file or printer, even though those fields were selected in the template.

5 - BUG FIX - if you ran a search and then began a second search, but pressed the cancel button before the search was begun, the program would just display the results of the
last search.

Changes in version 2.1.0

1 - Fixed a bug in the import functions - when the program imported a file it wouldn't set the file version, meaning that every time the program tried to open a file with imported records it would say that it had to convert it to the new BioBase format.

2 - I modified the import functions so that fields that begin with all capitol letters can be converted to lower case automatically. You can tell the program to do this by choosing "Options" from the edit menu and selecting "Make Imported Fields Lower Case". I also fixed a bug in the UNIX-SPIRS import that caused some fields to be truncated.

3 - I increased the speed for making the bibliography. The biggest gains occur when you are only using some of the records in your database, but even when making a complete
bibliography, it proceeds somewhat faster.

4 - BUG FIX - when you imported a file and then quit without saving it, you got an error because the program had the wrong directory information for the temp file.

5 - BUG FIX - The import procedures were adding the defaults whether or not the user wanted to when importing one of the text formats. I made it check for using the
defaults before it imports, now.

6 - I fixed one of the problems with the searches - when searching a range, the program was setting the range to be the maximum of the search minus the minimum, meaning that the searchlist was being set to being one record smaller than the true range (e.g. if min=100 and max=110, the range was set to 10, not 11 like it should have been.

7 - I added a spreadsheet form to the program, so that the you can see all your records reported in an abbreviated format. You can double click on the record of your choice
and the program will automatically go to that record for editing. The spreadsheet can be kept up at all times, so that you can refer to it while working. There is an update button on the spreadsheet form to allow you to bring up the newest information. The spreadsheet can also be used to display search results or as a place to display the report. To set the spreadsheet as your default method for viewing search results, choose "Options..." from the edit menu and select display "Search Results in Spreadsheet".

8 - Changed the "Edit Configuration" command on the Edit menu to the "Options" command.

9 - I fixed the problems with the AND / NOT searches when using the Multiple Search - it had the OR and AND mixed up for the NOT searches.

10 - Added context-sensitive help.

11 - I fixed the searches using the and/or and not options. For the F6 (search one) search, the code was reversed so an OR search did an AND and vice versa.

Changes in version 2.0.0:

1 - Found out why the RTF files produced by BioBase would make WordPerfect for Windows crash and gave users the option to produce files that are compatible with WP. (I don't look at this as a bug in my program, since every other program could open the RTF files fine! It didn't help that WP tech support couldn't help me in 3 years, either! Not that I'm bitter, no sir...but I digress...)

2 - Provided more import/export options, including some CD-ROM/Internet database formats, a user-controlled format and comma-delimited text import/export. This should make sharing information in SDB files much easier and allows importing records to save typing time. NOTE: WHEN IMPORTING FROM ANY OF THE NEW FORMATS, BIOBASE REQUIRES THAT THERE BE TWO (2) BLANK LINES AT THE END OF THE FILE OR ELSE IT WILL GET CAUGHT IN AN ENDLESS LOOP! I know this is a bug and I'm working on it, but this program has gotten such featuritis that I decided it would be better to release this version and not delay it any longer. I hope y'all don't mind. (:

3 - I added the ability of the program to recognize special control characters ("@", "*", "^" or "#") and change the formatting of specific words that are preceded by those characters. You can specify different formatting options for each code as well as which codes to use in the first place. This is useful to have BioBase automatically reformat special words (such as species names or Latin phrases) that need to display differently from the text around them.

4 - I added a second author field. Some users had requested that BioBase be able to change the order of initials etc. in the author field to conform to different journal styles. Unfortunately, this is not an option, so I added a second field so that you can type the two main formats you use and tell BioBase to use one or the other depending on which format you need. I know it requires extra typing but until every journal accepts one format for citations, these sorts of things will happen.

5 - The buffer size is now no longer under user control - it defaults to 1 record in memory at a time and it can't be changed. This may seem inefficient, but it was necessary to prevent some problems.

6 - The program allows more user control when searching for duplicate records. You can specify which citations to delete etc...

7 - I attempted to make the program work independently of the resolution of your monitor. For the most part, this works fine, but in some cases (which so far all seem to occur while running under Win95 in 800x600 mode) the resolution does not change correctly, so I've added the ability for you to change the resolution the program displays at manually.

8 - I changed the lengths of several of the fields - specifically, the Abstract, Comments and Keywords fields are all now longer than in previous versions. See the help file for the specifics.

9 - The program now allows you to specify more information about the formatting of the bibliography, especially the author fields. You can change the format of the author fields by clicking the Extra Options button on the Edit Style screen.

10 - The BIOBASE.INI file is now stored in the Windows directory. If you want to keep your old settings, just copy the INI file to the c:\windows or whatever directory you have windows installed in. Unfortunately, the Win 95 version stores the same information in the Registry file, and there is no way to import those values in your old INI to the registry easily. If you are comfortable editing the registry by hand, you can just edit the Registry to make the settings conform to what you used to have. The STL files are still kept in the BioBase directory.

11 - Several bugs were fixed in the search functions that would cause them to ignore matching records under certain conditions.

12 - The status of the report output (whether reports should go to the screen, a file or the printer) was working strangely, since the menu where you were supposed to have one of these items selected defaulted to having all 3 checked! I've fixed this now, and the information is now stored correctly in the INI file

13 - Win 95 native format program. The program works the same as the Win 3.x version, except for differences that are a result of the differences in Windows. For example, the main screen in Win 3.x can only display about 32000 characters, while the same screen in Win 95 can display about twice that many characters, but this difference is entirely a result of the change in Windows versions.

14 - A bug that showed up while displaying Articles in Book format citations was fixed. This bug caused the information in the city and editor fields to be reversed each time the citation was viewed/edited.

For New Users

What exactly is BioBase? BioBase is a bibliographic database for the various flavors of Windows. It allows you to enter the information on your references and then use that information to produce a bibliography/citation list in the format you specify. Currently, BioBase supports six main citation types: Journal Articles, Books, Articles/Chapters in Books, Theses/Dissertations, Meeting Abstracts, and Web Pages. Each of these citation types has several fields in common (Author, Year of publication, Keywords etc.) as well as some that are specific to that citation type. BioBase also allows you to import your citations in several different formats, including comma-delimited text and some formats used by online article databases or CD-ROMs (e.g. Silver Platter, MedLine etc.). In addition, you can specify an import format that coincides with an online database that isn't directly supported by BioBase.

The program can be customized to produce a bibliography that conforms to almost any format, and can make bibliographies in text format or RTF format or HTML. RTF and HTML formatted bibliographies can contain text formatting such as bold and italic text. The RTF format can be read by most Windows word processors and some Mac word processors as well, while the HTML format can be read by many newer word processors (as well as web browsers). The bibliography format is very user-customizable, and different formats can be saved so that you do not have to repeatedly make changes to produce your output in different formats.

The program can search through your data files in several different ways, allowing you to find specific citations quickly and easily. Searches can use "AND" or "OR" logic and you can have the program automatically perform some actions on the citations that match your search criteria, such as marking them for adding to a bibliography or deleting them from the data file.

For more information, I recommend checking the documentation (available online in Adobe Acrobat 4.0 format) or downloading the program and viewing the documentation and help files included with the program.

Download BioBase v3.4.5

Since Geocities has increased the quotas for all its users, I can now the files for download on my site. I have also found at least one extra place to put them so that you have an alternate download site. If you find that Geocities is having problems with the download, please try the alternate site. If that doesn't work, contact me, and I'll see if I can't find another place to put the files.

Note that SDB files created with version 3 cannot be used by earlier versions of BioBase (i.e. 2.5 or earlier).

This version of BioBase now comes with an installer program. This is necessary because Visual Basic requires so many files including several different DLLs that must go in your Windows\system directory.

The links below are to a couple of different sites on the web. I'll also try to get the archive uploaded to some of the online archives such as WinSite as soon as possible. Please let me know if you have any problems getting the program from any of these links.

Once you download the program, unzip the archive to a temporary directory and then run the "setup.exe" program to install BioBase to a directory of your choice.

There will be no changes made to the Windows 3.x version of the program, but it is still available for download, if you do not have access to a machine running a more recent version of Windows.

last updated 11 July 2000