Biota: The Biodiversity Database Manager
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Version History
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Version History: Biota Version 1.6.1 Version 1.6.1 replaces 1.6.0 as the diskette distribution version for new users of Biota, incorporating all changes in intervening updates (see below). All Biota Data Files created under previous versions of Biota are compatible with Version 1.6.1, which fixes a few bugs in 1.6.0. There are no new features. Bugs fixed in Biota 1.6.1. A problem with using 20-character Record Codes in the Collection and Locality tables was fixed (shorter codes caused no problems). A bug in the Loan Date entry field that did not allow days beyond 12 was fixed; this error has been present for a long time, but no one noticed it since all dates were entered normally when the Today button was used. A problem with finding existing records using the Import Editor with the Update option, when the Determination History option was enabled, has been fixed. |
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Version History: Biota Version 1.6.0 New Image Formats and Compression Options. With Version 1.6.0, Biota now offers crystal-clear, multi-format, cross-platform image handling on both Windows and Mac OS. On both platforms, Biota can now import and export images in ten different formats, including JPEG, BMP, PICT, Photoshop, and TIFF (GIF's can be imported, but not exported), whether compressed or uncompressed. In addition, a large number of image compression options are now available on both platforms, for compressing any existing Biota image, or for on-the-fly compression when pasting images from the Clipboard. All this is made possible by the integration into Biota of a third-party plug-in for 4D called QPix (http://www.escape.gr/), which accesses Apple's QuickTime, the premiere image-handling tool for Windows as well as Mac OS, to handle all these tasks. To enable these new tools, the Biota installer automatically places QPix plug-in files in the Win4DX or Mac4DX folder on your hard-drive. In addition, however, you will need QuickTime 4.x (or 3.x, but fewer formats are supported). If you do NOT use images, you need NOT have QuickTime installed; you can still use all non-image tools in Biota normally. Macs normally have QuickTime installed with the operating system, but many Windows users will need to download and install QuickTime 4.x from Apple's website (http://www.apple.com/quicktime/download/index.html) if they wish to use Biota's image tools; there is no charge for basic QuickTime. When you install QuickTime, be sure to choose the Full Installation option. The image screens themselves are identical to Biota 1.5.0 (which introduced a brand new set of image comparison and analysis tools), with the exception of new features in the Image Input screen (accessed from the Species Input screen): (1) the Save Image to Disk and Load Image from Disk buttons now offer multiple image formats in the navigation window. (2) To paste an image from or copy an image to the Clipboard, you now use a special miniature image window (rather than the main image display window). (3) A Compress button offers a large variety of compression options, for any image displayed in the Image input screen. (In addition, Mac users can continue to compress images on the fly while pasting from the clipboard; see the Manual, p. 352-3). (4) A new button, Check QuickTime, tells you what version of QuickTime you have installed. In addition, the Export Images tool (Im/Export menu) now supports all QuickTime image formats for batch export of image files, and allows you to create a folder to hold them. NOTE: With ten image formats (all in principle inter-convertible by QuickTime, and thus by Biota), two platforms, and six flavors of Biota, it has not been possible to test every possible combination and every transformation of image formats. Beta testers and I have checked JPEG, Photoshop, and PICT pretty thoroughly, and know of no problems. But I urge you to make frequent backups, check results carefully, and let me know if you encounter problems. WARNING: Importing (or pasting in) and saving very large images in Biota may damage your Data File. Biota is not intended for storing and displaying large images (> 1 MB, compressed). If you need to keep a high resolution image for publication or for other purposes, keep it in its own file and create a lower resolution version of the same image to display in Biota. There is little to be seen on a computer screen that cannot be displayed in an image of a few hundred KB, maximum, and Biota can compress images using JPEG or other efficient compression formats, on Windows as well as Mac OS. On the other hand, there is no limit to the NUMBER of reasonably-sized images you can keep in a Biota Data File, besides disk space the 132 GB Data File limit imposed by 4th Dimension, Biota's programming environment. Automatic Image Linking by the Create Web Pages Tool. As a result of the integration of new image handling capabilities (see above), the Create Web Pages tool (Export menu) now automatically produces JPEG image files and links them to the text pages. (Previously, PICT images files were created which had to be converted to GIF files with other software&endash;a nuisance!) Find and Replace Can Add or Change a Prefix or a Postfix. This new feature works even for Record Codes and other Key values. Previously, the Find and Replace tool (Special menu) was able to find Current Values using a wildcard search (see the Manual, pp. 220-225 and Supplement 1, pp. S43-44), but the entire Current Value was replaced by the New Value. In Biota 1.6.0, Find and Replace now works with the wildcard character (@) in either the Current Value or New Value fields, which means you can replace any part of a character string with any other character string in any alphabetic field. (The Help button in the screen provides examples.) If you select a Key field (e.g. [Specimen]SpecimenCode, [Species]SpeciesCode, [Genus]Genus, [Family]Family, [Personnel]ShortName, etc.) Biota reminds you that you must alter or add a prefix or postfix to already-unique values, retaining the unique portion by using the @ in the New Value field. Biota then automatically updates all links to child tables (lower taxon tables, Collection from Locality, Specimen from Collection, Determination History from Specimen; Notes, Aux Fields, and Images; all linked person fields from Personnel). In addition, where necessary, Biota updates Host links if the Host Specimen is changed, and updates Synonymies is Species Code is changed. Automatic Entry of Valid Species Code in the Import Editor. If you import new Species records using the Import Editor (Import by Tables and Fields in the Im/Export menu) with either the Import New Records or Merge Imported Records option, and you select the Species Code field but not the Valid Species Code field, Biota will inquire whether you would like the Species Code values copied into the Valid Species Code field. Automatic Recording of Determination Histories by the Import Editor. If you update existing records using the Import Editor (Import by Tables and Fields in the Im/Export menu, with the Update Existing Records option), and you update any field that changes the determination of a Specimen record--either directly or by changing a Species or Genus record (see the Manual, Chapter 19, and Supplement 1, p. S51), Biota will automatically create Determination History records to document the changes. To enable this feature, the Determination Histories box must be checked in the Preferences screen (Special menu). An alert box warns you that the records will be created; if this is not what you want, Cancel the alert and disable Determination Histories in the Preferences screen. Memory Feature and Date Options in the Export Specimen Flatfile Tool. The Export Specimen Flatfile tool (Im/Export menu) now remembers the fields you select, between uses within a Biota session. The [Species]Section field has been added (an inadvertent oversight). The Collection Date fields ([Collection]DateCollected and [Collection]DateCollEnd) can now be selected individually. If you select both, Biota offers you the option of either keeping them separate or combining them into a single Date Range (the previous default). Species Code Option in the Export Taxonomic Flatfile Tool. If you include the Species level in the option screen for the Export Taxonomic Flatfile tool (Im/Export menu), a checkbox is enabled to allow export of the Species Code. (Previously, only species names were exported.) This option facilitates combining the output from this tool with Auxiliary Fields data and other exported output. Locality Name Option in the Lookup Collection tool. When you use the Look Up Collection button (Specimen input screens), you can now find Collection records according the Locality Name of the Locality record to which the Collection records are linked. (Previously, you had to know the Locality Code.) Additional Wider Output (Record Listing) Screens. If your monitor is at least 800 pixels wide (or you can set it to display 800 pixels width), Biota 1.6.0 presents wider output screens than previous versions for the Determination History and Specimen Series output screens (to match the wider Specimen, Species, Collection, and Locality screens introduced in Biota 1.5.0). In addition, the Var Fields tool (which allows you to change the fields shown) has been added to the Specimen Series output screen. Bugs fixed in Biota 1.6.0. A Windows user discovered that if more than 256 values are found by the Look Up Collection tool (launched with the Look Up Collection button in Specimen input screens) or the Look Up Localities tool (Collection input screen), only the first 256 values are displayed. (This is not a problem with the Mac version.) Since this is a bug in the 4D popup menu tool for Windows, I have substituted (on both platforms, for consistency) my own scrolling display that has no list length limits. If more than 25 values are found when you click a selection button in either of these screens, a scrolling list appears instead of the popup list. Choose the value you want by clicking on it. If you need to see the scrolling list again, click the button again. A programming error previously made it impossible to use the Find and Replace tool for Auxiliary Fields and Notes (see Supplement 2, p. T-7). The bug has been fixed. |
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Version History: Biota Version 1.5.0 Version 1.5.0 replaced 1.4.0 (Windows) and 1.3.1 (Mac OS) as the diskette distribution version for new users of Biota, incorporating all changes in intervening updates (see below). Wider Output (Record Listing) Screens. If your monitor is at least 800 pixels wide (or you can set it to display 800 pixels width), Biota 1.5.0 (and later) presents wider output screens than previous versions, for the Specimen, Species, Collection, and Locality tables. The extra width allows you to read even the longest Record Codes in full in the output screens, as well as certain other long fields (e.g. Locality Name). Sort No Longer Lost When Records Deleted. In previous versions, if you sorted records using the Sort Editor in an output (record listing) screen, the sort was lost if you then deleted one or more records in the selection. In Version 1.5.0 and later, Biota maintains the sort even after record deletion. A blank row now appears where each deleted record formerly appeared in the sort, to confirm the deletion. (The blank row disappears as soon as you sort again or re-display the records from a menu.) New Image Comparison and Analysis Tools. A completely new set of tools was added in Version 1.5.0 to help you work with Images stored in Biota Data Files. If you need to compare images among species to speed identification of specimens or you use images in teaching or presentations, you should find these tools useful. You must have a monitor capable of displaying at least 600 x 800 pixels to use these tools. (Biota's original image screens are still present, if your monitor is smaller.) To access these Image tools, display the Species records you wish to work with in the Species output screen. Then click the Page button in the Display Images button group. (The other button in the group, Scroll, presents the original Biota Image output screen.) To learn how to use the new Image tools, click the Help button in the option screen that appears when you click the Page button, or the Help button at the bottom of the Page Images output screen itself. Note: All selection and zoom buttons in the Page Images screen require only a single click, not a double click. New options for Export Collections or Localities x Species Table. In Version 1.5.0 and later, both of these tools (Export menu; see Manual pp. 469-472 and Supplement 2, pp. T16-T18) offer options to include Collections or Localities with no Specimens (blank rows) and/or Species with no Specimens (blank columns). These options allow you to maintain the same columns and rows in exported text files for different subsets of your data, regardless of row or column content. Certain kinds of data analysis and spreadsheet manipulations are facilitated by this option. Additional Tools for the Synonymy System. Two new tools were added to the Synonymy system that are useful in generating taxonomic catalogs and in routine maintenance of synonymies: Find Species with Junior Synonyms and Find Junior Synonyms (both in the Find menu). You can search either the Species Record Set or all Species records. A related (existing) tool, Find Orphan Junior Synonyms, is an option in the Find Orphan Records tool (Find menu). Site Field in the Collection Table Enlarged. The [Collection]Site field was enlarged from 40 to 80 characters in length. A zoom button appears next to the field in the Collection input screen to display long values. This change has no effect on values for this field previously entered. (Note: This field is re-namable.) Quotation Character Warning in the Import Editor. Under certain conditions, when you save a file as Tab-delimited Text in MS Excel, Excel adds quotation characters (") to cell values that include commas or periods (but does not display these characters when you re-open the text file in Excel!). Biota 1.5.0 and later checks for quotation characters in the input stream when you use the Import Editor (Manual Chapter 26; Supplement, 1 pp. S57-60; Supplement 2, pp. T18) and presents a warning when if finds them. You can choose either to continue the import (including all quotation characters) or to abort the import. A Help button in the warning screen explains how to clean the text file and details the conditions under which Excel plays this dirty trick. Additional Component in the Auxiliary Fields Maintenance Utility. The Auxiliary Fields Maintenance Utility (Special menu, Maintenance Utilities) searches for and corrects linkage and other anomalies in Auxiliary Field tables that may arise from interrupted saves or imports. In Biota 1.5.0 and later, a new component checks for duplicate Record Code/Field Name combinations (ambiguous records), and helps you choose which duplicate to eliminate. Sound Error Feedback for Series Find and Series Find and ID Tools. When you use the Auto Accept feature of the Find Specimen Series and Find and ID Specimen Series tools (Series menu; see Manual pp. 234-242) and Biota cannot find a match for a Specimen code you have entered, you will now hear two beeps (or whatever alert sound you have selected in the operating system)--along with the onscreen error message. The feature is intended for those who use barcodes, and thus tend to miss error messages when they take their eyes off the screen. Several bugs were fixed in Version 1.5.0. The most significant is a potential conflict in date import options (registered users received a message about this problem early in 1999). Previously, if you specified that dates in the text input file were in International format, but the operating system was set to American format--or the reverse--the dates were not imported correctly. Dates are now imported according the to format you specify, regardless of the current Date Format setting of the operating system. A bug in the Make Guest Collection Records tool (Special menu) was fixed. Relatively minor bugs fixed include further stabilization of the progress indicator system, stripping of leading blanks in the Import Editor (see the Manual, p. 487), updating changed Specimen Codes in Determination History records, and several minor Windows report format problems. |
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Version History: Biota Version 1.4.0 Find and Identify the Specimen Record Set. In Version 1.4.0, a checkbox option was added to the Find and Identify Specimen Series tool (Series menu; see Manual, pp. 234-242) to indicate that you wish to apply a new determination to each record in the current Specimen Record Set. If the Determination History system has been enabled (see the Manual, Chapter 19), a record of the change, who made it, and when, will be created for each Specimen record in the Record Set. This new option is especially useful when you split a species, and need to re-determine one group of records while leaving the others untouched. Find Orphan Junior Synonyms. Providing enhanced support for the Synonymy System (Manual, Chapter 20; Supplement 2, pp. T15-T16), Version 1.4.0 offers this new tool at the bottom of the popup list of table names in the Find Orphan Records command (Find menu). An orphan synonym is a Species record for which the Valid Species Code does not correspond to any Species record in the Data File. Find Specimen Records for the Determination History Record Set. This new tool (Special menu) allows you to find all the current Specimen Records that correspond to a set of Determination History records. The principal use for this tool is to locate Specimen records for which the determination has been changed since a certain date, or by a certain person, or in a certain way (in the Species record, Genus records, Series, etc.). The corresponding tool, Find Determination History Records for the Specimen Record Set, has been available since Biota was first released (Manual, p. 375-377). Mailmerge-ready Format Option for Herbarium Label Export. In Version 1.4.0 (and later), you can elect to export the text for a set of herbarium labels to a tab-delimited text file, with fields as columns, records (individual labels) as rows. A header row is included, with field names. This format is directly readable by MS Word as a mailmerge data file, allowing you to design your own herbarium label layouts, manipulate the exported information, or add more information (such as exported Auxiliary Field data for the same records). This format option is offered in a special screen once the Herbarium Label export is launched. You must check the "Save label text to disk file instead of printing" checkbox in the Even More Options screen (see Supplement 2, p. T12). For more information on the Herbarium Label tool, see the Manual, pp. 255-258; Supplement 1, pp. S44-48; Supplement 2, pp. T10-T12. Export Specimens Examined List. In previous versions, if you wished to export a Specimens Examined List for the Specimen Record Set, you had to establish the corresponding Species Record Set as well (Manual pp. 463-470). In Version 1.4.0 (and later), this is no longer necessary. You can elect to base the List either directly on the Specimen Record Set, or base it on all specimens for the species in the Species Record Set. Version 1.4.0 eliminated a number of bugs. The most significant was a bug in the Update Existing Records option for the Import Editor; because of a field-length incompatibility in the code, several long fields in the Species table, plus [Locality]LocalityName, were not being updated. This problem has been fixed. A problem with the handling of subspecies and varieties by the Export Web Page tool has also been fixed. For Windows users, problems with Biota not finding the Input.4fi and Output.4fi ASCII map files while importing or exporting from text files have been eliminated; the installer now places these files in the Windows (system) folder, where Biota looks for them. In addition, minor bugs have been fixed in Print Locality; Print Collection; Print Loan Report (Windows); updating the [Loans]Borrower field by changing the Short Name in a Personnel record; and use of Show Synonymy after manual updating of Valid Species Code in the Species input screen. |
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Version History: Biota Version 1.3.1 Version 1.3.1 replaced 1.2.1 as the diskette distribution version for new users of Biota, incorporating all changes in intervening updates (see below). Image Link Option for Web Pages. In Version 1.3.1 (and later), an option in the Create Web Pages tool (Export menu) lets you choose how Species Images are treated in the web pages. Biota can either place the images "in-line" with text on Species Web pages (the default, as described in the Biota Manual, pp. 480-481, and Supplement 1, pp. S55-S56), or, alternatively, create hyperlinks on Species pages to images placed individually on separate Image Web pages, each launched in a separate window. The latter strategy is recommended for large image files, especially color images, which take a long time to display when several are placed on the same Species page. A dialog screen offering these options appears when you click the Include Images checkbox in the Create Web Pages setup. Other Changes in Version 1.3.1. Version 1.3.1 eliminated startup problems experienced by a few users, and incorporated a more reliable algorithm for displaying progress thermometers. A new utility (which you will probably never need) was added to the Maintenance Utilities screen (Special menu) to clear the arrays that control the progress thermometers. Bugs in the Synonymize, Record Code Prefixes, and Create Web Pages tools were fixed. |
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Version History: Biota Version 1.3.0 Data Export Options. In Version 1.3.0, two new features were added for exporting quantitative data files, enhancing Biota's interface with statistical and analytical software. The new Export Localities x Species tool is similar to the existing Export Collections x Species tool (see the Biota manual, pp. 469-472), but creates abundance or incidence matrices for Species in Localities instead of Species in Collections, based on the Species, Specimen, Collection, or Locality record set. A new checkbox option for both tools instructs Biota to export the data matrices in Cornell Condensed Format (required input for commonly-used statistical programs such as CANOCO and DECORANA), with several options for creating the required species and sample abbreviations. Both tools can export data in EstimateS format, as well. Progress indicators and abort options were added to both tools for large matrices. Image Zoom Windows. To accommodate large format, high-resolution images, Version 1.3.0 offers zoom windows for viewing single images at full size. (The window is 768 by 576 pixels, corresponding to the PAL video format.) To display an image in a zoom window, click the small zoom button in the lower right corner of the standard image window, which is accessed from the scrolling Image list in the Species input screen (Biota Manual, pages 350-351). To close a zoom image window, use the close box. Because each image zoom window is opened as a separate Biota process, you can open as many a like and close them individually when no longer needed. Synonyms. In Version 1.3.0 (and later), if you have enabled the Show Full Synonymy checkbox in the Preferences screen (Biota manual, pp. 385-388), clicking the Specimens button in the Species input screen with the record for a senior synonym displayed presents an option window allowing you to display Specimen records linked to all junior synonyms, as well as those linked to the record displayed. Other Changes in Version 1.3.0. A message window was been added to the relational algebra tool (Record Set Options Screen, Biota manual, pp. 13-15) to indicate how to display the result set. A bug affecting certain saved Aliases was fixed. Some minor bugs in the Herbarium Labels and Species Labels tools were fixed. |
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Version History: Biota Version 1.2.x Version 1.2.1 updated and corrected a minor bug in the Specimen Loan System in Version 2.1, corrected Help text for the Change Creator Type tool (Mac only), and added messages for Client/Server implementation (Biota4D only). Version 1.2.2 added a button in the Locality input screen for converting feet to meters (elevation or depth), added a Record Set option to the Find Valid Species command, corrected a bug in Valid Species input for carried Species records (the value previously had to be entered manually), and corrected some minor cosmetic problems. In addition, in Version 1.2.2 a new option was added for on-the-fly input of Linking field values (indicated by a double-bordered entry area in Biota input screens) that allows you to override the wildcard lookup of parent records. Version 1.2.3 incorporateed several significant improvements for non-U.S. users, non-English language users, and users of the Windows versions. All "high-ASCII" characters (characters with diacriticals and others) are now treated correctly when using the Import Editor or export tools on either platform. The non-U.S. date limitation described in the Manual and Supplement has now been completely eliminated. In Ver. 1.2.3, you can have your OS (Win or Mac) set to either International date format (dd/mm/yyyy) or U.S. format (mm/dd/yyyy); Biota Data Files remain completely cross-platform compatible and backward-compatible. Several new options and features have been added to the Herbarium Label tool. In addition, a number of minor bugs and some problems with Windows reports and labels were corrected in Ver. 1.2.3. Version 1.2.4 added Search Editor options for searching on the content of Notes. A warning now appears if you repeat enter a value for Locality Name that is already in the database. Field length were increased to 80 characters for the following fields: all four AuxFieldValue fields; the [Locality]LocalityName field; and in the Species table, SpeciesAuthor, SubspAuthor, VarietyAuthor, and CommonName. A"zoom" button appears next to each of these fields in input screens to display long values. This version corrects a serious error in the Export Web Pages tool that arose in Version 1.2, and a bug in the Import Editor (inappropriate error comments) that was introduced in Version 1.2.3. Version 1.2.5 added only one new feature, and was otherwise a refinement of 1.2.4 . The new feature was an additional export option for the Export Collections x Species tool. This option creates text files that can be direcly read by EstimateS, the freeware application (by Robert K. Colwell, author of Biota) for the statistical estimation of species richness and shared species from specimen-based sampling data. You can learn more about EstimateS and download a free copy of the software and User's Guide from http://viceroy.eeb.ucconn.edu/estimates. The layout for standard Locality reports were redesigned in Version 1.2.5 to include Locality codes. In addition to some obscure minor bugs corrected in Version 1.2.5, two more significant problems (for some users) were fixed. Record Code Settings for automatic entry of record codes are now saved correctly between Biota sessions (reversal of settings was a bug since 1.2, but only reported recently; settings worked correctly within a session). The option for saving herbarium label text to disk files (new in Version 1.2.4) now works correctly any number of labels. |
