Specify Download and Installation
Specify is available in two versions--Full and EZDB--for Mac OS X, Windows, and Linux computers. The Full version is recommended for most situations; it requires the additional installation of Oracle's MySQL database software. MySQL and Specify may be installed on the same workstation for users only on that computer, or a workstation with MySQL and Specify may be configured for access from users on a few additional computers, or MySQL may be installed on a dedicated server computer hosting MySQL for access from multiple Specify workstations.
Specify EZDB has the same code and functionality as the Full version, but it will automatically install MySQL in the background as part of the Specify installation process. Specify EZDB is recommended for small collection databases, which will be managed by only one or few users on a single workstation. Specify EZDB databases cannot be accessed from any other computer. EZDB is also useful for trial installations as it eliminates the need to install MySQL.
To consider institutional options for deploying MySQL, please see:
Both flavors of Specify, Full and EZDB, use the Java 7 Runtime Environment or "JRE" which enables Specify to run identically across Windows, Linux and Mac platforms. For Mac users, Java 7 requires an Apple computer with an Intel processor and Mac OS 10.7.3 (Lion) or above. Specify does not use the Java web browser plug-in. The Specify 6.5 installer puts Java 7 into the Specify program files directory on your workstation. If your systems administrator prefers to install Java 7 at a system level, Specify will detect and use the system copy. Linux workstation users need to independently acquire the Java 7 JRE; it is not included in the Specify Linux distribution.
For new installations of the Full version of Specify, the Oracle MySQL database manager must first be downloaded and installed. The MySQL Database Server Community Edition (free and open source) is available from Oracle at http://mysql.com/downloads. The Windows MySQL installer "MSI" file includes both 32-bit and 64-bit versions of MySQL. Once downloaded, the MySQL installer software chooses the version appropriate for your version of Windows.
Windows users should use this document as a guide for installing MySQL:
For Apple Mac OS workstations, MySQL is supported by Oracle for Mac OS 10.6 (Snow Leopard) and above, but because Java 7 requires Mac OS 10.7.3 (Lion) or above, Specify requires the Mac OS 10.7.3 or newer. Mac users should use this guide for installing MySQL:
Note that for full Specify installations on Windows workstations when you install MySQL you will be asked to specify a MySQL database "root" user password. In Specify's documentation we refer to the MySQL "root" user the 'Specify IT User." For full Specify installations the Specify Setup Wizard requires the root account password in order to set up a collection database and create Specify manager and user accounts. (For EZDB installations, where you do not separately install MySQL, the Setup Wizard will not require a MySQL database root user name or password.) The Mac OS installation of MySQL also has a user account called 'root' but the Oracle Mac MySQL installer does not ask for a password--MySQL is installed without a password on the MySQL root account. A password must be added, the document "Installing MySQL on Mac OS X for Specify" explains how to do that using a Mac OS terminal window.
(On shared or dedicated MySQL server computers, Specify does not require MySQL 'root' user access. The Specify 'IT User' in that case is a MySQL account with root-level privileges only for the Specify collection database being managed.)
On workstations, to install the full version of Specify, after you have MySQL installed and running, or to install Specify EZDB without a separate MySQL installation, download and then run the Specify installation package for your desktop platform. Download links to Specify installers are below.
Once Specify is installed, but before it can be used to manage collection data, there is an additional preparation step--running the Specify Setup Wizard. The Setup Wizard adds Specify's data tables to the new database and configures the initial database setup in several ways based on information you provide. The Collection Setup Wizard (SpWizard.exe) is included in the Specify 6 installation package and it is put into the Specify program installation "/bin" directory. Before setting up Specify for an actual, production database, read the Specify Collection Setup Wizard step-by-step guide linked below. In it you will find several configuration choices which determine how your collection's data will be represented within Specify. Those choices require some prior consideration.
Some software installation and Setup Wizard options may seem complicated or obscure. If you do not have local technical support for installing software or would just like to confirm your choices, contact us at the Specify Helpdesk at: (785) 864-4400, firstname.lastname@example.org. We would be happy to advise on the various options and walk through the steps for installing and evaluating Specify.
Software Applications in the Specify 6 Installation Package
||Specify 6 application (uses the Java JRE small memory model, best for most users)
||Specify 6 application (uses a 1 GB JRE memory model, for better performance if you have 2 GB or more of RAM)
||This is Specify's database backup and restore tool, for site administrators.
||Specify's version of iReport for creating and editing label and report formats for printed output
||The Specify Setup Wizard creates the first new, empty, Specify collection database in MySQL. Additional collection databases can be added later from within Specify.
||The Import File Splitter reduces large Microsoft Excel spreadsheet files into separate files of 5,000 record rows or fewer to enable specimen or taxon data import through the Specify WorkBench.
||Data Exporter exports a schema map made within Specify for the purposes of exporting data in a particular format for external use. The Data Exporter also exports Specify data in the destination (mapped) schema to an external file. This function is used to create an IPT server cache of data from a Specify database. This application was previously known as the "SchemaExporter".
Installation Packages for Specify 6.5.03 "Turducken", Database Schema 1.8
Released 27 November 2013
Specify 6.5.03 Release Notes
Specify (Full version)
(The Full version requires prior installation of MySQL.)
(MySQL is embedded within Specify EZDB and does not need to be installed separately.)
There is a compatibility issue with SpecifyEZDB on Windows 7 & 8. The Specify Collection Setup Wizard (SpWizard.exe) must be run in Windows compatibility mode for SpecifyEZDB installations. This can be done by right-clicking on the /Specify/bin/SpWizard.exe file and choosing: "Troubleshoot Compatibility", then follow the prompts to let Windows run the Specify Collection Setup Wizard in compatibility mode.
Specify Mobile WorkBench
The Mobile WorkBench is a standalone application designed to be used with laptop computers for portable, batch data entry. Mobile WorkBench records can be exported and then uploaded into Specify databases. The installation package is a zipped directory. Download, decompress and move it to a file directory for data, or install it on a USB flash memory drive. There is a bug with running the Mobile WorkBench on Windows 7. A workaround is to run the MWB in Compatibility Mode which can be started by right-clicking on the MWB exe file in Windows 7 and choosing: "Troubleshoot Compatibility" and then "Try Recommended Settings".
Specify Attachment Server
With Release 6.5, Specify has enhanced handling of image and document files linked as attachments to collection data records. Attachment files are not stored within MySQL but either in a specified local filesystem (or mounted server) directory, or on an institutional file or asset storage computer running the Specify Attachment Server and accessed through web service protocols.
The Specify Attachment Server offers a flexible option for storage of collection-data-related images and documents for institutions with multiple collections, a mix of workstation operating systems or that want to use the Specify Web Portal to publish attachment files to the web. The Attachment Server is an optional component, it handles transactions involving files linked to Specify database records, i.e. uploads, downloads, and deletions of attachment files. It is typically installed on an institutional Linux server. The Attachment Server's Python code is lightweight, it has been tested on Linux and should run on any platform supported by Python. Authentication allows repository access only from Specify workstations and from the Specify Web Portal. The Attachment Server Python code is available from GitHub. The settings file includes documentation as comments. Installing the Specify Attachment Server requires the technical expertise of a software engineer or system administrator.
Specify Web Portal
The new Specify Web Portal is a versatile interface for publishing collection information to the web. The Web Portal runs on a Linux server and shows collections information as tabular data, images, and as maps of geo-referenced specimen locations. See this site's Specify 6.5 release tab on this web site for examples of the Web Portal's interface. Specify Web Portal installation documentation is available here as a downloadable PDF and on this site's Documentation tab. The installation package is available here: Specify Web Portal Installation Software (ZIP). Installing the Web Portal requires the technical expertise of a software engineer or system administrator.
Specify 6 Release History
We regularly issue Specify software updates through our automatic update notification and delivery system. Less frequently we update the database structure or schema of Specify. The table below shows the history of updates for Specify 6.