ZeBase: An Open-Source Relational Database for Zebrafish Laboratories

Overview of ZeBase

The main window of ZeBase is shown in Figure 1. The major functions are grouped under five tabs at the top: Quick Stats, My Lab Fish, Search, Settings, and Scheduled Reports (Fig. 1, arrow 1), with the text for the currently selected tab highlighted in orange. All fields used in the database are defined in Supplementary File S1 (Supplementary Material is available online at www.libertonline.com/zeb), and some essential ones are discussed below.

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FIG. 1.

The main window of ZeBase. Along the top of the screen are five tabs (arrow 1) that correspond to the five major functions of ZeBase with Quick Stats tab selected by default. The three sub-tabs on the left (arrow 2) can be used to show additional survival information (see Fig. 2 and descriptions in text for details).

Quick Stats Tab

Under the Quick Stats tab are three sub-tabs on the left column: Overall Stats, Track Survival, and Current Survival (Fig. 1, arrow 2). The Overall Stats sub-tab shows the total adult fish count (Current Fish Count) and larval fish count (Current Nursery Count) in a facility.

Track Survival

Batch number, a unique numerical identifier, is assigned to each new clutch of fish added to the system. The Track Survival sub-tab displays the survival information for all batches of fish at a given point in time, regardless of laboratory affiliation and whether the fish are currently alive or dead. The table can be sorted by any field in ascending or descending order by clicking on the field title. It is also possible to select survival information for a particular month/year by using the ‘Show by Month’ drop-down menu (Fig. 2A, arrow 1). In addition, the corresponding data can be exported to a comma-separated values (CSV) file or printed by clicking on the Excel or printer icon respectively (Fig. 2A, arrow 2).

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FIG. 2.

The Track Survival and Current Survival sub-tabs under the Quick Stats tab. (A) The Track Survival sub-tab displays survival information for all batches of fish that have ever been housed in a facility. (B) The Current Survival sub-tab displays survival information only for currently alive batches of fish.

My Lab Fish Tab

The My Lab Fish tab shows all alive batches of fish that are possessed by the laboratory that the logged-in user belongs to (Fig. 3A). The ‘Add Batch’ icon (Fig. 3A, arrow 1), is used for adding all vital information pertaining to a new batch of fish in a new pop-up window (See the following paragraph for further discussion). Right next to it is the ‘All Fish’ icon (Fig. 3A, arrow 2), which is used to display all alive batches of fish in a facility regardless of laboratory affiliation in a new pop-up window. On the far right is the ‘Scan Mode’ icon (Fig. 3A, arrow 3), which can activate the optional scanner mode function for a quick retrieval of information for any batch by scanning the unique barcode. Barcodes are generated and printed on the labels that can be attached to the corresponding tank(s) (See the following paragraph for further discussion). To the left of each entry of the table are three icons (Fig. 3A, arrow 4) for deleting (red X), editing (pencil; also see next paragraph), and showing additional genotype information (magnifying glass).

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FIG. 3.

My Lab Fish window. (A) My Lab Fish tab displays all batches of fish that belong to the current logged-in user. (B) The pop-up window after clicking the ‘pencil’ icon (arrow 4 in (A)), in which information for a batch of fish can be updated. (C) A label with a unique barcode can be generated by clicking ‘Print Label’ (arrow 11 in (B)). See text for descriptions of the icons highlighted by the arrows.

When the ‘Add Batch’ icon (Fig. 3A, arrow 1) is selected, a pop-up window will appear and allow for entering all vital information for the new batch (not shown; but the basic arrangement is essentially Fig. 3B, see below). By clicking the ‘Insert’ icon in the pop-up window, a new batch number will automatically be assigned to this new batch of fish. After creating a new batch number, the mutant and/or transgene information can be added. First, search for the new batch number and open the corresponding record through clicking on the ‘pencil’ icon in the My Lab Fish table (Fig. 3A, arrow 4). The information of that batch will be displayed in a new pop-up window (Fig. 3B) for updating, with new options for adding existing mutant and/or transgene information. This can be done by either moving the available entries from the right column to the left individually using the ‘blue plus' icon or the ‘Add all’ option located at the top (Fig. 3B, arrows 5). Zygosity information can be added for each mutant or transgene through clicking the ‘Edit Genotypes' icon (Fig. 3B, arrow 6).

Tank location(s) can be added by clicking the ‘green plus' icon under the Batch Tanks sub-tab (Fig. 3B, arrow 7). To select the desired tank locations from a list of all possible locations in a facility, first type the location and/or room number in the search box, or select the information directly from the list; then, choose all applicable entries by clicking the ‘green plus' icon in front of them. After all tanks have been chosen, click ‘Insert’ to add these tank locations to the batch. If more than one batch number has been assigned to the specific location, these will be displayed under the ‘Multiple Batches' column (Fig. 3B, arrow 8). For example, to remove batch number 213 from an incorrect tank location, click the ‘red X’ icon (Fig. 3B, arrow 9) in front of that entry to add that to the remove list. After adding all incorrect tank locations, click ‘Remove’ to delete them from the batch record. Alternatively, the incorrect batch number assigned to the desired location can be selected from the ‘Multiple Batches' column, which will bring up the information of that batch of fish in a new pop-up window. Then, modification of this batch can be done as described above. In addition, this same procedure can also be used to delete tank locations when retiring a batch of fish from the database. Note all updates made to a batch record have to be finalized by clicking the ‘Update’ icon (Fig. 3B, arrow 10). To print a label for the optional barcode scanning, select the ‘print label’ icon (Fig. 3B, arrow 11). The image of the label will be generated in a pop-up window (Fig. 3C). The information that is shown in the label can also be customized.

Search Tab

The Search tab provides custom search functions (Fig. 4A). All different fields of the fish record can be used to do a search. The search results can be saved by entering a name in the Save Searches sub-tab (Fig. 4A, arrow 1). Next to the Save Searches sub-tab are two other sub-tabs, Quantity and Batch (Fig. 4A, arrows 2 and 3, respectively).

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FIG. 4.

Search window. (A) The Search tab displays custom search functions on the left-hand side of the screen. The search can be saved through the Save Searches sub-tab on the right-hand side (arrow 1). (B) The Quantity sub-tab (arrow 2 in (A)) displays the number of fish that belong to the current logged-in user (My Quantities) or the hosting laboratory (My Lab Quantities) (arrows 4). Other users and laboratories can be selected by the drop-down menus (arrows 5). (C) The Batch sub-tab (arrow 3 in (A)) displays all batches belong to either the current logged-in user (My Batches) or the whole laboratory (My Lab Batches) (arrows 6). Other users and laboratories can be selected by the drop-down menus (arrows 7).

The Quantity sub-tab (Fig. 4B) provides quantity reports from which one can quickly retrieve information related to the quantity of fish associated with the logged-in user or his hosting laboratory by selecting either ‘My Quantities' or ‘My Lab Quantities' respectively (Fig. 4B, arrows 4). The search results will appear in a new pop-up window, as shown on the right. There are additional options for searching quantity information associated with a specific laboratory or a specific user by using the drop-down menus (Fig. 4B, arrows 5).

The Batch sub-tab (Fig. 4C) provides batch reports similar to those in the Quantity search. To retrieve batch information associated with the logged-in user or his hosting laboratory select either ‘My Batches' or ‘My Lab Batches' respectively (Fig. 4C, arrows 6). Again, the search results will appear in a new pop-up window, as shown on the right. Additional options are also available for searching batch information associated with a specific laboratory or a specific user by using the drop-down menus (Fig. 4C, arrows 7).

Settings Tab

Under the Settings tab, there are three sub-tabs: Users, Tanks, and Other Attributes. Under the Users sub-tab, the full names, lab affiliations, contact information and administrative rights of all users are listed (Fig. 5A). The ‘green plus' icon in this tab (arrow 1), as well as in the two other tabs in Figures 5B and 5C, is used for adding a new entry. After entering the new required information, click ‘Insert’ to save the entry.

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FIG. 5.

Settings window. The Settings window provides information of all Users (A), Tanks (B), and Other Attributes (C) related to the Mutants, Strains, Transgenes, and Labs.

Under the Tanks sub-tab (Fig. 5B), all relevant information of each individual tank housed in a facility such as tank size, tank location, room number, and comments are saved. The size of each tank is recorded in liters, the tank location is a three-number code that is read as “rack-shelf-water spout” and indicates the exact location of a specific tank, and room number indicates which room the rack is located. This is the same room number that is shown in the add tanks window (Fig. 3B).

The Other Attributes sub-tab (Fig. 5C) consists of four additional sub-windows Mutants, Strains, Transgenes, and Labs. The Mutants sub-window displays all mutants that are housed in a facility, as well as the mutant allele, mutant gene, and strain associated with each mutant. The Strains sub-window shows all different strains housed in a facility and the source from which they are obtained. The Transgenes sub-window shows all transgenic fish that are housed in a facility as well as their promoter, transgene gene, transgene allele, and strain information. Lastly, the Labs sub-window shows all the laboratories that are using a facility.

Scheduled Reports Tab

To automate the process of report generation, a UNIX/Linux administrator can create a scheduled task on the server known as a cron job. A Windows administrator can use the Task Scheduler. A user can select a report to be emailed to him through toggling the user name selection on the left window (Fig. 6). The scheduled reports can also be run manually at any time by clicking the icon next to each report script in the list (Fig. 6, arrow 1). A standard report is included in the default install which includes quantity summaries for each user as well as the whole laboratory.

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FIG. 6.

Scheduled Reports window. A user can select to receive a scheduled report by email and/or run the report manually at any time by clicking the icon as indicated by arrow 1.

Implementation

ZeBase is implemented on MySQL 5.1.41, PHP 5.3.2, and an Apache web server, which can be installed in a UNIX/Linux or Windows environment. ZeBase is released under the Apache License, Version 2.0. Users only need to access the database through a web browser which can be run on PC, Mac, or UNIX/Linux. This can be a traditional server configuration or a workstation that is configured with Appserv (http://www.appservnetwork.com/), a simple installer that will install all server-side packages including Apache, PHP, MySQL, and phpMyAdmin. While all users can create and update new batch records, obtain statistics and reports, and control barcode scanner and label printer, only an administrator can delete and modify user accounts, Mutants, Transgenes, Strains, and Tanks. This avoids accidental modification of the critical information and ensures the consistency of the records. Codeigniter is used as the framework to organize and streamline the code and JQuery is used to create a full-featured graphical user interface. Advanced users will find phpMyAdmin helpful to directly access individual records and modify attributes of the database with a graphical user interface. An installer has been created to facilitate the setup of ZeBase, but it would be beneficial to have an IT administrator to help with scripting and implementation of the web interface. The most current installer and specifications of the database can be found at http://zebase.bio.purdue.edu

Availability and requirements

Cost estimation and management workload

The optional scanner and printer are the only costs associated with ZeBase if it is installed in a workstation. Current pricing is at $280 for a similar barcode scanner and $98 for a simple label printer as of January 2012. After the initial setup (estimated to be 2 hours of the IT service time), the database can be run with minimal routine maintenance, except for the implementation of new functions and updating of the current fish number. In our facility, all users are requested to keep track of and update the current number of their fish monthly to fulfil our institutional reporting requirement.