Table 1.
Examples of currently available zebrafish colony management applications.
Table 2.
Features of currently available zebrafish colony management applications.
Fig 1.
Schematic representation of FishNET configuration.
(A) FishNET can be used as a single unit installed in one PC alone or through a server that can support multiple computers and handheld devices. (B) Decision tree to determine if a single FMPA License is needed or multiple licenses hosted on a server are required. (C) The stationary, standalone desktop configuration for running FishNET consists of 1) barcode scanner, 2) Mac Mini, 3) keyboard, 4) mouse, 5) BBP33 Brady printer (Milwaukee, WI, USA), and 6) computer monitor. (D) The mobile configuration for FishNET consists of 1) 19” widescreen LED backlight LCD monitor, 2) barcode scanner, 3) dual-handle plastic enclosed shelf service cart, 4) DisplayPort to VGA adapter converter cable, 5) V-slot extruded aluminum stand for the monitor, 6) BBP33 Brady printer, 7) wireless mouse (far right, on top of cart), 8) a wireless waterproof keyboard (in cart drawer) 9) Mac Mini with, and 10) a Mac Mini security mount (stored in cart cabinet behind lockable doors). Not shown in the lower cabinet are the surge protector outlet power strip and an uninterruptible power supply (e.g., an APC UPS from Schneider Electric; West Kingston, RI, USA) to make the entire unit mobile. FMPA, FileMaker Pro Advanced; LCD, liquid crystal display; LED, light-emitting diode; VGA, visual graphics array.
Table 3.
Hardware required for the immobile, desktop FishNET configuration.
Table 4.
Hardware required for the mobile FishNET configuration.
Table 5.
Hardware, software, and cost comparisons between FishNET configurations.
Fig 2.
Step-by-step overview for implementing FishNET.
(A) The logic flow for configuring the database is shown, with essential steps in red and optional steps in blue. Simplified relationships are indicated by the directional arrows. (B) An overview of the resources that FishNET can relate and manage. (1) A tank with adult zebrafish is given a TUID. If two adults are crossed to produce offspring (2), a CUID is assigned to the mating. Embryos are collected (3) and given an NUID, and they can either be processed for experimental processes (4) and be given an HUID or (1) graduated to the main system and given a new TUID. CUID, cross unique identifier; HUID, harvest unique identifier; NUID, nursery unique identifier; TUID, tank unique identifier.
Fig 3.
(A) Activation of FishNET database from the FileMaker Server 17 administrator console can be done by selecting “Open” (indicated by red arrow). (B) FishNET App can be imported to FMPA locally by selecting “From Browser…” or from FileMaker Server selecting “From Hosts…” (indicated by red arrow). (C) FishNET landing page with full access privileges. FMPA, FileMaker Pro Advanced.
Fig 4.
Initial configuration of facility, rooms, and racks.
(A) Configuration page where the facility name (indicated with red arrow), tank size, and spaces occupied are initially defined. This page should be set up before using FishNET and should not be modified later. (B) An example of a Tecniplast fish rack (on the left) with a corresponding virtual rack layout (on the right) matching this commercial configuration. (C) After configuration, the Virtual Facilities button will now feature a dropdown list of Facilities to choose from on the landing page (indicated with arrow). (D) Within a facility, multiple separate rooms for housing zebrafish racks can be added by selecting “Add Room.” (E) Inside each room, multiple fish racks can be added to house zebrafish; to add a rack, simply select “Add Rack” (indicated with arrow) and chose the appropriate rack layout according to the manufacturer design.
Fig 5.
Creation of predefined and custom fish racks.
(A) Configuring the number and type of racks within a room of a facility. A dropdown list of predefined fish racks can be found, as well as pictures of each commercially available rack, by selecting the “Rack Layouts” button in the top, right corner of the menu header. Administrators for each room can also be added on the far right, main window. They can receive calendar notifications (fry to transfer to system, turnover of tanks, dead fish, etc.) via email, in addition to users. Racks are added using the “Add Rack” button and chosen from preconfigured options (that match commercially available racks) via the dropdown menu. (B) A picture of a rack and the corresponding virtual rack set-up for one of the predefined rack layouts (using the tabs at the top of the window). (C) Virtual view of the newly set-up empty rack. Each space can be labeled with its own barcode using the “Print Rack Labels” function (indicated with red arrow). (D) Example of a custom rack configuration. In each row, the number of tank spaces and how many spaces each tank occupies can be defined by the user. This can be changed to fit the custom rack specific layout by the facility administrator.
Fig 6.
Entering laboratories and individual users.
(A) Example of a new laboratory, where the name of the lab, the PI, institution, contact info, and IACUC protocol are all entered. Once lines and tanks have been entered, the lower part of this window will display the number of active tanks, active crosses, and tanks on the nursery for easy reference and billing purposes. Selecting the “Lab Members” button (indicated by the red arrow) will bring you to the next window. New laboratories can be added by selecting “+ New Record” option at the top of the FileMaker menu (indicated by a red arrow). (B) Individual lab user set-up. To add a new lab user, select the “+ New Record” option at the top of the FileMaker menu (indicated by a red arrow). Lab information is automatically populated from the general lab information window, and here individual contact details are entered. Users are defined as “active” or “inactive.” Later, tanks and crosses owned by this individual user will be shown in this window. (C–D) After adding laboratory accounts, an administrator can set up privileges for all users in that lab, as well as other labs, to restrict or permit visualization of lines and handling of fish (e.g., setting up crosses, etc.) by non-lab members. IACUC, Institutional Animal Care and Use Committee.
Table 6.
Setting up lab privileges.
Fig 7.
(A) The “Fish Lines” layout can be accessed from main layout dropdown menu, or by clicking “Fish Lines” on the main landing page (each indicated by the red arrows). (B) A new line information page can be created by selecting “New Record” (indicated by the red arrow in the header). Users can move through all records using the forward and backward arrows (top left of the header, indicated by the blue arrow). Each new record is assigned an LUID, indicated by the red arrow. This is an example of a fully annotated line record. Containers where external pictures or file attachments can be placed are indicated with an asterisk. Any tanks available for a given line will be displayed on the far-right side of the main window under the “Tanks Available” label. The tank labels are color-coded according to their age and mating status. Selecting the magnifying glass will bring up a pop-up window with a detailed overview of an individual tank (indicated by yellow arrow). Lines can also be browsed in list view (C) or compact view (D) for easy navigation, with more detailed information (TUID, tank size, number of fish, date of birth, etc.) easily available by clicking the magnifying glass icon. LUID, line unique identifier; TUID, tank unique identifier.
Fig 8.
Entering genotyping protocols.
(A) Genotyping protocols can be accessed from the landing page via the “Genotyping Protocols” button or via the dropdown menu under “Lines” and “Genotyping Protocols.” (B) An example genotyping protocol, where primers and PCR conditions and images, as well as phenotypic information, can be imported.
Fig 9.
(A) “List view” of all “Live” (active) tanks, in this case sorted by “Facility.” All active tabs for viewing are indicated by blue coloring. The age and status of each tank is indicated by color (see red arrow), while the sex of each tank is indicated by the background color (blue for male, pink for female, and purple/pink for mixed sex tanks, indicated with blue arrows). Selected tank is indicated by a bar changed to light blue (indicated by green arrow). (B) Detailed view of a tank with the derivative cross (C0831) and genotype/TUID of the parents, date of birth, date for turnover, and user/owner of the tank all indicated, as well as the facility and position. To view the virtual position of the tank, select “Locate Tank” (indicated by the red arrow) in the “Tanks Detailed View” layout, which will bring you to a new window. (C) The Room will be indicated on the upper left of the header menu (in this case, T032), while the Rack will be indicated in the center of the header menu (in this case, rack 3). The position of the tank of interest will be indicated by a blue label. In this case, TUID 0370 is in Room T032, Rack 3, Row C, position 15. Clicking on “Details” will show the genotype, sex, age, and number of fish in the tank, as well as the owner of the tank. All other tanks are colored according to their age and mating status (white ≤ 2 weeks old, yellow ≤ 3 months old/juvenile, green ≥ 3 months old/active, and red ≥ 1 year old). TUID, tank unique identifier.
Fig 10.
(A) Crosses can be set up from the “Detailed View” by selecting “Set Up Cross” button (far-left screen image), indicated by the red arrow, which will take you to a new screen (far-right screen image) where you can either manually or by barcode reader enter the TUID for the dam and the sire for the cross. Selecting the “Set Up Cross” function automatically generates a new CUID number and record for tracking purposes. The crossing function also allows you to record the success of the mating for tracking the fecundity of a tank (and overall mating at the level of a rack, room, or facility) (not shown). (B) The “Crosses” layout displays either “Active” or “All” crosses. The far-left column (indicated by the black arrow) displays the CUID of a cross at the top, with the status of the cross (either mating or retired) indicated below in the dropdown menu. Below that are the dates the mating was started, as well as the date the mating was ended. The blue background in the far-left column (indicated by the far left, red arrow) shows users which cross is currently selected (compare the blue background indicated by the red arrow in C0869 to the light gray background in the far left of C0867 for reference). Each cross is also color-coded for easy visual reference (indicated by the asterisk on the far-right side). Green = an active cross; red = an active cross, but more than 2 days have passed since it was set up; and gray = retired crosses. After a cross has been ended, in the top right corner, a user then selects to retire a cross (indicated by blue arrow), after which the background color on of a cross will automatically change to gray (compare the background color of C0867 between the left and the right images). The upper right header menu also has options to raise fry from the mating (indicated by blue arrow), to set up a new cross, to print more cross labels, or to print labels for petri dishes for embryos. (C) Selecting “Raise Fry from Mating” will ask the user for the number of embryos that will be kept in each tank/petri dish for raising. After selecting “OK,” a second window will ask if there are additional embryos to raise from the same cross (not shown). Once the user indicates that no more fry will be raised, a new NUID record (bottom image) will be created. Here, the NUID record, as well as the identity of the sire and dam, number of fish, and other details will be autopopulated from the CUID record. Once the fry are ready to move onto the main system, the user can select “Graduate to system” (indicated by the red arrow in the far-right image). This function creates a new TUID autopopulated with all of the pertinent NUID and CUID information (not shown). CUID, cross unique identifier; NUID, nursery unique identifier; TUID, tank unique identifier.
Fig 11.
Setting up calendar reminders.
(F) Once a new TUID is created (after graduating fish from nursery), a user can automatically set a reminder to turn the line over 1 year from the date of birth by selecting the “Set Reminder” button (indicated by the red arrow in the far-left image). The middle image shows the “Calendar” layout (in this case for the month of May, 2019 for room T032). More “Events” can be added (using the button indicated by the blue arrow). Clicking on the magnifying glass (denoted by the black arrow) will create up a pop-up window showing the details of an event. Months can be changed using the forward and backward buttons on the far right of the top header menu (indicated by the green asterisk). (C) Detailed “Event” layout, where FishNET has the capacity to email a reminder to the lab user and/or room administrator for any given event (using the contact details supplied in the laboratory set up). TUID, tank unique identifier.
Fig 12.
Using FishNET to track harvest records.
(A) Embryo harvest template. Creating a new record in the “Harvests” layout will create a new HUID record, where information such as the cross used to produce embryos, the genotypes and TUIDs of the parents, the date of collection, and number of embryos can be entered. Information regarding any chemical or genetic treatments, the age of collection, any genotyping to perform, and downstream tissue processing can be entered into this record as well. (B) After an embryo/adult quantity is added, a user can select the “Create Resources” tab to create a unique Harvest ID (H000X-1 if one resource, 1 and 2 if two, and so on) for each embryo group or adult fish that is processed. Selecting “Create Resources” will prompt the user to select the number of groups that embryos or adults are going to be divided into. If the original embryo quantity is 50, the user could make 2 groups of 25 embryos, each with a different experimental condition. (C) Viewing the resources takes the user to an individual record view of all “resources” associated with that harvest. Information regarding genotype, tissue processing and images of the embryos can store here to create permanent records of any experimental harvest. HUID, harvest unique identifier; TUID, tank unique identifier.
Fig 13.
(A) Screenshot of the Excel template used to import lines into FishNET. All fields should be filled accordingly. (B) Import Field Mapping showing the correct configuration to import new lines into FishNET.
Fig 14.
Generating fish statistics with FishNET.
(A) Navigate to the “Virtual Facility” from either the landing page (left) or the header tabs. (B) From the “Facility” page, selecting “View Stats” (yellow arrows) will take the user to a statistical report for either the facility, room, or individual rack. (C) shows the “View Stats” layout for an entire facility, with the “Current Status” of all tanks in that facility on the left and all individual fish on the right. From here, one can also view the “Vitality Summary” (indicated by the red arrow in the header menu) for the entire facility, room, or rack. “Generate Summary” (indicated by the red arrow) in the “Vitality Facility Summary” layout creates a report either for the past year, month, or week displaying all recorded fish born (embryos) from crosses, dead fish found in the facility, and fish euthanized for a comprehensive view of the vitality of a facility or room.
Fig 15.
Generating follow-up reports with FishNET.
(A) Individual fish within a tank can be brought to the attention of the tank owner and facility staff by creating a Follow-Up Report (indicated by the red arrow). A census of dead fish can be entered in the “Detailed View” of a tank (yellow arrow). (B) Both dead fish report and follow-up report list can be found in the List View Layout under Fish Reports (indicated with red arrow). A graphical overview can be found in the “Facility, Room, or Rack Statistics” under “Mortality Summary” (red arrow). (C) “Mortality Summary” shows pie charts with 1) a breakdown of Mortality Causes, 2) Symptoms of Fish Euthanized, and 3) Symptoms of Fish Found Dead. A bar graph of yearly, monthly, or daily dead fish is shown below as well.
Fig 16.
Importing water quality records.
(A) Example of virtual rack view, to see rack statistics, select View Stats (shown with red arrow) on the top right corner of the screen. (B) Scroll through the months with the arrows in each side of the header. Once in the current month, select “New Record” (shown with red arrow). (C) Days and values can be pasted in the two fields; FishNET can show either a single value per day (conductivity) or the average of multiple readings a day. (D) FishNET uses Google Charts to display data, and for that reason, an internet connection is needed to use the graphing functions. Once the user is done adding the days and values, select “Generate.” Graphs can be modified by selecting “Change.”