How to use the animal reporting module
This is an introduction to using the Animal reporting module (ARM). The module is only available to Premium customers and is enabled after sending a request, ideally via helpdesk.
The animal reporting module is designed for reporting the usage of animals for experimental procedures according to the Felasa recommendations and the 2010/63/EU directive on the protection of animals used for scientific purposes. According to this directive, each animal capable of independent feeding (in zebrafish, this applies to animals older than 5 dpf; days post fertilization) that has undergone one or more procedures with a severity level higher than threshold, must be counted and reported. The results are displayed in the Experiment report table as summary (EU). The prospective severity of the procedure must be defined before each experiment, and updated if changes in severity occur during or after the experiment. If an individual undergoes more procedures with various levels of severity during one experiment, only the highest experienced severity is reported. If more animals undergo procedures and it is not possible to distinguish the exact animals that were actually treated, then all the animals in the group are reported as having undergone a procedure with the highest severity of all experienced severities.
To cater to non-EU countries, the reporting system also records all procedures that the animals have gone through including all the severities. This means that one animal can be reported multiple times, once for each procedure it has undergone. This statistic is displayed in summary (all) in the Experiment report.
To start logging the animal usage, the facility admin first needs to set up a project or projects under which the animals will be reported.
Projects
Prior to starting the experimental work, outlining such projects is usually required by the authorities. These projects may run over several years and usually include the maximum number of animals to be used during this project and the list of experimental procedures and their estimated prospective severities. The experiment can start once the project has been approved.
Adding a new project to Zebrabase is possible in Projects/
This opens a New project form. The mandatory fields are a name and a code unique to the project, the project leader and the deputy (the same user can be filled in both fields). The optional fields are the Start and the Expiration dates of the project, Users and Used fish limit. The field Users serves as an informative list with no connected functionalities. The Used fish limit number is necessary for the capacity indicator bar to work. The actual project documentation or approval can be uploaded as a PDF attachment.
Finally, the Procedures that will be performed within the experiments in this project must be included. It is possible to use procedures that were already defined, or to create new procedures. The Maximum prospective severity of each procedure can be selected from the drop-down menu. The default values for procedure severity are: below threshold (0), non-recovery (1), mild (2), moderate (3), and severe (4). These settings can be changed in Admin/
After the project is successfully set up, experiments can be added.
NOTE: According to the regulations, breeding transgenic fish with burdened phenotype must be reported as well as the genotyping of all fish. For this purpose, we recommend setting up two separate projects that will serve as default projects for genotyping and reporting actions on burdened substocks that are not used in another experiment. For these projects, the procedures do not need to be defined; the procedure field can be deleted when creating the project by clicking on the bin icon on the left. If a substock is already subscribed to an experiment, the user can decide in the genotyping form under which project this genotyping should be reported.
ARM configuration
In the admin dashboard, there is the ARM configuration table which is designed to help with the configuration and give a warning if some of the important elements are missing. If an element is missing, there will be a red warning button, and if the element has not been set up yet, the button will be yellow. Ideally, all buttons should appear green. In the next step, after you have designed the default projects for genotyping and burdened fish breeding, please check this table thoroughly.
Configuration explanations:
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Mandatory configuration – Should not be changed!
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Observation period - The number of days after the final experimental procedure after which any death in a substock that has been in the experiment is attributed to the last experimental procedure. For the duration of the observation period, it is impossible to terminate the experiment. It is important NOT TO ADD ANY NEW PROCEDURES after the final one, because this would reset the observation period. Any deaths after the final procedure must be attributed to one of the already existing procedures.
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Burden checks - In every new fishline, there should be a check for burdened phenotype, the first check should be performed as soon as possible. This should be noted in the fishline detail (Edit burdens icon) and after a defined period, a second check should be performed to confirm the burden. The interval between the burden checks is set to 270 days by default (3 generations, i.e. F2), and can be changed in Configuration/
project.fishline_burden_check_interval.
When the ARM configuration is set up, you can start defining the individual experiments.
Experiments
Each experiment runs under a previously defined project and contains one or more procedures. A list of all experiments can be found at Projects/
When a new experiment is being set up, substocks can be added right away, or they can be added later. At the moment a substock is added to an experiment, the fish count is included in the project capacity indicator bar. If there are some unused fish at the end of the experiment, they are subsequently removed from the project capacity indicator.
NOTE: Once the project capacity is filled to 75% or more, the color of the indicator bar will change from green to red.
Quick reporting walkthrough
In some cases, the substock doesn't need to stay subsribed to an experiment, and can be removed from it right away. To make such reporting of individual procedures smoother, there is the option to go through all the necessary entries at once in a series of consequent action windows.
1. Add to experiment
In the substock detail, click the flask icon (Project experiment). This will open the Add to experiment action window, where you can choose under which project and which experiment you want to subscribe to the substock. The Continue to count button will save the action and open the next window in the sequence.
2. Count
In this window, you can specify the procedure and how many fish from the substock underwent it. The toggle button all fish will assign all fish in the substock. The severity of the procedure can be altered at this point. If you want to unsubscribe the stock from the experiment in the following step, click Save and leave the experiment.
If you need to make this action for a substock that was already assigned to an experiment, go to substock detail and click Count (Procedure) on the upper panel.
3. Remove from experiment
This action unsubscribes the substock from the current experiment. You can finalize the severity of the procedures (based on the actual observed severity) and specify the number of unused fish (a new substock consisting of the unused fish will be created, and the used fish will keep the original substock name and position).
If you need to make this action outside the sequence, go to substock detail and click Remove from experiment on the upper panel.
Before an experiment is finished, all substocks must be removed from the experiment.
Reporting tables
In the project detail, below the summary information, there are three reporting tables, Experiment report, Burdened fish report, and Genotyping report. These are detailed reports listing the substocks that went through a procedure, the date of the procedure, the name of the procedure, the associated severity of the procedure, the count of animals that were used, the name of the user, and any eventual note.
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When animals die during an experiment, the number of individuals is highlighted in red and appears with a minus. When the procedure severity exceeds the prospective severity, it is also highlighted in red.
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When a substock is added to the project before reaching 5 dpf, the number of fish is subtracted from the project capacity. Actions on or deaths of fish younger than 5 dpf are shown in the report, but the row is colored grey and the counts are not included in the project summary calculations.
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Substock actions on both burdened or not burdened substocks that happen within an experiment are reported in the Experiment report table. Actions on burdened substocks that are not involved in an experiment, but are subscribed to a project, are included in the Burdened fish report table in the project detail.
The yearly EU summary in the Experiment report is the sum of all animals that died or left the experiment after being treated in a procedure with higher than below threshold severity (i.e. mild or more severe procedures). Animals that have undergone at least one procedure with higher than threshold severity are marked as used by a recycle icon behind the name in the substock detail, or the word reused in the pop-up detail. If animals from one substock have gone through more procedures, only the highest severity is reported in summary (EU) and all procedures are reported in summary (all).
The fish usage is calculated as the sum of fish used in an experiment (all substocks added to the experiment minus the fish that were removed from the experiment unused or if they died before reaching 5 dpf - in the list of count types, this is represented as counts.to.experiment), plus the deaths or euthanizations of burdened fish (counts.as.burdened.death), plus the genotyped fish (every time genotyping is performed, even with the same substock). The notification after the limit was exceeded can be enabled by setting on project.fish_limit_exceeded.
NOTE: The numbers in the experiment report and on the project capacity indicator bar may slightly differ because of the order of operations and calculations performed in Zebrabase. This is not a bug. The project capacity indicator presents a rough estimate of used fish and is designed for the sole purpose of giving a warning and sending a notification when the project capacity has been exceeded.
WARNING: The numbers in the project capacity bar can also become inaccurate after some experimental action is subsequently deleted by the admin. If the project capacity is exceeded by a user error or there is generally a large difference between the capacity bar and the actual fish usage, please contact the help desk to have the numbers clarified and identify possible faulty actions. Always use the experiment report table for reporting fish usage to authorities, and not the capacity indicator.