Fish
The section Fish provides access to the lists of Genotypes, Fishlines, Stocks, and Substocks.
Genotypes
Genotypes are the elementary genetic modifications (e.g. mutations, transgenes), that combine to form a fishline.
New genotypes can be added by clicking the plus icon in the upper right corner of the list. This opens a new table, where you select the type of the genotype: transgenic, mutant (natural), or mutant (engineered), and specify further details about the modification. Add new parameters by clicking on the plus icon, or select a previously defined parameter from the list. In transgenic genotypes, the Driver and the Triggered gene are obligatory fields, and in mutant genotypes, only the Affected gene is obligatory.
Fishlines
Fishlines are combinations of genotypes that occur in your fish. You can either design them de novo (for example when obtaining new fish from a different facility), or create them during crossing: a new fishline with the corresponding genotype combination is automatically generated when out-crossing two different fishlines, or when assigning a new genotype during crossing (for example modifications done by microinjections).
New fishlines can be added by clicking the plus icon. It is mandatory to fill in either the fishline alias or the genotypes, other fields are optional. Additional documents can be added as attachments. The field Workgroups specifies the users who will be able to view the fishline and the derived substocks. All derived stocks and substocks will contain the Fishline suffix in their name.
Stocks
Stocks are the complete set of fish coming from one crossing. They further divide into substocks, which are groups of related fish bred in one tank. New stocks are generated automatically after a crossing (i.e. they are always connected to at least one existing substock).
Stock detail
The stock detail contains information on the fishline, date of birth, and the derived substocks. On the right side, there is the Observation log and Action log.
It is possible to add a generation number to a stock. The number can be manually set in Update stock (in stock or substock detail). With each in-cross, the number is automatically increased by one.
The Stock suffix is another information that can be maintained from the Update stock form. All derived substocks will contain the stock suffix in their name.
Substocks
Substocks are groups of related fish coming from one crossing, and bred together in one tank. They are the key units of the database, and most actions are directly connected to them.
Filtering the list of substocks is possible according to nearly any variable. The filter icon opens a form with filtering rules sorted into categories. There is also the option to load a custom filter that has been saved previously. Any filter setting can be saved as an instance default, user default, or a custom filter. Custom filters can be named and shared with other users (if saved as public). As a default setting, dead or terminated substocks are not included in the search results.
Another option is the Quick search, which searches for a string in the name or the ID.
In Standard and Premium plans, the columns that are displayed in the lists can be customized by clicking the cog icon in the upper right corner of the list. For substocks, there are over 60 different columns at the moment that can be selected. It is advisable to inspect which columns are displayed in the default setting and possibly customize the selection.
See more info on filters and lists here.
Founder substock
New substocks can be added by clicking the blue Founder substock icon. This function allows the creation of a new substock without a previous crossing and should only be used if generating the new substock by crossing is not possible (for example when obtaining fish from a different facility). It is recommended to always use the dedicated crossing function when creating new substocks from substocks already present in your facility. Only this will ensure that the pedigree is created and the information on parents and siblings preserved.
The form consists of two parts, the first part is dedicated to the respective Stock and the second part to the Substock. Leaving the Fish in each substock field empty will generate substocks with the fish count value "not set".
Substock detail
Clicking on a substock displays its Substock detail. All available information about the substock is displayed here, including the Parent tree, the Label preview and Action log that contains all actions performed with the substock or its parent structures (stock, fishline). All Siblings of this substock can be viewed as well.
The field Crossings contains information on the last three crossings performed with this substock (date, egg quality, egg quantity).
Substock actions
Actions are used to associate new information with the substock (e.g. number of fish, position, genotyping information). Records of all performed actions are stored in the Action log in substock detail, and the full list of all actions from all substocks is also available in Admin/
Users can access substock actions from multiple sites:
- In Substock detail - there is also the option to Update substock or Delete it
- In Substocks - you can select Action menu to be displayed in the list, to be able to access it directly from here
- In Facility view - select a substock in the View mode and the action bar will open
Scanning the QR code on a tank in your facility will lead you to the Substock detail of the substock in the tank.
The actions accessible from the action bar are:
Update
The function Update allows the users to change the basic information about the substock: Substock Use, Funding, Description, Substock suffix, Sex, Printing status, Project, Owners and Workgroups. A Note on the action can also be included.
Count & Terminate
This action enables efficient tracking of fish counts in the substock. Use the Count action to specify the number of fish in a tank, to report animals that were found dead or those that have been used for an experiment. The action offers a selection of various Count types that serve to distinguish between these situations. Terminate is used when all fish in the substock are terminated at once, and it supports the use of the same count types. If you declare all remaining fish in the substock as dead by using Count, the result will be the same as using the Terminate action - the substock will obtain the "deceased" status and its position will be unassigned.
1) Select a substock and click Count in the action bar
2) Set the Count type:
- Start count - the initial count of fish, other count types can only be selected once the start count has been set
- Died - fish that were found dead in the tank
- Euthanized - euthanized fish
- Used for Experiment - fish euthanized as part of an experiment - this count type is only available when ARM is disabled
- Correct - use it to correct a mistake in fish count
3) Write down the count (the number of fish this action concerns).
4) You can change the date when the action was performed, or add a note that will be visible in the action log.
5) Save the record.
See the section Animal reporting module to learn how to use Count to report animals used for experimental procedures with ARM enabled.
Crossing
This function serves for in-crossing and out-crossing substocks in the database. When out-crossing substocks of different fishlines, a new fishline with the corresponding genotype combination is automatically created.
1) Select the substock you want to cross, either in the Fish list or in the Facility view. If you wish to perform out-cross, find one of the parents first. Pick Crossing in the action menu. An empty crossing form can also be accessed by clicking the crossing icon in the top bar or by pressing Shift+X+X.
2) In case you are performing an out-cross, clear one of the parent fields and start typing the name or the ID of the second substock. The autocomplete function will show you the list of available candidates. In a large facility with a lot of records, prefiltering by room, rack or fishline might help to reduce the number of results. In that case, toggle the Prefilters button to reveal the filters.
3) Fill in the date when the crossing was performed. This will become the Date of birth of the child substock.
4) You can set the number of new child substocks and number of fish in each substock right away, or you can leave the field empty which will leave the value as "not set". It is also possible to specify the Sex for each of the parent substocks by using the drop-down menu.
5) Adjust the genotype, if needed. When outcrossing, if there is no fishline with a genotype set matching the combination of parent fishlines, the user has to create a new one during the crossing. If there are some suitable fishlines, the user can pick one of them or force-create a new one. When adding a non-parental genotype (for example by microinjection), specify it in the dedicated field.
6) Save action. By choosing Save and shelf, the newly generated substocks will be placed on the shelf in facility view, so they can be easily dragged to their new position.
In the Premium plan, the quality and quantity of eggs can be rated to keep track of your crossings. The predefined egg quality levels are: bad, mostly bad, average, and good. The egg quantity levels are no eggs, low, normal, and high. The rating can be amended retrospectively by the admin (in Admin/ Action log / Action type / Crossing / Select a specific crossing / Update). In the list of substocks, you can display either the quality and quantity of eggs in the last three crossings separately, or a general indicator that shows the average calculated from the last three crossings.
Split
This action allows splitting a substock into multiple smaller ones. You can assign additional information to the newly generated substocks, for example zygosities, positions, or owners.
1) Select the substock either in the Fish or Facility menu. Select Split in the action menu.
2) Fill in how many substocks you want to separate from the source substock and how many fish per substock there should be. You can also enter owners, projects, and workgroups, if they are the same for all newly generated substocks.
3) Pick Detailed split, if you want to assign information unique for each substock, for example position, fish count, or owners. An extended form listing all newly generated substocks appears.
4) Confirm by saving the action. Pick Save and shelf if you wish to put the substocks on the shelf in facility view.
If you are splitting fish because of genotyping or sorting, you can assign zygosity to any genotype that is assigned to that particular fishline in the detailed split form. You can also terminate any of the new substocks and record the number of fish you have euthanized.
The position can be either written down in the input field, or you can click the magnification glass icon to initiate the positional widget.
IMPORTANT: If the number of fish in the new substocks reaches the number in the original substock, the source substock will be terminated and will obtain the status “split out”. This warning will be displayed:
If the sum exceeds the available fish count, there is another warning with the option to auto-adjust the original substock count before splitting. The original substock will be assigned as "split out".
Merge
Merging serves to combine two substocks coming from the same stock into one. Only sibling substocks that are alive and not in an experiment can be merged. In the transfer mode, it is possible to perform merge by drag and drop.
Transfer
Transfer can be used to change the position of your substock, as well as assign and unassign it. You can also drag and drop the substock when in the facility view to change its position.
1) Select the substock you want to transfer either in the Substocks list or the Facility view. This can be a substock without a position or one already positioned within the facility. Click Transfer.
2) Choose the desired position in the position widget.
4) Save the record by clicking Save action.
If you choose a position that is already assigned to a substock, the position will be shared by both substocks. If you wish to perform another operation, like e.g. swapping of the positions or removing the original tank from its position, use the Transfer mode in facility view.
Productivity
This function allows you to change the productivity tag of your substocks. Fish can be reported as productive or unproductive. By default, new progeny substocks are unproductive until they are reported productive. Productive substocks can also be reported during crossing, by ticking the Change productivity of parents to "productive" toggle.
1) Select the substock either in Fish or in Facility view. Select Productivity in the action menu.
2) Fill in the date.
3) Change the tag. The options are Unproductive juvenile and Productive.
4) Save the record.
Genotyping
Genotyping assigns zygosities (+/+, +/- etc.) for each of the genotypes present in a substock. It also allows to specify the genotyping method and report the procedure when the ARM module is active.
1) Select the substock either in the Fish or Facility menu. Select Genotyping in the action menu.
2) Select zygosity for each of the genotypes from the drop-down menu. When a new substock is generated, its default zygosity is unspecified (?). This can be changed to any of the following options:
3) You can select the genotyping method that was used. New methods can be defined in Admin/
4) If ARM is in use, it is obligatory to specify the project under which the procedure should be reported.
5) Save the record.
ARM project and genotyping method can be retrospectively amended by the admin in Admin/
Tags
It is possible to add a tag to your substock, to associate some additional, quickly accessible information with it (such as low productivity, illness, single fish in tank...). Tags are visible either in substock detail next to the name of the substock, or in facility view.
New tags can be designed in Admin/
Conditions
Diet and light regimes can be updated here. Define your custom values in Admin/
Experiment
This is a part of the ARM module. You can add the substock to an experiment here, or create a new experiment for the substock.
Date of execution boundaries
Each action must have an associated date stating when it was performed. In the forms, this date is called Performed (date of execution). To preserve the logic of the database, the date has certain boundaries. The automatic limit is the date of birth of a substock - no action can happen before a substock has been born. There are additional boundaries specific to some action types:
- count + terminate, split, merge - limited by the date of the last split, merge, or count
- transfer - the date of the last transfer
- genotyping - the date of the last genotyping
- productivity - the date of the last productivity change
Batch actions
Some actions can be performed on multiple substocks at once, i.e. in a batch. You can initiate the batch mode either in the list of substocks, or in the facility view, by clicking Batch actions, or Batch select. After selecting the substocks, use one of the available actions: update substock, record count action, crossing, genotyping... Selected substocks can also be added to a marked list.
In Substocks, batch mode is switched off and the selection is wiped out after navigating to a different page of the list.
The marked list
The marked list is a list of selected substocks that persists within the session (it is not accessible after logging out nor from a different computer). Only one marked list can be held in a session. A marked list can be created in the batch mode, either by selecting individual substocks and clicking Add selected to marked list, or by clicking Add filtered to marked list to add all filtered results.
The link to a marked list appears in the Fish submenu after it is created. The list can be used to perform batch actions on a larger number of substocks, or to export the data into an XLS file. Batch actions called on a marked list are applied to all substocks in the list.
Action log
The action log is a field in the substock, stock and fishline detail, that holds information on all performed actions, within the structure or its parents. For example, any actions performed on structures higher than substock (stock or fishline) will be projected into the respective substock action log as well. You can filter individual action types in the log, or view the detail of an action by clicking the icon on the right of the name. The info button opens a short version of the detail.
Action log of the whole facility can be viewed in Admin/
Observation log
The observation log serves to keep track of various information concerning the husbandry of your fish (for example about the health, treatment with medication, medical checks etc.). It is available for substocks, stocks, and fishlines. The field is designed to hold any written information - custom observation types can be designed in Admin/
Observations are logged (include the date and the user who created it). In the admin action log, individual logs can be viewed and corrected.
Known bugs
- Available actions in substock menu don't reflect the user's permissions or substock status.