Initial facility configuration

This chapter explains the steps required for the initial setup of rooms and racks in the facility layout, creating new fishlines and substocks, adding users and defining user rights. It is advisable to go through the setup process step by step before you start using Zebrabase but you can also come back later to re-define any part of the configuration.

Please, be aware that the facility configuration is only accessible to administrators. For the initial setup, use the admin credentials you have received via e-mail.

Sections:
1. Fishlines
2. Founder substocks
3. Rooms
4. Racks
5. Species parameters
6. Diet, Light
7. Tags
8. Users
9. Workgroups
10. Projects
11. Printing

1. Fishlines

Fish / Fishlines / Add fishline

In Zebrabase, each fish substock is assigned to a specific fishline that is defined by genotypes and/or an alias. It is mandatory to fill at least one of these two fields. If an alias is available, it will be used preferentially for creating stock and substock names.

Entering wild-type fishlines

1) Enter fishline alias

This is the only compulsory field for WT lines. The recommended format of an alias for a wild-type line is “WT (AB)”, where the background is in brackets.

2) Fill in other optional parameters and fields

Genotypes
Origin - who created the fishline
Source - who provided the fishline
In facility since - date
File Attachment - protocol, image, publication etc.
Suffix - this is an additional note or descriptor for your fishline; for instance, if you have two fishlines with identical genotypes, you can distinguish them by attaching a suffix to one or both of them
Responsible user - this person will appear as a responsible person for any fish belonging to the particular fishline
... and more, see image:

Entering genetically-modified fishlines

1) Select genotypes

Genetically modified or mutant lines are defined by their genotypes. Each genotype describes one mutation/transgene, and their combination describes the fishline. If the genotype is already stored in the database, start writing into the genotype field and select from the suggested options. If you need to assign more genotypes, repeat the procedure.

If the fishline you are creating carries genotypes that have not been previously defined in Zebrabase, you will need to define them first. To do so, click the plus sign next to the Genotype field and:

Select the modification category (transgenic or mutant) from the drop-down menu.
For transgenic lines, enter driver, triggered gene, and optionally the allele/mutation, e.g. mitfa:BRAFV600E or gata1:DsRed.
For mutant lines, define the affected gene and optionally, allele/mutation.
Save the genotype.
To add another genotype, click the plus button again and repeat the process.

You can also define genotypes independently in Fish / Genotypes / Add genotype.

Optionally, you can also create a new modification category in Admin / Codebooks / Mod Category. This can be an “Enhancer trap”, for example. You will need to specify if the modification category “behaves” like a transgenic (driver and triggered gene) or mutant (affected gene) genotype.

Editing genotypes

If you wish to edit some of the genotypes that have already been assigned to one or more fishlines, you can do so in Fish / Genotypes / Edit. If you edit a genotype, it will be updated for all the fishlines that have it assigned.

2. Founder substocks

Fish / Substocks / Founder substock

Substock is the basic functional unit in Zebrabase. It represents a group of fish that originate from a single crossing and are kept together in a tank. A substock, together with its sibling substocks from the same crossing, form a stock. All the fish from one stock share the same parents and date of birth (DOB), but they are rather a virtual unit in Zebrabase, i.e. not many actions are connected directly to stocks. The real functional subunits, i.e. the fish of a defined origin in a tank are called substocks.

Usually, substocks are created automatically by the Crossing action. Founder substock should be created only in case it is necessary, e.g. when receiving fish from another facility, or when setting up Zebrabase.

In the Founder substock form, it is mandatory to select the fishline and the date of birth. The rest of the fields are optional. Substocks ascribed to a specific workgroup are not visible for users outside the workgroup (they will be greyed out and locked in the Facility view).

3. Rooms

Facility / Rooms / Add Room

In Zebrabase, you can reflect the layout of your facility by defining Rooms and Racks.

Create the first room of your facility and then press Save and add another to define more rooms or simply Save and continue to the next part of the facility configuration.

4. Racks

Facility / Design Rack

Once you have your rooms defined, you can fill them with racks. In Step 1, you can define the number of rows and columns independently for each rack you add to your facility. In Step 2, enter the name of your rack and select the room. To use the rack setup for multiple racks, click Add rack form and fill in the new form. Please, note that Zebrabase currently supports tanks occupying up to 4x standard tank width.

When you are finished designing your rack, hit Save and your newly designed racks will appear in the Facility view. Both rooms and racks are in alphabetical order.

NOTE: After saving, the layout of the racks cannot be edited. Delete the old rack and create a new one instead.

5. Species parameters

Although the default settings connected to species are pre-set for zebrafish, they can be tweaked based on the facility's practice, or changed to suit a different species. These parameters include the age when the animals become juvenile/adult/retired, or the threshold densities of animals in tanks (used for color-coding tanks in the Facility view). They can be configured in Admin / Configuration under the following keys:

substock.age.juvenile - age in days when fry becomes juvenile (default value: 7)
substock.age.adult - age in days when juvenile becomes adult (default value: 90)
substock.age.retired - age in days when adult becomes retired (default value: 549)
substock.count.verylow - upper limit for the count of fish in a tank to be color-coded as "very low" (default value: 5)
substock.count.low - upper limit for the count of fish in a tank to be color-coded as "low" (default value: 15)
substock.count.standard - upper limit for the count of fish in a tank to be color-coded as "standard" (default value: 25)
substock.count.high - upper limit for the count of fish in a tank to be color-coded as "high" - above this limit, the value is "very high" (default value: 35)

If you have the multi-species extension active, you can define these settings for multiple different species. Please see Multi-species module for more details.

6. Diet, Light

Admin / Codebooks / Diet Admin / Codebooks / Light

If you are planning to assign different diet and light conditions to different substocks, first you need to define them to be able to use them for your fish. Go to Admin / Codebooks, and select either Diet or Light. You can input new conditions by clicking the blue plus button in the upper right corner.

You can change the diet and light setting for each substock in the action Conditions (in the action panel in stock detail). It is also possible to change multiple substocks in bulk using batch actions. Default diet is also one of the parameters associated with your species.

7. Tags

Admin / Codebooks / Tag

Tags are used to associate additional, quickly accessible information with your substocks (such as low productivity, illness, single fish in a 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 / Codebooks / Tag. You can define the name and the color of the tag, and write a short description. The name should be short (ideally one word). Tags are most useful when only one or two of them are associated with a substock.

8. Users

Admin / Users / Add user

Adding a new user account The user name and a functional email must be defined, as well as the first name and the last name of the user. Type of the user (person/machine) must be selected. After saving the record, an email is sent to the new user's address with the automatically generated password. The users can change their password after logging into their account by clicking on their username and the Change password icon.
Define additional details Adding the Slack user name is optional, as well as the projects the user participates in. Permission groups determine the access rights the user is going to have. In the default, there are four permission groups: guest, user, facility, and admin. The rights of each permission group can be reviewed by the admin in Admin / Permission groups. If a workgroup has been selected for the user, he/she will only see the data belonging to his/her workgroup. Users without a selected workgroup will only see the substocks and fishlines that do not belong to any workgroup. In the table at the bottom of the form, the notification settings can be defined. Each type of notification can be sent by one or more of the three types of channels: Slack, e-mail, and system notifications (inbuilt Zebrabase messaging system).
Select Save, or Save and add another

User accounts can be edited in Admin / Users by clicking on the edit icon on the right side of the page or by clicking on the user and clicking on Update. An admin can ban a user by clicking on the Ban user icon in order to prevent the user from logging into the database (this will delete the user profile, however as most deleted items in Zebrabse, it can be re-enabled later).

9. Workgroups

Admin / Workgroups / Add workgroup

Workgroups allow the separation of fishlines and users into multiple workgroups (these may be for instance different labs). The data belonging to a specific workgroup are then only visible to the corresponding members. All fishlines assigned to a specific workgroup will be displayed only to its members. Fishlines with no workgroup assigned will be visible to all.

Add fishlines to workgroups: Fish / Fishlines / Edit and select one or more workgroups from the options.

Assigning users to workgroups: Admin / Workgroups / Edit, or in the user profiles: Admin / Users / Edit.

10. Projects

Admin / Codebooks / Project / Add Project

Projects can be used to specify different project licenses/IACUC codes/permission IDs or simply to separate fish into different projects. Enter the name and optionally also description and attachment for each of your projects and then Save or Save and add another.

Note that if you have the Animal reporting module extension active, there is an additional setup needed for your projects. Please navigate to the Animal reporting module configuration in that case.

11. Printing

Zebrabase allows you to print substock labels with your local label printer. You can use the predefined Zebrabase templates, or create your own. A printing template is also displayed in the substock detail - you can change the template used in the substock detail by changing the configuration key substock.detail.label_template.

You can find more info in the section Printing.