Create a freezer in OpenSpecimen
Create a freezer structure by describing the shelves, the racks, and the boxes within it.
OpenSpecimen allows you flexibility to describe your freezer space to the specifications, or lack thereof, of each section of your freezer. You can be as detailed and organized as you wish. A container is just a two-dimensional representation of what you see in your freezer.
OpenSpecimen also allows you to create ‘Dimensionless’ containers for those instances where a container has no defined structure. For instance, you have some bags full of tubes and they are placed in a bin or section of a shelf, with no organization.
It’s also possible to build a freezer in one single step by utilizing ‘Container Types’. That process will be covered separately. It is rare to find a freezer that is completely uniform across all shelves and racks. And building a freezer from the top down is a good way to learn how to describe containers.
Understanding the container level fields
Containers are just compartments that hold other compartments or specimens. Empty compartments can be created linearly as one-dimensional units or two-dimensionally with rows and columns. Each empty compartment can either hold another compartment or it can hold specimens.
For example, specimens can be stored in boxes in a two dimensional manner. Typically, each cryobox has a divider in it that splits it into rows and columns. A typical 9x9 crybox can be described as 9 rows by 9 columns.
Characteristics that can be described about the box are:
1D or 2D (is it a linear container, such as a slide box, or a 2D box?)
Number of rows and number of columns
How to label the rows and columns (using an alphabet or numbers).
Perhaps you prefer to label each position linearly 1-81.
How do you want to populate the box? Do you want to start from the top, left corner and add specimens horizontally or vertically?
Is the box restricted to hold specific sample type(s) or can it hold samples from only one collection protocol?
These concepts are then used to describe how the box is stored in the freezer. You don’t just put a box in the freezer. If you have hundreds of boxes in a freezer, you need to be able to describe where in the freezer any given box is placed. Therefore, we build racks or drawers to describe the box location. A drawer exists in a rack. A rack exists on a shelf. And a shelf exists in a freezer. Freezers are unique and can accommodate different numbers of shelves, and each shelf might hold a different number of racks depending upon the width of a rack. So we can describe each of these levels as a new ‘container’ in OpenSpecimen. These fields will be described for each level of container created (freezer, shelf, rack, or drawer).
Parent container vs. subcontainers:
A freezer is a parent container. What defines it as such is the fact the the Parent Container field is blank. Any parent level container will appear in the main Container List for your Site. This list should only contain freezers, refrigerators, or perhaps a shelf that holds room temperature boxes. All other containers, will have a defined ‘Parent container’ that is selected upon creation. These containers will not be displayed in the main Container List.
Container Fields
When creating a container, you need to describe characteristics about that container. The list below describes each of these fields and will help you to understand how to describe your container.
You can choose to create a single container or multiple containers if they all share the same characteristics.
This menu is used regardless of whether the container will hold specimens or hold other containers. The field called ‘Store Specimens?’ will define whether the container hold samples directly or not. It is a common mistake to check ‘Yes’ to this for parent level containers. Only boxes should be checked as ‘Yes’ in this field.
All fields with a red asterisk * are required.
If a container Type is chosen, then these 4 fields will be pre-filled with the values described for that specific container type:
Dimension
Position Labeling
Labeling Scheme
Position Assignment
For example: 9x9 Box will prefill these as 9x9, Row and Column, alpha x number, horizontal, top to down, left to right. Once you choose a type, you can edit any of the characteristics.
Some types might have a unique naming scheme predefined. If the Unique Name field disappears, then you can remove the container type and the defined dimensions will remain and you will be able to define your own unique name in the field.
Field Name | Description | Required |
|---|---|---|
Type | Pre-fills the dimensions, labeling scheme, & position assignment | No |
Used For | Storage or Distribution Storage containers are used for any sample being stored in a freezer. Distribution containers are created to temporarily hold specimens that have been added to a distribution protocol (sample request). | Yes |
Display Name | Non-unique descrition of the container | No |
Unique Name | Name of freezer and each container must be unique across the entire system and all Sites. Choose a naming convention for your lab that will ensure unique container names, such as incorporating your Site name or PI intials. JonesLab.FR1.S2.R3 (Freezer 1 in the Jones Lab, shelf 2, rack 3) | Yes |
Barcode | At the UofU, we use the official Location Code of the room in which the freezer is located. See https://location-lookup.app.utah.edu/ to find your code. Because the barcode must be unique, if you have more than one freezer, use a suffix after the location code, such as .FR1 or .FR2 | No |
Dimension | Number of Rows and Columns | Yes |
Position Labeling | Linear or Row and Column. Linear will always be numerically represented, 1 to X, where X is the total number of compartments in your container. Row and column will allow you to assign a vertical and horizontal labeling scheme (numeric or alpha). | Yes |
Labeling Scheme | You must define how the rows and columns are to be labeled. | Yes, if you choose ‘Row and Column’ for Position Labeling. *Linear will always use Numbers. |
Position Assignment | Tells the system how to add samples to the box or additional compartments to the container.
| Yes |
Approximate Capacity | Describe the number of samples the container can hold | No |
Temperature | Describe the storage conditions | No |
Store Specimens | Choose ‘Yes’ if the container can directly store specimens. Choose ‘No’ if the container will hold other smaller containers. Example: you will not store specimens directly on a shelf, so if building a shelf, choose ‘No’. Only choose ‘Yes’ when creating a box or other containers where specimens will be directly stored. | Yes |
Display in Map | Lets you choose what field you want to see on the 2D container map: Person ID, the specimen label, or a specimen barcode. | Yes (will default to ‘Specimen Label’, if not specified). Field only present at parent container level. |
Automated Freezer | This field is only used for labs using an automated system to store and retrieve samples. | No |
Collection Protocols | If the box can hold only specimens from one or more protocols, this can be defined here. | No |
Specimen Types | To limit the specimen types that can be stored in the box, choose the type from the dropdown list. | No |
Instructions
Define your freezer structure.
To create a structured freezer you must first understand how your freezer is organized. It is recommended to organize your boxes prior to starting to build your freezer if at all possible. If you cannot obtain actual racks to store boxes, then organize them in stacks.
Examples of freezer compartments and how they are represented in OpenSpecimen
Freezer (top-level container) examples:
Example of a basic 4 shelf Freezer
This is a simple freezer that has 4 shelves.
In OpenSpecimen, it would be built as 4 rows and 1 column.
Example of a side-by-side refrigerator with 5 shelves per side.
Example of a side-by-side refrigerator with 5 shelves per side.
This refrigerator could be configured in OpenSpecimen as 5 rows by 2 columns.
An asymmetrical side-by-side refrigerator/freezer with door shelving
An asymmetrical refrigerator/freezer with door shelving
To represent a container like this asymmetrical refrigerator with space in the doors for storage, you could create a freezer with 4 columns. Each column would be assigned a separate structure in the ‘shelves’ section.
Container 1 will be the left freezer door, 2 will be the left-side freezer section, 3 will be the right-side of the fridge and 4 will be the right fridge door shelving.
Top/Bottom asymmetrical freezer
Combo freezer with shelves on top and side-by-side drawers on the bottom compartment.
In OpenSpecimen, this freezer would be built as two compartments: 2 rows by 1 column.
After adding the shelves (top) and bins (bottom)
The top compartment would then be configured as 3 rows and 1 column.
The bottom compartment would be configured as 3 rows and 2 columns.
Subcontainer examples:
This is an organized shelf that holds 5 racks, so this container would be designed as one row (vertical dimension) and 5 columns (horizontal direction).
In OpenSpecimen, the shelf would look like this:
Each of the slots 1-5 can hold another container. To each of these, for the image above, you can add a Rack. If one of these slots was not a rack but a space for a stack of boxes, each space can be assigned it’s own unique structure. The containers in the slots do not need to match.
Example of a small shelf that holds a rack and other items
This shelf could be described in OpenSpecimen as three compartments (1 row by 3 columns)
The column on the left would hold a stack of boxes (as many as could be accomodated in the future), the compartment on the right would hold the organized rack and the middle compartment could be described as ‘dimensionless’. The dimensionless compartment can hold either containers or specimens, depending on how the lab wants to design it.
This Rack can be described in one of two ways.
Two-dimensionally: (also used to describe a rack without drawers)
Configured as a 2-D container that can hold 24 boxes
6 rows (vertical direction) and 4 columns (horizontal direction).
Benefit: all slots can be viewed on a single screen.
Rack and drawers displayed in 2D: 6x4Each compartment can hold a box.
One-dimensionally as a rack that holds 6 drawers:
Rack: 6 rows (vertical direction) by one column (horizontal direction).
Drawers: 1 row (vertical) by 4 columns (horizontal)
Define each drawer separately, need to expand the rack to see the drawers.
One dimensional Rack with drawersThen each drawer is defined as a container of 1 row and 4 columns. Each compartment can now store a box.
1D drawer that can hold 4 boxes
Perhaps your boxes are stacked one upon another from bottom-to-top and back-to-front on a shelf. A stack of boxes can be created in OpenSpecimen using the same technique as if it were a rack. Determine how many boxes high and deep the stack of boxes can be and design a 2D container to represent it.This is a single stack of boxes, but these might exist on a shelf 3 stacks deep. Typically these would be populated from the bottom-up (vertically) from back-to-front (left-to-right).
In OpenSpecimen, if there were 3 stack of boxes, we could represent it as a 2x2 container of 4 rows and 3 columns.
Specimens are typically stored within boxes or racks. You can design a 2D box or rack by determining the number of slots available to hold a specimen.
The most important step is to define this container as a container that holds specimens!
9x9 box: 9 rows by 9 columns
Blood tube rack: 4 rows and 10 columns
You can even design a linear container to hold fixed tissue blocks. Each lane might accommodate 30 blocks: This column of this container could be designed as 30 rows. Each of the 30 compartments would hold a single tissue block.
Create the freezer and compartments:
Once you have an idea of your freezer structure, you can begin to build it in OpenSpecimen.
Start by building the parent level container.
The parent container will typically describe the number of shelves that exist in the freezer. So a freezer with 4 shelves will be 4 rows by 1 column.
Expand the Containers page
Click ‘Create’.
Enter a Unique Name for the freezer
Choose the Site from the dropdown list, you will only see the Sites you have access to. Choose your lab’s Site.
Type in the number of rows (these would be how many shelves are in your freezer)
Type in the number of columns (most freezers are 1 column unless they are side-by-side.
Position Labelling: Choose 'linear' if a single column or row is used. If more than one column or row, you can choose to row and column which will give you two coordinates.
Position Assignment lets you choose the direction samples or other containers will populate your container.
Click ‘Horizontal, top to down, left to right’.
Store specimens: Click ‘No’ to tell the system that you cannot store a specimen directly on a shelf. This will allow you to put other containers on the shelves.
Display in Map allows you to choose the field to display in the container map. Click ‘Specimen Label’.
Click ‘Create’ to create your freezer.
This is the top-level configuration of the new freezer with 4 empty compartments. You can now describe the shelves in the empty comparments.
Create the shelves
Once you have the freezer compartments created, you can describe each shelf independently or you can create all shelves at once if they all share the same format (the number of racks they hold).
Shelves are typically described by the number of racks that can be placed on a shelf from left to right. If all shelves hold the same number of racks, you can create all 4 shelves at once. If one is used to hold a different type of container, you can describe it differently. In this example, we will create 4 identical shelves, each of which will hold 6 racks from left to right.
Navigate to the Locations tab of the freezer created in the first step to see the empty compartments in which you will describe your shelves.
Click the '+' symbol in the top compartment to create the new container.
To create multiple identical containers, click the ‘Multiple Container’ button.
Enter the unique names of the shelves in the ‘Names’ field, separated by commas, tabs, or ‘newline’.
Optionally add Display Names of the shelves to see a more descriptive name.
Choose ‘No’ in the ‘Dimensionless?’ field to be able to create structure for each shelf.
Decribe the number of rows and columns for the shelves. Typically, shelves consist of a single row of racks. The number of columns will describe the number of racks on a shelf.
Describe the Position Labeling of the shelf as ‘Linear’.
Describe the Position Assignment of the shelf (populated from right-to-left, or left-to-right).
Choose ‘No’ for ‘Store Specimens?’ because you do not want to place a single specimen in this container.
Click ‘Next’ to navigate to the next page where you will review the position assignment of the shelves.
Review the Shelf names and positions and edit if necessary. Click ‘Create’ when complete.
This is the display at the freezer level of the new shelves that were created.
Select ‘Shelf 1’ and the ‘Locations’ tab to view the structure of the shelves on which the racks will be created.
Create the racks
Racks can be described two different ways, depending upon your needs. You can have a 2D rack that holds boxes. Or you can describe a one dimensional rack that holds drawers. Then the drawers will hold boxes. This is an individual preference. However, if your drawers are used to segregate samples by protocol or specimen type, then it is recommended to create drawers to hold boxes as each drawer will have a separate description and restrictions, if desired.
Example of a 2D rack: Holds 4 boxes high and 5 boxes deep. This will be described as 4 rows and 5 columns. In this tutorial we will create 6 identical racks (4x5) on shelf 1 of the Demo Freezer.
Navigate to the Shelf where the racks will be created.
Click on the shelf where the racks will be created.
Click the '+' sign in the first open position.
To create multiple identical Racks, select the ‘Multiple Container’ button.
Enter the unique names of the containers. Note that the number of containers created will be determined by the number of values in the Unique Name field.
Enter the Display Names if different from the Unique Names.
Enter the number of rows and columns.
In position labeling choose either ‘Linear’ or ‘Row and Column’.
Row and Column (alpha x number), left-to-right, bottom-to-top example
Linear example:
If Row and Column, choose how to describe the rows and columns using numbers or alphabet.
Choose Position Assignment to determine the order of how boxes will populate the grid.
Example of a bottom-to-top method of placing the boxes into the rack. In this case, boxes would be created from the bottom-most rack at the back of the container, and placed horizontally from back to front. When the first row is filled, the boxes would begin at the back of the second row from the bottom and populate forwared.
Choose ‘No’ in the ‘Store Specimens?’ field.
Click ‘Next’ to proceed to the review screen.
Review names and positions and click ‘Create’ when complete.
To view the completed Rack, expand the shelf and select the Rack.
Select ‘Locations’ to view the 2D grid.
Once complete, boxes can be created in the available slots.
Because we have chosen bottom-up, left to right, the lower left corner is labeled (1,1) and the upper right is labeled (4,5).
Example of a Rack with 5 Drawers. Each drawer holds 4 boxes.
In this case the Rack will be 1 column of 5 rows. Each row will hold a Drawer that is 4 columns by 1 row.
Create the Racks on a shelf as linear 5 rows by 1 column.
Select the Shelf and choose the first position to create the Racks
Click ‘Multiple’ to create more than one Rack.
Enter the Unique and Display Names
Describe the number of rows and columns and how to name and populate them. A rack that holds drawers will always be 1 column and the number of rows will represent the number of drawers.
Choose ‘Next’ to review the positions and click ‘Create’ when complete.
Create the Drawers in the Rack.
Expand the containers to select the Rack in which the drawers will be created and select the first empty slot to populate the drawers.
Select ‘Multiple Container’ and enter the Unique and Display Names for each drawer.
Enter the dimensions of each drawer and the position assignment and labelling schema.
Select ‘Next’ to Review the names and positions, then click ‘Create’ when complete.
Editing container characteristics
If one of the shelves is different than the others, you can edit that shelf’s structure. For example, if Shelf 4 holds 3 bins used to collect bags of samples of odd sizes, then you can edit it to have only 3 compartments.
Note that if all compartments within a container are occupied, then you cannot decrease the container size. You must either delete those containers or move them to another open position to be able to decrease the number of rows or columns in a container.
Navigate to the overview tab of shelf 4.
Click ‘Edit’.
Edit the number of columns to represent the new number of containers to be created.
Type ‘3' and click 'Update’.
New structure of ‘Shelf 4’.
Create the boxes
In this example we will create a box to hold specimens. But technically any type of container can be created to hold specimens, such as a blood tube rack, banker's box that holds envelopes, or a slide box. The only difference between a box that holds samples or a box that holds other containers, as described in the steps above, is whether the ‘Stores Specimens?’ box is checked ‘Yes’ or ‘No’.
If it’s checked ‘Yes’, then the system will show the container as available to store a sample. If checked ‘No’, then the container can only be used as a parent container for new sub-containers.
Boxes can be created all at once to populate a rack using the same methods we used to create racks on shelves. However, if you create empty boxes all at once without restricting the protocol or specimen types that the box can hold, you will be able to see all available boxes when trying to store samples. This can make the process of choosing an available box more difficult. Good practice is to only create the boxes that you currently are using. If you do choose to create additional unused boxes, you can block all available positions until they are ready for use.
If you choose to create a single box at a time, you can choose anywhere in the rack to place it. You do not have to go in the order defined by the parent container. That feature is used when creating multiple containers at once.
Example of a 9x9 box
Navigate to the rack or other parent container into which the box will be placed.
Select the empty slot in the Rack where the Box will be located.
Enter the Unique Name and Display Name (optional).
Enter the dimensions of the Box and the labelling and position descriptors.
Click ‘Yes’ in the ‘Store Specimens?’ field.
Select Protocol and Specimen Type restrictions.
Select ‘Create’ to create the Box. If only one box is being created at a time, there is no review page to show.
To see the box structure, select the box and click the ‘Locations’ icon.
Example of a 3x4 box to store saliva containers.
Follow the same steps, but enter different Box descriptions
3 rows by 4 columns, Alpha x Numbers, Horizontal, top down, left to right.
Two dimensional depiction
Dimensionless containers
Dimensionless containers can be created at the primary container level (as complete freezers or maybe a cabinet that has no structure to it). It can by used to store other containers with or without structure. Or it can be created within a structured container. You can choose if you want it to be able to hold specimens directly or if it can be used to store other containers using the ‘Store Specimens?’ field.
This example will be used to create a dimensionless container as a ‘Bin’ on a shelf. In the example freezer created, there are 4 slots to create new containers. We will create those as dimensionless bins which can store samples. The bottom half of this freezer contains 3 rows of dimensionless bins.
Create a dimensionless container that holds specimens, within an organized parent container
Navigate to the parent container level to create the dimensionless container.
Enter a unique name and display name for the new container.
Choose ‘Yes’ for ‘Dimensionless’. The 4 fields for describing rows and columns and position assignment will disappear as these cannot be described for a dimensionless container.
Choose ‘Store Specimens?’: ‘Yes’ if the container will store specimens directly. Or ‘No’ if the container will be used to hold other containers.