Repository

Research laboratories make use of several types of containers to store biological material. In LAS container concept is everything that can contain other containers or biological entities (i.e. sample). So we can figure out the repository like a tree in which there is a root that contains some objects, which in turn contain other ones until stopping at the leaves represented by the samples. Besides the LAS divides all containers in four categories (generic types): starting from the root we have freezer/cabinet, rack/drawer, plate/box, tube/bio cassette. The order in which categories have been presented is related to the containing relationships (i.e. a freezer contains a rack), but we can have some exceptions. For example a plate can directly contain some biological entities. Every category is in turn divided in other container types. For instance in the category freezer/cabinet, we have -196°C freezer, -80°C freezer and cabinet at room temperature. For every container type it has been defined a series of mutual interactions (i.e., which container type can host another one), that can change according to characteristics such as the layout and the laboratory procedure. For instance, a plate of a given manufacture and model may be able to host only some kind of tubes.

Then for every container type we have container instances univocally identified by a barcode. Every container has a geometry composed by number of rows and columns used to correctly visualize the container in the interfaces. Besides user has to specify for every container which types of biological entities (e.g. viable, RNA later, snap-frozen) can contains. They can be more than one.

In LAS, containers can be managed like independent entities, but also like grouped objects. For example plates and their tubes are grouped entities and in some LAS interfaces, when it is required to position a sample created, it is possible to see a plate and its tubes simply loading the plate.

The Repository Management Module allows managing any kind of container by defining and applying different rules to them. In the following the main functionalities are described.

New container

The insertion of new containers instance can be done individually or in batch. In the first case, user has to go to “Single container” menu and set the features of each new container that he wish to insert. This procedure can turn out useful, for example, in the creation of empty plates (i.e., without tubes).

In the second case, “Load batch” menu presents an interface in which loading files with the container data. In the interface there is an example to explain how this file has to be formatted. After clicking on “Next step”, the system requires features to be assigned to every new container. To assign the same characteristics in batch to multiple containers, it is possible to select the containers of interest by using the checkboxes positioned to the right of each container, and choose the values from the menu on the right side of the screen.

New container type

The LAS allows to insert new container type. User has to select the name, the generic type (i.e. freezer, rack, plate, tube), the geometry and the relationships among other container types that is the type it can contain and the type in which it is contained. In addition there are other optional parameters.

Change container features

This procedure allows to change some features of a container. In particular user can change the generic type, the container type, the biological entities contained and the geometry of a container. User can also choose if make it disposable, that is in case the biological content is over, container will be thrown away. Container features can be changed only if the container is empty. For example, in order to be updated, a plate should not contain any tubes.

Archive container

This interface can be used both to navigate containers and to archive them. For the first purpose, user can navigate the containers structure starting from one container and going to the children or to the father through the “zoom +” and “zoom-” buttons.

To move/archive containers, the user can drag one container from the source over the destination; a block of containers can be selected by clicking on the starting block of the series in the source container and then on the final block. For example, by clicking on A1 and then on B2 the containers in position A1, A2, B1 and B2 will be selected. To move the selected container to the final destination, it is sufficient to click on an empty place in the destination. When moving a container the system verifies the archiving date of all contained samples. If the archive date is not available, it is set to the current date.

Automatic placement of container is also available. When loading a source container, if the destination has already been defined, the system checks if the first can fit in the second and, if so, it executes the automatic movement to a free position. For example, if the user wants to place a series of tubes in an empty plate, he/she must load the plate as the destination and then just enter the barcode of the tubes. If the user is unhappy with the position assigned automatically, the block can be moved manually. If this automatic procedure is not desired, click on “Deselect container”.

The system provides an area called “Temporary place” where some containers can be moved temporarily. This is useful when working with a completely full container, to rearrange the blocks inside of it.

Return

In laboratory when a researcher takes a sample from the storage to execute an experiment, he has to put it away once he finished his activity. The LAS tracks this and whenever an aliquot validation occurs in a biobank interface, it was saved that the aliquot has been taken by a certain operator. When the operator puts away the tube has to do a “return” procedure in LAS. The interface shows all containers taken by that operator and, to return them, user has to insert containers barcode. After the confirmation a final report is shown.