Overview	Top

This document provides various examples designed to help you understand the capabilities of the Array Management OOB Actions and their usage scenarios.

Master Plate Creation and Content Loading	Top

A typical use case is the creation of master plates (based on instrument generated files) that define data mapping. For example, once Samples have been placed on the Instrument (Decapper), a series of activities will result in a csv file detailing the creation of a master plate and mapping of Samples to individual wells. See the file format below and the semantics of the relevant columns.

The data from the csv file can be imported into LabVantage using Data File Definitions.

The following examples discuss various scenarios that illustrate how data from instrument files can be uploaded into LabVantage using Data File Import functionality and OOB Array Management API Actions.

The position for each of the tubes (cells) is specified for all wells (1 through 96), in sequential order.

1.	Create a Data File Definition with the style specified as Simple Grid. Note that most of the Array Management Actions allow for processing all the cells of the Array in a single call to the Array Actions, and hence the Process Block Size can be set to "All Items".

The position for each Tube is specified as an Array Item Label, the list does not include all the cells of the Array, and can be in any order.

The DFD definition in Example 2 is almost identical to Example 1, except for the call to the LoadArray Action. It is replaced with a call to LoadArrayByPosition. This example highlights the fundamental difference between LoadArray and LoadArrayByPosition. The LoadArray allows for loading contiguous cells of the Array from a specified "Start Item" based on a "Load Direction", while LoadArrayByPosition allows you to choose wells in any order and they can be listed explicitly by their labels.

The inputs to the LoadArrayByPositon action are as follows:

The table below illustrates the similarities and differences between LoadArray and LoadArrayByPosition.

Positions are specified as an ordinal number and the positions may be in any order and cherry picked.

In this case the positions are identified by Ordinal Number i.e. well A1 -> 1. A2 -> 2, A12 -> 12...;. B1 -> 13 and so on. The example file is shown below.

The DFD in this example is very similar to Example 2. The LoadArrayByPosition action is used, but the field position specified as "Ordinal Number" needs to be converted to arrayitemid to be input to the action.


The arrayitemid uses the groovyutil class "arrayutil" and calls the method positionToArrayItemId as follows:

[$G{arrayutil.positionToArrayItemId( action0.arrayid, fields.position.toString(), 8,16,"H" )}]

The groovy function takes the following inputs:

Instrument file includes information to load a Reagent for the Entire Zone.

Suppose the excel file in Example 1, includes the details of the reagentlot to be loaded for the entire zone.

Define cell fields for the three fields highlighted below.

Assume that the MasterPlateExample is defined as follows:

The DFD in Example 1 needs to be modified to add the following steps after the Array is created.

The GetSDITrackItem Action step determines a Trackitem for the ReagentLot specified. Note that the Mode must be specified as "self".

The LoadArray action is called to do the zone level loading for the unload zone to load the reagent lot specified. Note that the inputs specified to the LoadArray action.

Master Plate Content Management	Top

In the previous section, we discussed various Loading use cases. Loading is a "complex" operation which has many intrinsic assumptions about the way things work:

There may be a situation when you require finer control on the contents and exceptions to the rules mentioned above. The following sections discuss various content management scenarios.

AddArrayContent is the OOB action that can be used in situations such as the caller does not want to use the automatic volume calculations and does not want to honor arrangement rules for some specific contents.

In the image below, we depict the properties that need to be specified to AddArrayContent action to add content at item level. This example assumes that we are adding samples to three specific cells A1;B1;C1. The inputs can be specified as:

Note that to add contents at the Zone level, the input properties that change are:

AddArrayContent, when invoked with the level as item, the difference between LoadArrayByPosition and AddArrayContent is highlighted below.

When the AddArrayContent is called for level = 'zone' the difference between LoadArray and AddArrayContent is as follows:

The call to AddArrayContent to load content at zone level looks very similar to Example 1, except:

Note that EditArrayContent is analogous to AddArrayContent to modify contents that were previously added via LoadArray actions or AddArrayContent. Content can be edited at Item level or Zone level.

DeleteArrayContent allows you to "delete" content items added by Loading or AddArrayContent Actions.

It does not take care of volume restoration to the source or the totalvolume in arrayitem.

The input properties are:

Master Plate Data Entry	Top

Once Arrays are loaded, they are sent to instruments for analysis to capture data for each parameter of interest. Instruments typically generate text/csv files that need to be uploaded into LabVantage to be reviewed by the user. The following sections describe various formats of data returned by instruments that can be uploaded using the OOB Array Data Entry Action via Data File Import functionality.

The OOB DFD "ExampleArrayResults" can be used for this purpose. The format of the excel data, mapped on to various fields is illustrated in the screen shot below. The results are entered a cross tab grid of the Array item labels and the results for the Array item for each parameter. The list of parameters is not fixed and can be extended to add more parameters.

The processing rules uses the ArrayDataEntry action as shown below.

The OOB DFD "ExampleArrayZoneData" is used for this purpose. This example illustrates the upload of Array Zone level results. The grid shows the Minimum/Average/Maximum Parameter results to be uploaded to Positive Control and Negative Control Zone. Efficiency specified in Cell B2 is uploaded to (Full Array) zone.

The processing rules has two calls for ArrayDataEntry. The first call is to upload results at "zone" level for "Positive Control" and "Negative" control zones.

The second call to ArrayDataEntry uploads the Efficiency to "(Full Array)".

The OOB DFD ExArrayDataBy2DImage can be used for this purpose. The example represents the Array data represented as an image of the Array. The header column is the Row labels, A, B ...; P and the header row is the Column labels 1, 2, 3...;

The results range shows the result for each well. The param name is specified in cell B4.

In this case the ArrayDataEntry action is called without any item labels. The results are ordered by sequence of wells, one of the three ways that ArrayDataEntry matches results to wells.

Custom Plate Transfer	Top

Consider the following Example where the source Array needs to be mapped onto two targets.

A custom Transfer Method is defined as follows:

The source column defines a source Array bar code. The assumption in this example is the barcode is actually used as arrayid for the Arrays created (using CreateArray action).

Each source plate needs to be applied a "Plating" transfer method that does the following.

The first 48 wells are transferred twice into 96 wells of plate 1. The next 48 wells are transferred twice into 96 wells of plate 2.
Arrays as follows:

The DFD to import the Plating.csv file is defined as follows: 

1.	Note that the process block size is one, to perform transfer operation on one source Array at a time
2.	The fields of the DFD are defined as shown in the illustration below:
3.	The processing rules are defined as follows: In action0 CreateArray, the target Arrays for the current sourcearrayid being processed are created In action1 Transfer Array, the sourcearray is transferred using the Plating TransferMethod to transfer contents to the two destination plates The details of the properties passed to the CreateArray action step are as follows: • Either the arraymethod or a arraylayout is specified for the target Array • The number of copies is specified as 2, to create the two destinations • The override arrayid is the concatenation of the [destination1] and [destination2] separated by a semicolon. (IDs of the two arrays to be created)

The next action step is to do the Transfer.

The inputs to the Transfer action are as follows: