Preparing to Use Array Management	Top

Master Data Setup discusses the master data that must be defined in order to create and manage Arrays. For details about creating and managing Arrays once this information is defined, see the Array Management Overview as a starting point.

To create and load an Array, you must first define details about the types of Arrays you intend to create. Consider the physical characteristics of the Array, such as dimensions and layout. Determine what content goes where, and what results need to be gathered. Each of these components work together to create and process Arrays. When preparing to use Array Management, you must define the following:

System Level

Define these system-level attributes:

Array Type

Define the physical properties of an Array:

Array Layout

Define the following features of an Array:

Array Method

Array Methods define the content that can be loaded into Array Items and Zones and how to handle results. Define the following in Array Methods:

Array Transfer Method

Array Transfer Methods define a set of rules for moving content from source Arrays to target Arrays. There are two types of Transfers:

Array Types	Top

Use Array Types to define the physical properties of Arrays (Plate, Racks, or Gels). Later, when defining Array Layouts, these Array Types will be available as options. To add or maintain Array Types, navigate to the Array Type List at Lab Admin → Arrays → Array Types. The Array Type List page opens:

Here you can Add, Edit, View, Delete or Copy Array Types. You can also create a New Version of an existing Array Type. Click "Add" or select an existing Array Type and click "Edit" to make changes.

Clicking "Add" opens the Add Array Type page. Here you define the physical characteristics of the Arrays you plan to use. 

Following is an example of how the Physical Array will appear using the values entered in this example.

Click "Save" to add the Array Type.

Array Layouts	Top

Array Layouts allow you to predefine different content layouts and loading patterns for loading Arrays:

To add or maintain Array Layouts navigate to Lab Admin → Arrays → Array Layouts. The Array Layout List page opens.

From the Array Layout List page, you can Add, Edit, View, Delete or Copy an Array Layout.

Click "Add" or select an existing Layout and click "Edit" to make changes. You can also create a New Version of an existing Array Layout.

Click "Add". The Add Array Layout page opens.

Define basic information about the Array.

"Save" the Array Layout. The physical Layout (as defined by the Array Type) displays. Each well is considered an Array Item.

In the Array Tab, map the contents of each Array Item either individually or by Zones. Click "Add Zone", then choose one or more Zones (the list of available Zones is defined in the Array Zones Reference Type).

Note: You will not be able to add the same Zone more than once. If you want multiples of the same Zone, you will need to define a unique Reference Type for each.

Click "Ok".

Zone to Array Item Mapping

Once you have identified the Zones, you will need to map them on the Array. Assign Array Items to Zones either individually or by groups. Choose the Zone you want to define, then highlight the Array Items you want to include in that Zone.

Array Item Selection Options

The following grid selection tools are available for highlighting Array Items:

Highlighted Array Items will appear green during selection.

Reserving Zones

With the Zone you want to Reserve selected, and the Array Items you want to include in that Zone highlighted (green), click "Reserve". The Zone will change to the color you specified. Notice that each Array Item now contains a letter and number which represents the Zone (the first letter of the Zone name) and its position, the Arrangement String. The Arrangement String represents what will be loaded into an individual well. You will see only the contents of the Array for the Zone selected.

Column 1 was reserved for the Positive Control.

Columns 2 through 11 are reserved for the Unknowns. Note that Unknown Zone has 80 Array Items available.

Optionally, fill the entire Layout or leave Array Items unassigned. You can also create overlapping Zones, including an Array Item in multiple zones. There is a many-to-many relationship between Array Items and Zones.

Clearing Zones

To clear the Reserve, first choose the Zone containing the Array Items you want to clear. Select the Array Items within that Zone (they will turn green), then click Clear. The highlighted items will be cleared.

Viewing Content

Arrays Layouts can be zoomed in and out using the options provided on the toolbar. In the case of very large Arrays, a smaller version of the entire Array is displayed to the right to show into which portion of the Array you are zoomed. You can move the red bordered box over the entire grid to zoom to a particular location.

Zoom using the scroll wheel on the mouse is also supported. You can pan the grid by clicking within the grid then moving the viewport around or using the reference grid.

Once you have identified the Zones on your Array, you must define the relative positioning of Array Items for replication or serial dilution and how Array Items should be loaded. Using the Arrangement tab, define Arrangement Rules for loading Content into an Array. Define the following for a Zone:

Following is an example of how you might choose to load an Array. Suppose you want to load 24 samples with 4 repeats each into a 96 position Unknown Zone. Below is an example of 2 possible ways to load the Samples.

In the first example, you see the distinct sample repeated vertically. The second is a Horizontal repeat. Use Dimensions to define these and other loading patterns.

Dimensions

LABVANTAGE provides three dimensions for defining Arrangement Rules.

Loading boxes are provided to easily add dimensions to the Arrangement. Click the dimension you want to add and drag it into the Horizontal or Vertical loading area. Add as many dimensions as needed to a loading box and rearrange them as necessary once placed in the box. You can also give a dimension priority over the others. Initially a simple arrangement with only the Content Dimension is defined (as below).

Once defined, the Arrangement is shown in each Array Item. In the following example, only Content is defined in the Horizontal loading box, one distinct sample per Array Item within the Unknown Zone, positioned one after the other horizontally. The Arrangement is shown as U1 (Unknown 1), U2, U3, U4 etc. to fill the entire Zone. With this Arrangement, there are 80 available Array Items.

You can optionally click and drag additional Dimensions to either loading box (vertical or horizontal). The left-most dimension in the horizontal loading options box (or top-most dimension in the vertical loading options box) will be given Priority.

Priority determines which dimension is given consideration over the others, in other words if you choose to make Content the priority with a repeat of 3, the Sample is given priority and you would see (as an example): U1 U2 U3 repeated 3 times. If the Repeat has the priority you will see U1 U1 U1 U2 U2 U2 etc. for each sample.

When there are multiple Dimensions in a Loading Box, arrows are available to change the Priority or Orientation of each Dimension. To remove a Dimension from a Loading box, either drag it out or click the X at the top of the box. The Content dimension cannot be removed.

You can also drag the boxes to change Priority or Orientation. Following is a description of each Dimension.

Content

You can load as many distinct Samples as will fit within the Array Zone as defined in the Array Layout. The number defined here determines the number of Array Items filled for each distinct Sample (this number does not represent the Loading order). For example, should you decide to change the Content to 2, you will be loading each Arrangement twice for every distinct Sample you choose when Loading. You must then consider the number of available Array Items in the Zone and the Arrangement to ensure you will have enough Array Items to accommodate the Arrangement.

Using the Layout above as an example: If you were to change Content to 2, you will be able to load 40 distinct Samples (40 Samples, loaded twice).

As you add Repeats and Dilutions, you will need to factor those additional Array Items per defined Content number. For example, if you were to add a Repeat of 5 and the content was 2, the entire arrangement is loaded twice (number of distinct samples 2, times the number of repeats 5) each distinct Sample will require 10 (content 2, 5 repeats each) Array Items in the Zone. If you have 80 Array Items available, you can load 8 distinct Samples.

Repeat

Load each distinct Sample multiple times for averaging or for quality checks.

In the example below we added a Repeat of 5 for the Unknown Zone. The Samples repeat 5 times in the Horizontal direction. In the Unknown Zone, as we defined it in the Layout, there are 80 available Array Items. With this Arrangement, a repeat of 5 and Content 1, we will be able to fit 16 samples, 80 divided by 5 (number of repeats) = 16. If the Arrangement will not fit within the specified Zone you will receive an error message stating this is not a valid combination of Dimensions.

Dilution

Serial Dilution is the process of changing the concentration of the content across different Array Items.

Following is an example of a typical Serial Dilution. A distinct Sample is diluted across a specified number of Array Items by a specified concentration amount.

To create the following Serial Dilution in Array Management: 8 Samples at 6 different concentrations repeated twice: Define the following Arrangement: Notice that the dilution is the Priority therefore for each sample the dilution is displayed one after the other Horizontally then repeated. The next Sample begins in Array Item B1. Each distinct Sample will fill 12 Array Items filling all 96 Array Items.

Using the Dilution box, enter the number of diluted Array Items and the dilution factor (expressed as the denominator of the dilution ratio). Optionally check Dilute First to indicate whether or not the first Array Item is full strength (if unchecked the first Array Item is full strength).

Categories Tab

A Category allows you to group Arrays into Categories you define. Defining a Category here will group Array Layouts into the defined Category (see Categories).

Save the Layout

Once you have finished the Arrangement, "Save" the Layout. Optionally click "Add" to add another Array Layout from this page directly.

Once you have added a Layout or created a different Version, you can Approve that version. Approving a Version changes the status to Current and the fields in the Array Layout tab are no longer editable. Click "Approve Version" on the Add Array Layout page.

Array Methods	Top

The Array Method defines the procedure for the execution of a Laboratory technique. This includes both how the Array is to be loaded, as well as how it will be analyzed and on which instrument. The Array Method has two distinct sections, content and parameters. The content defines:

The information defined here is copied to the Array and used throughout the Array life cycle. Before loading an Array, you must apply an Array Method. You can do so either when creating an Array or after the Array is created using the Apply Array Method button.

You can Apply multiple Methods to an Array. Each time a Method is Applied (instance) it is listed on the Array (see Applying Array Methods).

To add an Array Method navigate to: Lab Admin → Arrays → Array Methods. The Array Method List opens:

Here you can Add, Edit, View, Delete or Copy an Array Method. You can also create a New Version.

Changes to the Method will not affect Arrays to which the Method has already been Applied. You would need to create a new Array and Apply the Method again. Once applied to an Array, the Array Method cannot be deleted.

Click "Add". The Add Array Method page opens:

Define basic information about the Method.

There are three types of Array Methods: Array Methods that define the Loading directives only, Array Methods that define the Analysis directives only, and Methods that define both. The "Defines Array Loading" and "Defines Array Analysis" checkboxes determine which you are defining. Both are assumed, but you have the option to de-select either.

Define Array Loading

Define Array Analysis

Save the Array Method. Once saved, the additional fields and tabs become available. In the following example, both the Array Loading and Array Analysis fields are checked.

In the Content Detail Tab define which type of Content is available in the Source pane when loading an Array.

Optionally, define specific query parameters to restrict the content that is available during loading. For example, you can specify that only Samples with a certain Sample Type are displayed, or to display Trackitems from specific Reagent Lots. If no specific criteria is defined Users can perform an Advanced Search during Loading to find Content.

To define Content for each Zone click "Add". The Array Method Content Editor opens. Depending on the Type of Content you choose in the Content Editor, different options are available.

In the Zone dropdown, you will find a list of the Zones defined in the associated Array Layout. Choose the Zone for which you want to define Content details.

In the Content dropdown choose the type of content you want to load for the Zone you selected. Following is a description of the options available for each Content Type.

Content Type	Description
Unknown	Place an unknown Sample into an Array Item. Use specific Queries or Workflow Queue to determine which Samples are available when loading Arrays. Query Define specific search criteria for filtering the Samples available when loading. Choose a Query from the dropdown list. Available queries are those defined with the ArrayQueryforUnknown checked. Depending on the Query you choose click Query Params to define specific criteria for the search. In the example, we chose to populate the list with Samples of a specific Sample Type. In the Query Param Editor we selected the Sample Type "Whole Blood". If no Query is specified here, an Advanced Search is available during Array Loading. Workflow Queue Choose either a Primary or Secondary Workflow Queue. If you intend to Load Arrays based on Workflow Input Queues you should set this to Primary queue.
Control	Place a known entity into Array Items (such as Controls, Standards or Blanks). Samples or Reagents can also represent Controls. Choose to search for these Controls using a specific query or choose to load Reagent Lots associated with a specific Reagent Type. Query Define specific search criteria for filtering the Samples available when loading. Choose a Query from the dropdown list. Available queries are those defined with the ArrayQueryforControl checked. Depending on the Query you choose click Query Params to define specific criteria for the search. If no Query is specified here, an Advanced Search is available during Array Loading. Query based on Reagent Trackitem Define search criteria for filtering Reagent Lots based on either a Reagent Class (such as Buffer) or Reagent Type (such as H2SO4). A list of all Reagent Containers for the specified Class (or Reagent Type) displays. Reagent Type Specify a Reagent Type. Reagent Lots associated with the Type specified will be available when loading Arrays. The Version is displayed.
Treatment	A Treatment is an additive for each Array Item, which can be done individually, or against the entire Zone (such as Dye or a spiking Reagent). When choosing the Source for Treatments you can define a specific Reagent Trackitem (Container), specific Reagent Type, lookup a specific Treatment or define a Treatment Category. Choose a specific Treatment in that Category when Loading. Available queries are those defined with the ArrayQueryforTreatment category.
Operation	Operation is a procedure performed either on the entire Array; for example, Incubating, Spinning or Freezing or in individual wells like Mixing. Choose to define a specific Treatment or a Treatment Category. Queries are not available when loading an entire Zone at a time. When defining an Operation for Zone Level loading be sure to choose a specific Treatment.
Transfer	The Transfer option allows you to define criteria for determining available Content when Cherry Picking. Cherry Picking allows you to select specific Array Items to Transfer onto a Target plate. The Content Detail for Transfers allows you to further define which Arrays display in the list. Choose to populate the list with results from a specific Query. Queries displayed are those defined with an Array Category. The Workflow Queue contains the source Arrays from which you can Cherry Pick. Here you also define a Transfer Rule. Define in which direction Array Items selected in a block (such as a 3x3 grid of Array Items) should be loaded. This Transfer Rule determines which Array Item is loaded first, next and last. Choose: Horizontal Array Items are ordered Horizontally starting with the selected item. Loading moves from one row to the next beginning each new row at the first column. Vertical Array Items are ordered Vertically starting with the selected item. Loading moves from one column to the next, beginning each new column at the first row. Horizontal Snaking Array Items are ordered Horizontally and snake through the selected items. When snaking, after the last Array Item in a row is filled loading moves to the last Array Item of the next row and moves back toward the first column. Vertical Snaking Array Items are loaded vertically and snake through the selected items. When snaking, after the last Array Item in a column is filled loading moves to the last Array Item of the next column and moves back toward the first row. If multiple Array Items are selected individually, the selection order is remembered and those Array Items are loaded in the order in which they were selected.  Define the Content to be included with the Transfer. Choose to propagate: Unknowns, Controls, Transfer, Treatment, Operation and/or Master Mix (see Transfer Rule).
Master Mix	Master Mix is a premixed solution containing Taq DNA polymearase, dNTPs, MgC12 and reaction buffers at optimal concentrations for efficient amplication of DNA templates by PCR. Specify Master Mix content by identifying either a Reagent Type or specific Reagent Trackitem, or a Treatment Category or specific Treatment. Queries are not available when loading an entire Zone at a time. When defining a Master Mix for Zone Level loading (such as Positive Controls or Full Array) be sure to choose a specific Reagent or Treatment.

When you are finished defining the Content Type, click "OK". The remaining detail fields display.

Each Array Item has an SDIData structure that is defined in the Parameters tab on the Array Method (not a Parameter List). When Data Entry is performed (either by an instrument or manually into the Array), it is against these Data Items. In the Parameters tab, define the testing parameters for analyzing the data.

Click "Add", choose the Parameter you would like to include, then click "Select and Return".

Simple Push

The Push Results Rule allows you to push results from the Array Item structures to the loaded content Samples. Using the Push Results Rule Editor, define whether to push data to specific columns on the Sample, Parent Sample or a Trackitem, or to a Parameter on an associated Parameter List.

Click the Push Results Rule lookup on the Array Method Parameters tab to open the Push Results Rule Editor. Choosing "To Column" gives you the option to promote results directly to specific columns on the Sample, Parent Sample or Sample's Trackitem. Choose the Column to which you want to push results.

Choosing "To DataItem" allows you to choose the Parameter List and Parameter to which you want to push results.

The values available in the ParamList and Param dropdown are determined by the Test Method defined in the Content Detail tab. The Test Method data type must be compatible with the Parameter for which you are defining the Push Results Rule. You cannot use the Push Results Rule if you have defined Serial Dilutions.

Click "Ok" to add the Rule.

Calculation Rule

Define calculations that use data from Array Items to perform a calculation. You can define the following types of Calculations:

The above 3 calculation types are calculations within an Array. These are not to be confused with a calculation used to pull Array data from the Array to the Unknown Sample. That is defined in the Sample's Parameter List and is a Complex Pull. See Complex Pull for more information.

In the Parameters tab, clicking the lookup icon in the "Calculation Rule" field opens the Expression Editor.

Click the Cross SDI Helper in the Parameters box. The Array Item option of the CrossSDI Helper displays where you can specify a Calculation Rule. The Parameter List defined here with the Calculation Rule is added to the Test Method that is applied to the Zone when the Content Type is Sample.

Cross SDI Tab

In the Cross SDI tab define:

Param Tab

In the Parameter tab define the parameters to be used in the Calculation.

Click "Ok" to add the Rule.

You can define a Calculation rule for Item level and Zone Level parameters of an Array.

Example Calculation Rules

Complex Pull

When performing a Complex Pull, Array data is pulled from the Array and used in a Calculation defined on the Unknown Sample's Parameter List. Consider the following when deciding to use a Complex Pull or a Simple Push:

Whether or not Calculations defined on the Sample are considered depends on your decision in the "Execute Sample Calculation when Promoting" option. When checked, the Calculation is evaluated when the Promote Results button is clicked. Results are then pushed back to Data Sets on the Samples. See Results Handling for more details.

Example Sample Paramlist Calculations

Optionally, you can define details for additional Zones before saving the Method.  

Apply as many Array Methods as needed to an Array creating overlays. Doing so creates a new Array Method instance. At any given point, only a single Array Method is in play at a time on an Array. Each time a new Method is Applied, the previous Applied Method must have a status of either Completed or Reviewed, if not, that instance will be cancelled and the latest Method Applied will be the Active Method.

When all Applied Methods are Complete, the Array is complete. You can manually Cancel an Applied Method using the Cancel Array Method button on the Plates and Gels list page. If all applied Methods are cancelled the Array is cancelled.

Clicking the Array link in the Plates and Gels list or selecting the Array and clicking "Edit" displays general details about the Array including any Applied Methods and their status.

 Each Applied Method contributes to the Status of the Array. The following chart details the Status of the Array depending on the Status of the active Array Method Instance.