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Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 101 of 202 Intelli Sense Selecting the entry in this menu will then enter this keyword into the Code pan e. The Intelli Sense menu will only appear if the text entered cannot be resolved into a name. If it can, the keyword will automatically be filled in. For example, if Create O was entered followed by pressing the key CTRL-SPACE on the keyboard, the keyword Create Object would be completed automatically. It is always clear that Intellisense recognizes a keyword as when it is completed, it will be highlighted in blue. It should also be noted that pressing CTRL-SPACE where the cursor is not beside any text will b ring up the Intellisense menu with every keyword for the selected language. 4. 10. 2 Using Overlord variables in Scripts A more useful script would be one that takes the data just generated by a plate reader (Data. txt) and renames it with the barcode of the plate a nd stores this on a network drive (e. g \\LIMS\Assay Data \). The following code would do this The difference here to the previous example is that the variable [Barcode] has been used for the new name of the file. It is assumed th at the variable [Barcode] would contain the barcode of the plate on the reader when this script is run. If [Barcode] contained the value “B12345”, then the file would be copied to \\LIMS\Asssay Data and would be called “B12345. txt” Variables can be added to the location of the cursor in the code pane by clicking on the Edit section of the Toolbar in the Script Editor and then clicking on the 'Insert Variable' button. If a new Overlord variable is required at this point, the 'Add Variable' button next to 'Ins ert Variable' can be clicked which will allow a new variable to be added. Set obj FSO = Create Object ("Scripting. File System Object" ) obj FSO. Copy File "C:\Data. txt", “\\LIMS\Assay Data \” + [Barcode] + “. txt”, true Set obj FSO = Nothing

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 102 of 202 Add Variable 4. 10. 3 Code Snippets Code snippets are blocks of common functions that can be added into any part of a script and be easily customized for the task in hand. Right mouse cl icking on the menu brings up the context menu and at the bottom is 'Insert Code Snippet'. Selecting this will bring up a sub menu of available snippets

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 103 of 202 Insert Snippet Each folder in this list contains different categories of snippet type. Selecting t he 'Set' folder would allow the 'Set Statement' entry to be selected. Once this is selected, by pressing ENTER on the keyboard, the snippet will be inserted into the Code pane. When a snippet is added, any additional text that is required to be entere d to customize the snippet will be surrounded by a green box or hlighlighted in light red. In the example above, the text obj FSO and Scripting. File System Object could be modified. The part of the snippet that can first be changed is highlighted in light red. The current text obj FSO is fine so we can move on to the next part by pressing ENTER on the keyboard. The highlight will then move onto Scripting. File System Object so that this can be changed if necessary. Again, in this case, the current text is fine and pressing ENTER again will confirm the snippet is complete. Now an instance of the File System Object has been created (or instantiated), it can be used. In Overlord scripts this is commonly used to work with files as seen in the examples above. Selecting th e code snippet File  Copy File Method will add this method call which can be against the obj FSO object.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 104 of 202 T his time the default text entries on the snippet will need modifying as follows Name  obj FSO Source Path  “C:\Data. txt” Destination Path  \\LIMS\Plate Data \ + [Barcode] + “. txt” True (Overwrite?)  True With the snippet complete another line can be typed in this time that sets the object obj FSO to equal nothing. We now have the same code that was used in the example in Section 4. 10. 2 Using Overlord variables in Scripts. Using code snippets allows scripts to be written much quicker and also reduces the chances of syntax errors since code, that is known to work, is used.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 105 of 202 4. 11 Timers The Timers procedure step allows the user to manipulate time during the run. The edit window is shown below: The Timers edit panel There are 5 options: Duration; set the timer Description; Adjust Time; Return Time; Wait For Timer

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 106 of 202 4. 11. 1 Duration Select the variable to be set as the timer: Choosing the variable to use as the timer The user should then select either Run timer for or Run time until to set the timer duration. The timer can be an absolute time or a timer determined by the variables in the drop down list. To detect the end of the timer period either check the Wait for timer to complete option or use a loop with the timer option set with the timer variable selected:

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 107 of 202 Set a timer and then wait for it to elapse in the loop And the individual loop procedure step looks like this: Loop test for the end of the run 4. 11. 2 Description This allows the user to define a name for the timer. This is advisable when there are multiple timers in a run.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 108 of 202 Add a descriptive name to the timer

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 109 of 202 4. 11. 3 Adjust Timer This allows the user to make changes to a timer setting during a run. Adjust time option The user should choose whether one timer ( For one timer ) or all the timers ( For all dynamic timers ) will be affected by this procedure step. Then the user should then decide if the timers should be increased in time ( Add) or decreased ( Subtract ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 110 of 202 4. 11. 4 Return Time This allows the user to get a time value into a variable for manipulation. Return time edit screen Select the timer that the value is requ ired, choose the Time remaining or Time elapsed option, the unit for the time to be reported and finally the variable to which the information is to be assigned.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 111 of 202 4. 11. 5 Wait for Timer This allows the user to halt the Overlord2 procedure until a selected timer ha s elapsed. Wait for a timer to elapse Select the timer to wait to elapse. 4. 12 Loop This allows the user to halt the Overlord2 procedure until a selected timer has elapsed. 4. 13 Move Command The Move Command provides a simple interface to allow basic users t o move Labware around a system, without having to define the steps required in detail. The system should be setup by an advanced user, but once this is complete changes are only required if the system changes, for example if a new instrument is added. 4. 13. 1 Setup The Move Command is used in a Standard or Schedule Procedure the Setup dialog must be completed. To open the Setup dialog select Devices from the Command Palette, click the right-hand part of the Move button, then click Setup (Select Move Command Setup ):

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 112 of 202 Select Move Command Setup The Move Setup dialog will appear. Initially two entries will be listed for each device on the system (Move Setup Initial State). Each device will have a Get and a Put type entry. Move Setup Initial State The Move Command works by linking pre-defined Procedures (Move Command Procedure-. mcp files) together at runtime to move a Labware item from one location to another. The following explanation uses the example of moving Labware from a Thermo Cytomat storage device to a Bio Tek EL406.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 113 of 202 4. 13. 2 Move Type The entries in the Move Setup list can be one of three types: Get, Put or Direct Move. By default each device on the system has a Get and Put entry. Direct Move entries are for advanced use and not required on all system. They are explained in more detail later in the section. Get-A Get Move Command Procedure should contain the Actions necessary to move Labware from the initial storage location (e. g. Thermo Cytomat) to a safe point. The Proced ure should end with the Labware being gripped by the robot, ready to move to the destination location. Put-A Put Move Command Procedure should contain the Actions necessary to move Labware from a safe point, with the Labware already gripped by the robot, to the destination location (e. g. Bio Tek EL406). Direct Move -A Direct Move, Move Command Procedure, should contain the Actions necessary to move Labware from the initial storage location (e. g. Thermo Cytomat) to the destination location (e. g. Bio Tek EL406). The empty Procedures for all Moves can be generated automatically. Click the Auto-Generate Files button. A dialog will appear to check that the user wants to go ahead and generate the files (Auto-Generate Files). Click Yes to continue and generate files. Auto-Generate Files Once the files have been generated the Setup dialog will be updated to show the names of the auto-generated Procedures (Auto-Generated Files Displayed).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 114 of 202 Auto-Generated Files Displayed 4. 13. 3 Initialize Procedure This defines the Procedure that is called at runtime if the Move-Initialize action is called. It provides a way to make sure users initialise all devices on a system with only one Action. 4. 13. 4 Change Selected Procedure To change to Proced ure that is used for a particular Move, either double-click the entry, or select the entry and click the Select Procedure button. A file browse dialog will then allow any. mcp file to be selected. 4. 13. 5 Direct Moves The default behaviour for a system is to link Get and Put moves together. This is done so that we do not have to define every combination of moves on the system. However, in certain cases it may be desirable to define a single Procedure to move Labware to one location to another. An example of this is a Stacker device, where the Stacker Action moves the Labware in one Action. To define a Direct Move, click the Add Direct Moves button. The Add Direct Moves dialog will appear (Add Direct Moves):

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 115 of 202 Add Direct Moves Select the two l ocations required for the move. Click OK. Two entries will be generated in the move items list, one for each direction of travel-A to B and B to A (Direct Moves Added): Direct Moves Added Direct Move Procedures can be generated in t he same way a Get and Put Procedures, using the Auto-Generate Files button (Auto-Generate Direct Move Files).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 116 of 202 Auto-Generate Direct Move Files When a Direct Move has been defined this will override the Get and Put Procedures for that s pecific move at runtime. In the example, if the user selects a move from Thermo Cytomat to Bio Tek EL406, at runtime a single Procedure will be run-Thermo Cytomat to Bio Tek EL406 Direct Move. mcp. However, when the user moves Labware from the Thermo Cytomat to the REMP TPM it will link two Procedures-Thermo Cytomat Get. mcp, followed by REMP TPM Put. mcp. A Direct Move entry can be removed by selecting the entry in the list and clicking Remove Direct Move. 4. 13. 6 Advanced: Enable variable selection on Move Edit dia log This is an advanced feature that adds Overlord Text Variables to the Labware, From Location and To Location drop-down lists on the Move Command Edit dialog. Tick the box to enable to feature. The feature is explained in further detail in the Edit dialo g section.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 117 of 202 4. 14 Move Command Procedures The Move Setup section explained how to define which Move Command Procedures to use for each Device Get and Put. The next step of the configuration process is to complete the Procedures created using Auto-Generate Files. 4. 14. 1 Get Move Command Procedure Open a Move Command Procedure Get file. By default Move Command Procedures are generated in a sub-directory of the Procedures directory called Moves. The Procedure should be empty (Empty 'Get' Move Command Procedure): Empty 'Get' Move Command Procedure Add Actions to the Procedure to get the Labware from the storage device, pickup with robot and move to safe point. In the example, this means adding an unload Cytomat Action (Cytomat Unload Action), followed by a robot Action to pick up the Labware Robot (Get Labware From Hotel Action). It is important to use the variable [Move. Position] in any Storage Device position related Actions. This is because the value of [Move. Position] is set at runtime based on th e system configuration.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 118 of 202 Cytomat Unload Action Robot Get Labware From Hotel Action The Procedure should now resemble Completed 'Get' Move Command Procedure. Make sure the Procedure is saved:

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 119 of 202 Completed 'Get' Move Command Procedure 4. 14. 2 Put Move Command Procedure Open a Move Command Procedure Put file. In this example we will complete the Procedure to move the Labware to the Bio Tek EL406. This is simpler than the Storage Get procedure as only the robo t Action to put the Labware on the device is required.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 120 of 202 Empty 'Get' Move Command Procedure Robot Put Labware On Device

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 121 of 202 Completed 'Put' Move Command Procedure The Move Command Proceudres should be completed for all Get and Put moves. Any Direct Moves Procedures can be completed in the same way, making sure the Labware is moved completely from the source to the destination location. 4. 15 Adding a Move to a Standard or Schedule Procedure Once the Move Setup and all required Move Command Procedures have been defined Move Actions can be added to Standard or Schedule Procedures. To add a Move Action to a Procedure drag-and-drop the Move onto the Procedure flow from the Devices pane of the Command Palette (Drag-and-drop Move Action).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 122 of 202 Drag-and-drop Move Action The Move Edit dialog will appear (Move Edit). Select the Labware move, along with the From and To locations. The Labware listed is defined in Labware Setup (see Labware Setup sect ion). The From and To locations list either the device alias or the Positions Set alias, both set via Command Setup. Where a device has more than one position defined the Position item allow selection of the position. However, when a device is a robot, sta cker or storage device the Position item is disabled, as the position will be set atomically at runtime.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 123 of 202 Move Edit 4. 15. 1 Process Number When a Move Action is added to a Schedule Process the Process number option is disabled as this value is calculated automatically at runtime. When a Move Action is added to a Standard Procedure the Process number option is enabled and an Overlord Numeric Variable must be selected. At runtime this variable must be set to the Process you want to carry out the move for. This is important for moves from and to storage devices, so that the position to unload ([Move. Position]) can be calculated correctly. 4. 15. 2 Return Barcode The Return barcode to option is only enabled if the Get Procedure contains an Action that uses t he [Move. Barcode] variable. This means that the option can only be selected when the Procedure will return a barcode.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 124 of 202 For example, from the earlier example of Thermo Cytomat Get. mcp, adding an additional robot action to move the Labware past a barcode rea der, followed by a Barcode Reader action to return the barcode to [Move. Barcode] ('Get' Move Command Procedure To Return Barcode), will enable to option on the Move Edit dialog ( 'Return barcode to' Option Enabled) 'Get' Move Command P rocedure To Return Barcode

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 125 of 202 'Return barcode to' Option Enabled Tick the box and select a variable to return the barcode value. 4. 15. 3 Use Wait Time The Use wait time option is available only for Storage devices (including robot and stackers) during Scheduled Processes. To enable the option the move To location must be a storage device (Use Wait Time). The Use wait time box can then be ticked and a duration, in seconds, entered. At runtime, once the plate has been loaded into the storage dev ice the system will wait for the given duration before the next Move Action is executed for the process.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 126 of 202 Use Wait Time

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 127 of 202 5 Main Overlord3™ screen 5. 1 Running Overlord3™ When Overlord3 is launched from the start menu, file explorer or desk top, the Overlord3 main screen is displayed ( Main Overlord3 screen ): Main Overlord3 screen The Overlord3 main screen has the following areas (clockwise from lop left): File options (Section 5. 2File ribbon options ) Tab area (Section 5. 2. 2) Design (Section 5. 3. 1) Runtime (Sectio n 5. 3. 2) Setup (Section 5. 3. 3) Environment functions (Section Error! Reference source not found. ) Variables (Section 5. 4. 1) Help (Section 5. 4. 2) Variables Section 3. 5. 1 Runtime information Section 3. 6 Environment functions Section 3. 4 Flow Section 3. 7 Command Palette Section 3. 7 Plug-Ins Section 3. 7 Plug-Ins Section 3. 7 Setup tab Section 3. 3. 3 Runtime tab Section 3. 3. 2 Design tab Section 3. 3. 1 Procedure Work Area Section 3. 8 File and ribbon options Section 3. 2 Devices Section 3. 5. 3 Help Section 3. 5. 2

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 128 of 202 Devices (Section 5. 4. 3) Runtime information (Section 0) Command palette (Section 5. 6) Flow Plug-Ins Devices Procedure work area (Centre, Section 0) The user also has a number of Overlord3 environmental options, such as docking sub windows, hiding sub windows and colour options. 5. 2 File ribbon options The top left of the Overlord3 screen, has two sections, the standard file manipulation options (Section 5. 2. 1 File options ) and the ribbon options (Section 5. 2. 2 Ribbon options ). 5. 2. 1 File options To use the file options, select the blob in the top left of the Overlord3 main scr een (File options selection ). The file options menu then appears ( File options menu ). File options selection File options menu

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 129 of 202 The user can then perform one of the many standard file options: New Open a new Overlord3 procedure for editing Open Open an existing Overlord3 procedure for editing Close Close the current active open Overlord3 procedure Save Save the current active open Overlord3 procedure with the sam e procedure name Save As Save the current active open Overlord3 procedure with a different procedure name Save All Save all the current open Overlord3 procedures Print Preview Throws up a dialog box showing how the procedure would look if printed Print Print the current active open Overlord3 procedure Exit Exit The user is also offered a list of recent opened Overlord3 procedures on the right hand side of the panel. 5. 2. 2 Ribbon options The ribbon options button is located next to the File options button (Ribbon Options, Figure 17-Ribbon Options ). To add quick access icons to the quick access ribbon, follow the instructions below. The user can manipulate the ribbon options drop down box ( Ribbon drop down list ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 130 of 202 Ribbon Options Figure 17-Ribbon Options Ribbon drop down list 5. 2. 2. 1 Customize Quick Access toolbar To Customize Quick Access toolbar, select that option on the drop down menu. This will bring up the configuration menu ( Figure 18-Toolbar configuration options ). Select the Run option ( Choose run toolbar to edit ). Figur e 18-Toolbar configuration options Choose run toolbar to edit The options on the run menu then can be selected to be included in the quick access ribbon ( Add icon to quick access ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 131 of 202 Add icon to quick access Selecting Add moves the Run icon to the right hand pane ( Run icon added ). Run icon added Selecting OK will add the Run icon to the quick access ribbon ( Run added to the quick access ribbon ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 132 of 202 Run added to the quick access ribbon The Run option is available for easy access. 5. 2. 2. 2 Place the Quick Access Toolbar below the Ribbon Selection of this option allows the presentation of the options in a diff erent order. The Place the Quick Access Toolbar below the Ribbon option is available from the menu ( Ribbon drop down list ). option is accessed from the drop down Before the selection the top left of the screen is show n (before selection ) after the selection the icons are reorganized ( after selection ). before selection after selection This can be achieved in the editing dialog box ( switch order in dialog box ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 133 of 202 switch order in dialog box This can be reversed by clicking the option again and selecting Place the Quick Access Toolbar below the Ribbon from the menu, or deselecting the option in the dialo g box ( switch order in dialog box ). 5. 2. 2. 3 Minimize the Ribbon The Minimize the Ribbon option ( Ribbon drop down list ) removes the ribbon completely ( ribbon minimized ). The ribbon can be restored by selecting Maximize the Ribbon from the same menu (ribbon maximized ). ribbon minimized ribbon maximized 5. 3 Top panel-tab and buttons 5. 3. 1 Design tab The Design tab allo ws access to all the editing functions ( Design tab for procedure editing ). Design tab for procedure editing

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 134 of 202 The design panel offers similar functions to any editor. Selecting an action or actions in a procedure is completed by clicking the mouse left hand button in one position, keeping the mouse selected and bounding the action or actions, then releasing the mouse ( bounding an Overlord3 action ). The selected action or act ions then appear with a yellow perimeter ( the Overlord3 action is selected ). bounding an Overlord3 action the Overlord3 action is selected This action can then be manipulated with the other commands. Any of the icons may be greyed out as that function may not be available. 5. 3. 1. 1 Cut Cut a single or multiple actions in an Overlord3 procedure. Taking a demonstration Overlord3 procedure, it is possible to remove an action by bounding the element ( the Overlord3 action is selected ) and selecting the Cut icon, the unwanted action will be removed ( the action is removed ) and stored for later use (Section 5. 3. 1. 2 Copy135, Section 5. 3. 1. 3 Paste ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 135 of 202 the Overlord3 action is selected the action is removed 5. 3. 1. 2 Copy Copy a single or multiple actions in an Overlord3 procedure. Select an Overlord3™ action ( the Overlord3 action is selected ) and select the Copy icon. The action is stored for later use and the copied action or actions can be pasted in this or another Overlord3 proce dure (Section 5. 3. 1. 3 Paste ). Control-C also works to copy an action or actions to the copy buffer.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 136 of 202 5. 3. 1. 3 Paste The paste icon only becomes available when an action has been copied or cut in a previous act ion. Select with the mouse right hand button the location where the action or actions are to be pasted, the link will turn yellow ( select a position to paste an action ). Click the Paste box, and the stored action will be pasted into that position ( action pasted in selected position ). select a position to paste an action action pasted in selected position The user can also select an action in a procedure ( select a position to paste an action ) and choose the Paste icon ( action pasted in selected position ). Control-V also works to paste the copy buffer to the required position in the pro cedure.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 137 of 202 select a position to paste an action action pasted in selected position 5. 3. 1. 4 Delete To delete an action in a procedure ( the Overlord3 action is selected ), select the action or actions to be deleted, a nd select Delete ( the action is removed ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 138 of 202 the Overlord3 action is selected the action is removed 5. 3. 1. 5 Undo If the user wishes to undo the last action, just select the Undo action. This has multiple layers of undo. 5. 3. 1. 6 Redo If the user uses undo too many times, just select the Redo action to retract the last item.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 139 of 202 5. 3. 1. 7 Zoom Out Zoom In Zoom Out allows the user to see more of the procedure at the expense of clarity. See below for the effect of Zoom Out before (Error! Reference source not found. ) and after ( Error! Reference source not found. ) selecting the Zoom Out button. Zoom In allows the user to see less of the procedure at the expense of quantity of information. See below for the effect of Zoom In before ( Error! Reference source not found. ) and after ( Error! Reference source not found. ) selec ting the Zoom In button. 5. 3. 1. 8 Zoom to Fit The user can get the whole procedure on one screen at any time using the Zoom To Fit button. This is at the expense of procedure details. See below for the effect of Zoom To Fit before ( before Zoom To Fit ) and after ( after Zoom To Fit ) selecting the Zoom To Fit button.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 140 of 202 before Zoom To Fit after Zoom To Fit

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 141 of 202 5. 3. 1. 9 Properties The Properties button allows access to the details o n any Overlord3 procedure step (the edit screen). This is the same as double clicking on the procedure step. 5. 3. 1. 10 Action View Action View allows the user to see the comments relating to the Overlord3™ procedure step rather than the graphic representatio n. Selecting the Action View command, allows the user to choose in a menu between Graphic Only and Text Only ( Action View Menu ). The graphic only ( Action View, Image Only ) can be compared with text only ( Action View, Text Only ) below.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 142 of 202 Action View Menu Action View, Image Only Action View, Text Only

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 143 of 202 5. 3. 2 Runtime tab The Runtime tab allows access to all the runtime functions ( Runtime tab for runtime control ). Runtime tab for runtime control The Runtime panel offers similar functions to any DVD player. When the user has completed the procedures for the required automation method, the pro cedure is ready to run. 5. 3. 2. 1 Run Run the current procedure. 5. 3. 2. 2 Run Stepwise Run the current procedure step-by-step. After each procedure action has been completed, Overlord3 will expect the Run Stepwise icon to be pressed. Run continuously or Stop are also active for use at each step of the procedure. 5. 3. 2. 3 Pause Pause the current running procedure. Run continuously, Run Stepwise or Stop are possible options after pausing the run. 5. 3. 2. 4 Stop Stop the current running procedure. The user will be prese nted with a dialog box ( Stop the run dialog box) to confirm the cessation of the run (select Yes) or to continue from the stopping point (select No).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 144 of 202 Stop the run dialog box 5. 3. 2. 5 Validate Validate the commands in the current pr ocedure. The bottom left of the screen will show two messages, either Validation succeeded (Validation succeeded ) or Validation failed (Validation failed ). Validation succeeded Validation failed 5. 3. 2. 6 Analyz e Schedule Analyses the current Scheduled Procedure file to show the estimated order of actions at runtime. This includes estimated uration for the run. 5. 3. 2. 7 View Logfiles View the runtime log files. This is explained in more detail in a later secti on.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 145 of 202 5. 3. 3 Setup tab The Setup tab allows access to all the environment functions ( Runtime tab for runtime control ). Setup tab for system configuration 5. 3. 4 Environmental controls, main additional options The main options f or the environment control are found in the artist palette icon ( Main environment control ). Main environment control This options allow selection of the color scheme. The user can have either a favorite environme nt configuration or the default configuration. If the user has reconfigured the environment and wishes to return to the factory settings, they should select the Restore Default option and answer Yes to the dialog box ( restore default environment ). restore default environment To save a favorite environment, select Save Favorite, and answer Yes to the dialog box ( save environment as favorite )

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 146 of 202 save environment as favorite To restore a favorite environment, select Restore Favorite, and answer Yes to the dialog box ( restore favorite environment ) restore favorite environment 5. 3. 5 Environmental controls, help The user has access to Help at any time with the help icon ( Help). Help This shows the Help dialog box ( Error! Reference source not found. ) with standard access to the Contents, Index and Search functions. 5. 3. 6 Environmental controls, about The current verion of Overlord3 can be determined from the About dialog box. The About dialog box is displayed with version number and copywrite information.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 147 of 202 5. 4 Right panel 5. 4. 1 Variables There are 4 types of variable: Text, this is da ta that is alphanumeric, it is used to handle textual information. Numeric, this is data that has number information only (100, 10, 1, 0. 1, 0. 01 are all numbers) True False, the is also known as a Boolean operator with values of True and False, this is use to describe the state of an object, e. g. the plate is lidded, True or False Object, this is a more complicated structure for programmers to use in scripts, in order to use an Object created in one script in another. The Object would typically be a C# or V B. NET Object, for example a System. Collections. Generic. List(Of String) Object to store a list of barcode values. The user should be aware that the number 1 and the text value 1 are completely different entities and should be treated differently by the user and are treated differently by Overlord3. The numeric value 1 can be compared to other numbers such as 0. 1 or 10. The text value 1 is a statement of information only. The variable panel ( Main screen-Variables ) lists the variables that are available to the user in the current Overlord3™ environment. Main screen-Variables

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 148 of 202 To add a new variable select the green plus (add a variable icon ). add a variable icon The u ser should see a dialog box to enter the new variable name. The user should enter the new variable name, in this example test_variable and choose the variable type from the drop down list, in this example Text (add variable dialog box ) add variable dialog box The user can then select OK to continue (continue to add a variable ). continue to add a variable

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 149 of 202 This will update the Overlord3 main screen variable list (updated variable list on main screen ). updated variable list on main screen When the list has a large number of entries, it is useful to sort the list, there are two options, by name using the Name button (variables, sort by name ). variables, sort by name And by variable type with the Type button (variables, sort by type ). variables, sort by type

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 150 of 202 Once Overlord3™ has been started the variable values persist until changed by the system. For example, it is necessary to initialise the variables at the beginning of a run to ensure that all the numbers are initialised to zero, and all the strings are set to no characters. To change the value of a variable manually, select the variable of which you wish to change the value. (changing the value of a variable ) changing the value of a variable Enter the new value under the Name text entry box, and select Update . (variable value changes ). variable value changes The variable value will now be set to the new value. (new variable value ) new variable value

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 151 of 202 To delete a variable select the variable name and then click the red cross . (delete selected variable ) delete selected variable 5. 4. 2 Help The context sensitive Help is available for most areas of the screen, command and runtim e information. The help screen is updated depending on the screen area last selected. Main screen-help If another section of the screen is chosen, for example the Loop command in the Flow command area, the help box information changes ( Help panel, Loop command ). Selecting one of the information lines in the Help area will bring up an information dialog box ( Using the help panel for the Loop command ). Searching for information on a set subject, chose the Search tab from the Help area. The standard keyword search panel is displayed ( Searching the Help file ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 152 of 202 To search for a keyword, select the Index tab of the Help area. ( Searching the keyword index ). To view the Contents of the help file, select the Contents tab (Searching the Contents ). Help panel, Loop command

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 153 of 202 Using the help panel for the Loop command Searching the Help file

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 154 of 202 Searching the keyword index

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 155 of 202 Searching the Contents 5. 4. 3 Devices The devices area of the main screen displays the currently installed instruments/devices on the system (Main screen-devices ). To add, remove or change this list, move to the section relating to setup. This information box acts as a runtime information box, showing if the instruments are Idle (Main screen -devices ), Busy (Devices-Busy attribute ) or in an Error status. The instrument is highlighted red on error. Main screen-devices Devices-Busy attribute

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 156 of 202 Devices-Error attribute The Device Position Viewer allows the user to see the curren t status of all the equipment on the system, and the plate load status. Select #Device Position Viewer to see the information, choosing the drop down box ( Position Viewer, change instrument ) to change instrument. Position Viewer dialog box

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 157 of 202 Position Viewer, change instrument 5. 5 Runtime information/Error list The runtime information box and runtime error list are stored as a tabs by default ( Runtime Output ). Runtime Output Hover over or the tab to reveal the contents ( Runtime Output tab expanded ). Runtime Output tab expanded To view more of the panel, expand with the stretch tool ( Runtime output resizing box ),

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 158 of 202 Runtime output resizing box 5. 6 Command palette Command palette These commands are listed into three different categories, Flow, Plug-ins and Devices. The start default is Flow ( Figure 1. 4-Flow palette ). Clicking on the Plug-Ins icon on the Command Palette will show the available Plug-In commands ( Figure 1. 5-Plug-Ins palette ). If you wish to see and used the installed instruments, select the Devices palette ( Figure 1. 6-Devices palette ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 159 of 202 Flow palette Plug-Ins palette Devices palette Each command can be dragged onto the Procedure flowchart to generate an Action, which uses the Command in a particular way. The follow section describes all of the common commands available and how they would be used within a Procedure. These functions are explained in the Commands Section 4.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 160 of 202 5. 7 Favorites area Selecting the favorites option ( View Favorites palette option ), allows a user to move frequently used commands into one area. View Favorites palette option The Overlord Favorites palette, is initially empty ( Favorites empty ), however selecting an icon in another palette (e. g. Loop in Flow ) and using he mouse in the drop down arrow on the right hand side of the Loop icon to bring up the drop down menu to select Add to Favorites (Loop, add to Favorites ), allows the user to add a new option to the Favorites palette ( Loop added to Favorites ). This Favorites option can be removed by using he mouse in the drop down arrow on the right hand side of the Loop icon to bring up the drop down m enu ( Remove Loop from Favorites ) and selecting Remove from Favorites.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 161 of 202 Favorites empty Loop, add to Favorites Loop added to Favorites Remove Loop from Favorites

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 162 of 202 5. 8 Palette configuration The palette layout can be configured. Palette options The options are: Show More Buttons, this will move the Favorites palette from an icon to a palette bar ( Show More buttons ) Show Fewer buttons, this will move palette bars to ico ns (Show Fewer Buttons ) Navigation Pane Options, this allows ordering and removal of palettes as required ( Navigation Pane Options ) Add or Remove Buttons, easy addition and remova l of palettes ( Add or Remove Buttons )

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 163 of 202 Show More buttons Show Fewer Buttons Navigation Pane Options Add or Remove Buttons

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 164 of 202 5. 9 Overlord3™ window controls There are a number of icons available on the Overlord3 screen that allows manipulation of the environment and work area. 5. 9. 1 Environmental controls, thumbtacks The thumbtack in the top right of a panel ( Thumbtack selection ) allows that information panel to be converted to an a uto-hide tab. Pass the mouse over the thumbtack and click and the panel will disappear off the screen and be replaced with a tab ( Replacement tab ). Thumbtack selection Replacement tab The panel can be made visi ble, and used, by passing the mouse over the tab ( select tab and thumbtack to make panel visible ). The panel can be made visible permanently by passing the mouse over the tab and clicking on the thumbtack ( panel visible again ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 165 of 202 select tab and thumbtack to make panel visible panel visible again All the thumbtacks can be selected and the resulting tab makes a very clean interface ( full thumbtack selection ) compared to displayed panels ( before thumbtack selection ). full thumbtack selection before thumbtack selection 5. 9. 2 Work Area controls, Multiple Document Interface Overlord3 has a flexible multiple document interface. This means the user can have many Overlord3 procedures on the screen simultaneously, with the option of each procedure being displayed or on a tab. For example, open four new procedures (Selection 5. 2. 1 File options ) to get four procedures to manipulate ( Load four procedures ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 166 of 202 Load four procedures The presentation of the procedures to the user can be manipulated. To see Procedure 1 and Procedure 4, click on the Procedure 1 tab and keep the mouse button down ( Grab the Procedure 1 tab).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 167 of 202 Grab the Procedure 1 tab Move the mouse and the location icon will appear ( windows location icon ). The user can choose the location where the window will reside ( Figure 19-add new window at top of screen, Figure 20-add new window at right o f screen, Figure 21-add new window at bottom of screen, Figure 22-add new window at left of screen, Figure 23-add new window to tab list, Move mouse and location icon will appear ). windows location icon Figure 19-add new window at top of screen Figure 20-add new window at right of screen Figure 21-add new window at bottom of screen Figure 22-add new window at left of screen Figure 23-add new window to tab list When an icon is selected, the area is greyed out to show the user what the screen might look like if that option is selected.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 168 of 202 Move mouse and location icon will appear Examples of positioning left ( position left ), right ( position right ), up ( position up ) and down ( position down ) are shown below. position left

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 169 of 202 position right position up position down

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 170 of 202 The Procedure 1 tab can be repositioned in the tab row by dragging the tab to the centre of the positioning icon ( return to the tab row ). return to the tab row The use of these tools can position the procedures in a user favourable way. Examples are shown below (different page payouts for 4 procedures ). different page payouts for 4 procedures

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 171 of 202 5. 9. 3 Tooltips By passing the cursor over any of the flow chart steps, Overlord3 wi ll show what that step will do at runtime by displaying a tooltip ( Tooltips after passing mouse over procedure step ). Tooltips after passing mouse over procedure step

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 172 of 202 5. 9. 4 Getting and changing properties of a procedure step To change the parameters of a procedure step, the user should select the procedure step ( Changing the properties of a procedure step, double click ) and double click to display the properties ( Dialog box to view/change properties ). Changing the properties of a procedure step, double click Dialog box to view/change properties The user can then view and or make changes to the properties of the procedure step before selecting: OK to exit and save the changes. Cancel to ignore the changes.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 173 of 202 5. 9. 5 Cut, Copy, Paste, Delete, Properties In addition to the toolbar functions to edit the procedure flow chart, the user can also use the mouse edit function by passing the mouse over the required step and single right hand mouse click han d mouse click (Mouse editing menu ). Mouse editing menu The options are described in other sections of the manual: Cut (see Cut) Copy (see Copy) Paste (see Paste ) Delete (see Delete ) Properties (see Properties )

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 174 of 202 6 Creating Procedures Procedures are created by dragging Commands across onto the flowchart to build up Actions. The way the procedure runs Actions can then be controlled by using Overlord variables. The following sections describes how all of these components work together to run an Assay and is followed with an example on how a simple procedure can be built up. 6. 1 Opening a new procedure From the circle menu ( Overlord3™ screen, top left) select New (New Procedure ). open a new procedure The user is offered a choice of procedure type to create ( Choose procedure type ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 175 of 202 Choose procedure type There are three types of procedure: Standard Procedure Move Command Procedure Schedule Process Procedure See scheduling section for details on the different scheduling types. 6. 2 Standard Procedure A standard procedure produces an even t driven procedure. These procedures have the complete set of Overlord3 functions available. These procedures are identified with the <filename>. ovp filename type and are saved in the normal way. 6. 3 Move Command Procedure These are automated moves that are used by the Schedule Procedure type process. The Schedule Procedure type reduces the user input by inferring that a process that has a diluter as stage 1 and a plate reader as stage 2 will require a robot or stacker move to transfer the plate from the di luter to the plate reader. These moves are called Move Commands and defined in the Move Command Procedure function. Not all Overlord3™ commands are available in a Move Commands Procedure, please see the list below.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 176 of 202 Flow Loop  Exit Loop  Decision  Call Procedure  Exit Procedure  Exit Run  Wait For Device  Plug-Ins Initialise Variable  Set Variables  Message Box  User Input  Timers  Script  Controlled Stop  Labware Definition  Position  Devices All  This all ows Move Commands Procedure complex functions to be performed, for example, if there is a lid on the plate remove and park the lid, before placing the plate on an instrument. Move Commands Procedures don't have a runtime mode. These procedures are identifi ed with the <filename>. mcp filename type and are saved in the normal way.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 177 of 202 6. 4 Schedule Process Procedure A Schedule Process Procedure is a time driven scheduler that will run a dynamic scheduling mode. The time dependency of the process of the standard Overlo rd3 means that Overlord3 functions that might lead to a non-determinant time frame are not available. Non-determinant times make the initial scheduling process impossible. Flow Loop  Exit Loop  Decision  Call Procedure  Exit Procedure  Exit Run  Wait For Device  Suspend Process  Plug-Ins Initialise Variable  Set Variables  Message Box  User Input  Timers  Script  Controlled Stop  Labware Definition  Position  Devices All 

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 178 of 202 6. 5 Procedure Flowchart When Overl ord3 starts, it opens with an empty procedure that consists of a Start Action, an empty Action and a Finish Action. All procedures contain a Start and Finish Action and these cannot be removed. Commands are dragged in between these two Actions to build up the procedure. A new procedure, if there isn't already one open can be created by going to the File Menu and selecting 'New Procedure'. This should load the following window ( New Procedure ). New Procedure A Command can then be added into the empty Action box or inserted between existing Action boxes. The place where the command will be added will be highlighted so when the mouse button is released, it is clear where the command and resulting Action will be placed. If a Loop com mand is inserted between the Start action and the Empty Action, the procedure will expand to include this new Action ( Add Loop Command ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 179 of 202 Add Loop Command Add a Message Box command onto an empty box and the procedure remains the sa me, the only difference being the Action in that place is updated. If you add a command onto a box that already contains an Action, a dialog will appear asking if you want to overwrite the existing Action. The basic rules are, dragging onto an arrow will insert the Action ( Insert ), dragging onto a box will overwrite the Action ( Overwrite ). Insert Overwrite Existing Action boxes can also be moved within a procedure or deleted.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 180 of 202 6. 6 Overlord Variables Overlord variables have a very important role in Overlord3. They control how procedures execute at runtime and they pass data around between devices on the system and with the outside world. There are 2 default variables on every system, [Plates] and [Barcode]. The y have the following uses. Variable Use [Plates] Represents how many plates are to be run. Typically used to control how many times a Loop action should loop around. [Barcode] Normally used within a Barcode action. The read barcode is stored in this variable. This can then be used in a script to rename a file with the barcode of the plate. The current list of variables on the system is listed in the Variables pane which is normally in the top right of the main window ( Variables pane ). Variables pane Extra variables can be added by clicking the green cross. The name of the new variable and its type can then be added ( Add Variable ). Add Variable The type of an Overlord variable refers to the type of data it contains. There are four types of variable available.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 181 of 202 Type Description Numeric For variables that store numbers such as the current plate or the volume to dispense. Text For variables that store text such as the data path to write new generated plate data to. True/False Variable that is either true or false. Used typically for variables that indicate if the plates have lids or not. Object This variable type is used on more advanced setups and is used in association with Scripts. It allows Objects tha t were created in a Script to be persisted across multiple scripts. An example would be an instance of the Excel Application Object. This would mean this object would only need to be created once if we were using multiple times within a procedure. 6. 7 Actions Each time a Command is dragged onto the Procedure flowchart, an Action is created. At runtime, each Action will execute a specific task using the Command it was created with. If a Robot command (e. g. Mitsubishi Robot) is dragged onto the flowchart an Ed it screen will appear for that Command. If the robot program “Get Plate From Incubator” is selected, then at runtime, that program will be executed. Alternatively, if a Loop command is dragged onto the flowchart and Edit screen will appear for setting options on how to loop. If the loop is set to loop around 3 times, at runtime, it will do exactly that. Refer to Section 6. 7 Actions for details on how all the Overlord3 core commands work. Refer to the Readme files that come with each Overlord Driver, available from the PAA website , for details on what options are available. Each Action is similar in that they each h ave a set of properties. By highlighting an action and then right mouse clicking, the context menu will appear. At the bottom of this menu will be the entry “Properties”. Selecting this will bring up the Action Properties dialog ( Action Properties ). Action Properties

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 182 of 202 The table below describes each of the properties that are available and what they do. Property Description Wait until Idle By default, when an Action is executed at runtime, the procedure execution will wait for t he Action to complete. If this property is turned off, the Action will be started, but the procedure will carry on running moving onto the next Action. If the procedures are built up properly, Actions representing Devices (instruments) can be run in parall el which improves the throughput of the system that Overlord3 is running. Breakpoint If the Breakpoint property is set, the execution of the procedure will pause when it comes up this Action. This feature is typically used when testing the procedure for the first time. Typically, you turn a breakpoint on, on a Robot Action that was about to move a plate into an area of the Workcell where a collision could occur if the devices was not in the right state (e. g. a pippetting station with its arm in the positi on where the plate would be loaded) Enabled By default, an Action is enabled. If this property is turned off, at runtime it will not be executed. Retry on error If an error is generated on this Action at runtime and this property is turned on, the Action will automatically run again until an error is actually generated. The number of times it 'Retries' is set in the text box labelled 'Retry Count' Comment The comment box allows a better explanation of what the Action is doing, to be associated with it.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 183 of 202 6. 8 Example Procedure This section will go through step-by-step how to create a procedure that will move a set of plates from a Thermo Kendro Carousel ( Thermo Kendro Cytomat Carousel ) onto a Molecular Devices Aquamax (Molecular Devices Aqua Max ) using a Mitsubishi RV-2AJ (Mitsubishi RV-2AJ robot ). Thermo Kendro Cytomat Carousel Molecular Devices Aqua Max Mitsubishi RV-2AJ robot The procedure will be setup as follows. 1. There will be a mai n procedure that uses sub-procedures that move plates to and from the Aquamax 2. The procedure will allow a variable number of plates to be run 3. The procedure will allow the user to enter which program to run on the Aquamax 4. The Kendro will be setup to automati cally retry on error 5. Each robot action will have break points for testing purposes It is assumed that Overlord3 is already setup with devices described above. The commands (drivers) for these devices can either be downloaded from the PAA website or by contacting PAA directly. It is also assumed that the Mitsubishi has already been programmed with the following 4 programs GPCYT-Get Plate From Kendro Cytomat PPCYT-Put Plate onto Kendro Cytomat GPAQ-Get Plate from MD Aquamax 1. PPAQ-Put Plate onto MD Aqumax The procedure requires 2 new Numeric variables. Add a variable called ' Cur Plate' and another called ' Aquamax Program'. Refer to Section 6. 6 on how to add n ew variables. 2. Starting with a new Procedure, add a User Input command that asks the user how many plates they want to use. Store this value into [Plates] (User Input for Number of P lates).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 184 of 202 User Input for Number of P lates 3. Follow this with another User Input command that asks the user what Aquamax Program they want to run. Store this value into [Aqua Max Program]. Add a Loop command after the last User Input action and configure this to be a fixed loop that loops [Plat es] times. Set it up so that the variable [Current Plate] is updated with the current Loop number (Fixed Loop ). Fixed Loop 4. At this point the procedure should contain 2 User Input commands and an empty Loop ( Empty Loop). The next step is to fill in the loop with the Actions that will be run on each plate

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 185 of 202 Empty Loop 5. Add a Kendro Cytomat Series command from the Devices palette into the loop ( Setup Cytomat to unload ). Select the option t o Unload a plate from the position [Current Plate] (Setup Cytomat to unload ). If the loop is setup to loop 5 times, then the first time through the value of [Current Plate] will equal 1. 2nd time through it will equal 2, 3rd time through it will equal 3 and so on until the final loop through, the 5th time through where [Current Plate] will equal 5. With this setup, each time we go through the loop, a different plate is unloaded from the Kendro Cytomat. Setup Cytomat to u nload

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 186 of 202 6. Next add a Mitsubishi Melfa RX command to pick up the plate from the Kendro since at this point, the plate would be sitting on the Kendro Transfer station. Select the robot program to pickup a plate which in this case is GPCYT. 7. Add another Mitsubish i Melfa RX command to place the plate onto the Aquamax. Select the program PPAQ. 8. Add a Molecular Devices Aquamax command to run a program on the Aquamax ( Run Aquamax Program ). This should be configured so that is runs a program represe nted by the variable [Aquamax Program]. When selecting the program make sure the 'Wait until Finished' checkbox is selected. It is very important this checkbox is selected when using Overlord1 Drivers in Overlord3. Run Aquamax Program 9. At this point in t he run, the Aquamax would have finished running the program so the plate can be returned to the Cytomat. 3 commands are required for this. Two Mitsubishi commands are required to pickup the plate, GPAQ, and place onto the Kendro, PPCYT. Finally the plate c an be returned into the position within the Kendro it originally came from. Add a Kendro Cytomat Series command to load the plate into position [Current Plate] 10. The program is now complete and should be saved. Save this as MAIN-Run Plates on Aquamax. ovp. T he Kendro Cytomat actions need to be setup to retry automatically upon error plus a breakpoint is needed on the first Mitsubishi action. Select the first Kendro Cytomat set the Retry on error property so that if there is an error the Cytomat will automatic ally retry before reporting an error (See section 6. 7 Actions ). Repeat for the other Cytomat action. Select the first Mitsubishi command and set the 'Breakpoint' propert y.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 187 of 202 11. At this point, all of the Actions are with one procedure. One of the requirements for building up this procedure was to use sub-procedures for moving plates to and from the Cytomat. Imagine if we also on this system had another procedure that was ident ical to the procedure created above, but instead of an Aquamax it used a Biotek Washer. If down the line we wanted to add in a barcode reader step, we would need to modify both procedures to add this change. However, if we use sub-procedures, we only need to make this change in the sub-routine since both Main procedures would be using this. Building up sub-routines is good practice since it reduces the chance of writing the same blocks of actions over and over again. Create a new procedure and dock this nex t to the existing procedure ( Create Sub Procedures ). Select the Cytomat Action and the Mitsubishi command that unloads a plate from the Cytomat and picks it up ( Get Plate from Cytomat Sub-Procedure ). Cut and paste these into the new procedure and save this as 'Get Plate from Cytomat'. Add a Call Procedure command into the Main procedure to call this new procedure. Create Sub Procedures

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 188 of 202 Get Plate from Cytomat Sub-Procedure 12. Create another n ew procedure and then remove the last Mitsubishi action and Cytomat action from the Loop in the main procedure. Cut and paste these into the new procedure and save this as 'Put Plate on Cytomat. ovp'. Add a Call Procedure command into the Main procedure w here these two actions were removed that calls this new procedure. 13. The procedure is now complete, we have one main procedure, using two sub procedures, that moves a variable number of plates onto an Aquamax and runs an Aquamax program that is set by the user at runtime ( The Final procedure(s) ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 189 of 202 The Final procedure(s) 6. 9 Advanced Procedure with Incubations and Data Handling Incubations can be run in Overlord3 by using the Timers command. By allocating a Timer to a plate and telling it to run for a period of time, we are effectively doing the same as if the plate was being run manually using a stopwatch for the incubations. With a stopwatch, you wait until the required time has elapsed before carrying on with the next steps in the assay. In Overlord3, you do exactly the same, you tell the Procedure to wait until the timer in question has elapsed before moving onto the next set of Actions. There are also other ways to monitor timers. Decisions and Loops can work against the state of a T imer. However, for this example we will just be using the Timer command option “Wait until Complete”. Taking the previous example (Section 6. 8),

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 190 of 202 Example Procedure : this will be extende d so that after the plate is run through the Aquamax it will be incubated for 1hr in the Cytomat before running it through a Molecular Devices Spectra Max using Softmax Pro. Finally, the plate will be moved back into the Cytomat. The plates will also now be bar-coded so a barcode reader is required. The data generated by the Specta Max will need renaming with the barcode and stored onto a network resource for a LIMS to pickup. See the flow diagram below for an illustration of the assay we are looking to autom ate. Metrologic Barcode Reader Molecular Devices Spectra Max Plus384 Plate Reader Before modifying the existing procedure, the Metrologic Barcode reader and MD Spectra Max commands (See above) need to be downloaded fr om the PAA website and added. It is also assumed that the Mitsubishi has been programmed to additionally contain the following 3 programs. GPSM-Get Plate From Spectra Max PPSM-Put Plate onto Spectra M ax BARCODE-Move Plate past barcode reader (always gripping the plate) 1. Open the procedure MAIN-Run Plates on Aquamax. ovp and save as MAIN-Incubation Demo. ovp 2. Add a timer command after the step that puts a plate back into the Cytomat ( Add Incubation Timer ). This resulting Action will be telling the procedure that this plate needs to be incubated for one hour. Set this action so that is uses the Timer represented by [Current Plate] and sets it to run for 1hr. Using [Current Plate] means that on the first time around the loop when we are using Plate1, it will be assigned Timer 1. Plate 2 will have Timer 2; Plate 3 will have Timer 3 and so on. Move plate back to Cytomat and Incubate Plate for 1 hr Load plate onto Spectra Max and start Luminescence Method Load plate onto Spectra Max and start Lumin escence Method Move plate back to Cytomat and store Plate data on Network Move Plate from Cytomat to Aquamax and Dispense Reagent Aquamax Move pla te from Cytomat to Barcode Reader

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 191 of 202 Add Incubation Timer 3. Once all the plates are back in the Cytomat they will each have the ir own timer, each one elapsing slightly later than the next. If we were running 5 plates, 5 timers would have been created. Assuming the first plate was loaded into the Cytomat at 10. 00am and the time to move a plate to the Aquamax, run a program and back to the Cytomat takes 2 minutes, the Incubation elapse cycle would look as follows. Plate Timer Elapse Time (Incubation time of 1hr) Plate Timer 1 11:00 am Plate Timer 2 11:02 am Plate Timer 3 11:04 am Plate Timer 4 11:06 am Plate Timer 5 11:08 am The next part of the Overlord procedure needs to wait for relevant timer to elapse before moving the plate to the Spectra Max. Add another loop into the procedure after the existing loop that again loops [Plates] times and uses [Current Plate] to represent th e current loop number ( Add new Loop ). Add a Timer command inside the loop and select 'Wait for Timer'. This should wait until the timer represented by [Current Plate] has completed. The desired effect here will be that the procedure wi ll not move plates to the Plate reader until the Incubation has completed.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 192 of 202 Add new Loop 4. The steps to move the plate to the reader and back need to be added after the Timer command. Add a Call Procedure command and select the OVP file 'Get Plate from Cy tomat. ovp' which was created in the previous example'. 5. Add a Mitsubishi command to read the plate on the barcode. Select the Robot program BARCODE. Follow this with a Metrologic Orbit command to take the barcode that was just read and store it into the Ov erlord Text variable [Barcode]. 6. After this add a Mitsubishi command and select the program PPSM. It is assumed that the Spectra Max drawer is already open at this point. Follow this with the Spectra Max command. Select a method that has already been created in Softmax Pro, the software for running the reader in stand-alone mode. Set it up so that with each read the data file C:\Plate Data \Data. txt is created. 7. Once the reader has finished, the drawer will open automatically. Add a Mitsubishi command to pick up the plate, PPSM. Add another Call Procedure command after this and select the program 'Put Plate on Cytomat. ovp' All of the instrument calls are now complete. The only thing is missing is a way of renaming the generated plate data with the barcode of the p late and then moving this onto a network resource. This can be done by using a Script command. Add this after running the Spectra Max. Assuming the command has been setup to use VBScript use the following code. 8. The procedure is now complete. This exampl e shows how incubations can be added into an Overlord procedure by using timers. The entire assay has effectively been divided into 2 sub processes, Run plates through Aquamax and Incubate followed by Run plates through Spectramax. A general rule of thumb is that the number of incubations plus 1 is the number of sub processes required. Set obj FSO = Create Object ("Scripting. File System Object" ) obj FSO. Copy File "C:\Plate Data \Data. txt", “\\LIMS\Assay Data \” + _ [Barcode] + “. txt”, True Set obj FSO = Nothing

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 193 of 202 7 Running Procedures 7. 1 Standard (Event-driven) Procedures Procedures are run from the window that they were created in. This section describes how a procedure can be run and als o how it can be validated before a run even begins to ensure it is setup correctly. This section also describes how errors are handled in Overlord3 and how a run is logged. 7. 1. 1 Run Once a procedure has been created it can be run by simply clicking the Run butt on on the Ribbon toolbar. The procedure must be saved at this point and a message box will appear asking for the procedure to be saved if it isn't. Before the run starts, the procedure and all of its sub-procedures will be validated to ensure all the Actio ns can be executed. If this passes, the procedure will begin running). Overlord3 at Runtime At runtime the Command palette that is normally on the left hand side of the screen disappears, but apart from this the screen will appear the same as it doe s at Edit time. As each Action is highlighted it will be executed and will stay highlighted until the execution is complete. If a sub-procedure is called, this will be loaded onto the screen and execution will continue through the sub-procedure, as seen in Calling a Sub-Procedure at Runtime ). The main procedure will stay open at this point and the Call Procedure action that made the call will remain highlighted so it is clear where execution will resume once the su b-procedure has completed ( Calling a Sub-Procedure at Runtime ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 194 of 202 Calling a Sub-Procedure at Runtime When an Action that is running a device, is executed, the status of this device will be updated in the Devices palette that is typic ally on the right hand side of the screen ( Executing a Device Action ). Executing a Device Action The run can be paused at any point during the run by clicking the pause button on the ribbon toolbar. Pausing wil l stop the execution at its current point and will not execute any subsequent actions. If there is an action currently running, or devices that are busy, these will continue running. Pause just stops the execution of new actions, it doesn't pause current ly running Actions. To resume the run, click on the Run button on the ribbon toolbar. Alternatively, the stepwise button can be clicked. This will move the execution onto the next Action but will then pause the system again. This is useful when running a procedure for the first time to ensure each Action completes as expected before moving onto the next Action. The procedure will also pause when it comes up to any Action that has a breakpoint set.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 195 of 202 7. 1. 2 Validation Validation checks that the procedure and all of its sub-procedures contain Actions that will run properly at runtime. Below is a list of just some of the things Validation checks Procedures that are being called actually exist Variables that are used in an Action actually exist on the system That co nfiguration settings have been made for certain devices Syntax errors in VBScripts, VB. NET and C# Code Snippets Validation can be run by clicking on the Validation button in the Runtime section of the Ribbon toolbar. It will also be run automatically when the Run or Stepwise button is clicked. If there are any issues with any of the Actions in the main procedure or its sub-procedures, these will be listed in the Error List palette that typically is located at the bottom of the window ( Validation Error list ). Validation Error list The list explains what procedures and commands have issues and a description for each one of what the problem is. Double clicking on the entry in the list will open that procedure if it isn't already open and highlight the action with the issue. If there are Validation errors, indicated in the list by the red circle with a white cross, the procedure cannot be run and will not run until the issue is resolved. Entries in the Validation Error list can also be Warnings. Validation warnings are listed alongside a yellow triangle with an exclamation mark inside. Warnings simply alert the user to double check that everything is setup as this action may fail if certain conditions are met. An example would be an Acti on that uses a device that has a dependency on a certain file existing in a certain folder. The warning for this action would simply tell the user to double-check that when the procedure gets to this action, that key file will exist. This wouldn't be a Val idation Error because it maybe that the procedure creates this key file at runtime. 7. 1. 3 Error Handling Although validation does it best to prevent errors, errors will still come up during a run. These can be due to many different things such as the following. Faulty instrumentation Incorrect correct configuration (e. g. Device setup up on the wrong COM Port) Data files not generated in the correct format Labware loaded into the wrong position This list could easily be much longer. There are many different types of error that can happen on any system. Overlord3 will trap all errors that are encountered at runtime and will give the user the chance to respond to the error in three different ways Ignore -The error will be ignored for this Command

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 196 of 202 Retry -The Actio n will be sent to the command again and depending upon the command will either start from the beginning or will resume from where the error occurred Abort -The entire run will stop There are 2 different ways that errors are reported and it depends upon wh at type of command the error is generated in. If the command is a device (e. g. robot, plate reader, pipetting station etc) then the error will be raised in the Device List palette by highlighting in red the relevant error. If this is the only device in error, the Error palette will be filled in with the details of the error. The Retry and Ignore buttons will also become available giving the user the chance to respond to the error as seen in Device Erro r). If there i s more than one device in an error state at the same time, clicking on each device will bring up its error details in the Error palette ( Device Error ). Device Error If the command is a non-device, a Flow or Plug-in command (e. g. M essage box, Script, Loop etc) then the error message will be brought up as Message box with the Abort, Retry & Ignore options available to the user. All error responses are recorded into the Logfile. 7. 1. 4 Logfile Every time a procedure is run, an entry is creat ed in the Overlord Logfile so you can see exactly how the run proceeded ( Logfile Viewer ). The logfiles are accessed by clicking on the Logfile button in the Runtime section of the Ribbon toolbar.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 197 of 202 Logfile Viewer Each time a run star ts a new Logname is created using a time/date identifier with the format <dd/mm/yyyy> <hh:mm>. Every run that has ever been started will appear in the Log Name drop down list and is listed in reverse chronological order, newest first. Selecting the log you wish to view will populate the Log grid which lists all of the activities which occur during a run. There are different activities that happen during a run, known as Run Log Types. These are listed below. Run Log Type Description Run Start When the Run begi ns Run Finish When the Run completes Action Start When an action is first executed Action Finish When the action completes Action Error If there is an Error with the Action User Response Ignore The user has responded to the error be selecting Ignore User Re sponse Retry The user has responded to the error by selecting Retry User Response Abort The user has requested the system to Abort The Run Log Type column on the Log Grid sometimes also lists the name of a variable type, Numeric, Text, True/False or Object. T his is because the Log also records when variables value changes. Each entry in the Log is listed with the time that it occurred. There is also an additional column next to this called Timer ticks. This is for trouble shooting systems where there is a timi ng issue and we need a log recording resolution less than 1 second. This functionality is only for advanced users.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 198 of 202 There are various drop down boxes below the Log Name drop down box. These are all filters which allow the Logfile to only display relevant in formation. For example if the Kendro Cytomat is selected in the Commands Filter drop down box, only entries in the Log that report usage of the Kendro Cytomat will be displayed ( Filtered List ). This filter can be reset by selecting 'A ll' in the filter list. Filtered List 7. 2 Running Schedule Process (time-driven) Procedures

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 199 of 202 8 Frequently Asked Questions Question Answer How can I check communication with an instrument, because it doesn't work? If the instrument comes with its own softw are it is often best to check through this. Most communication errors are due to the wrong cable being used. If the instrument software is generating a Timeout error, its most likely to be this. If the instrument doesn't have its own software and it uses Serial communications, Hyper Terminal or VBTerm can be used to send raw commands to the instrument. The commands to use are often listed in the user manual for the relevant instrument. Again, if there are no responses at this point, it suggests it is a Time out error. If I have an issue, what files should I send PAA to begin with? The following files should be sent The OVP file(s) that are being used C:\Program Files \PAA\Overlord3 \Overlord3. mdf C:\Program Files \PAA\Overlord3 \Overlord_log. ldf How can I backu p my system in case the PC dies? Copy the following All files in C: \Program Files \PAA\Overlord3 All files in C: \Overlord C:\Windows \Overlord. ini Backup of the registry key HKEY_LOCAL_MACHINE \SOFTWARE \Process Analysis & Automation. This can be done by goin g to the program REGEDIT, accessible by typing this into the Run prompt in windows. What do I need to do to transfer Procedure files from one system to another? Overlord3. mdf and Overlord_log. ldf must be copied across Can I use Overlord3 to emergency sto p a robot? No. Overlord can only stop a procedure from running, it cannot halt actions that are already running. See Section 7. 1. 1 Run for more details

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 200 of 202 My instrument isn't connected with original manufacturer supplied cable and I don't have their software. But why doesn't Overlord work anyway? Overlord will only work if all the instruments are connected with the correct cables and the correct instrument software. If instruments do not work in stand-alone mode through their own software, they will not work in Overlord. When setting up any system. Check each instrument works on its own before integrating as part of an automated system. The instrument Type in Command Setup is not Serial. What do I need to enter as the port value? The other types or command communication are USB and TCP/IP. USB doesn't require any port setting, the instrument will be picked up automatically. For TCP/IP, either the IP address or the name o f the PC connecting to should be used. Refer to the Readme file for each command, found on the PAA website for details on setup. What do I use the Script Command for? See Section 4. 10 Scripts How can I use a plate barcode to name data files? See Section 4. 10 Scripts When running a procedure I get a “Input string was not in a correct format” This is most likely because an old software license key is being used on the PC. Contact PAA for a new key. How do I disable an action / add a breakpoint? See Section 6. 7 Actions