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Peak A nalysis & Automation, Inc 3330 Fillmore Ridge Heights  Colorado Springs Colorado  CO 80907  USA t: 1-719-598-3555  f: 1-719-548-9227 Peak Analysis and Automation Ltd 6 Armstrong Mall  Southwood Business Park Farnborough  Hampshire  GU14 0NR  UK t: +44 1252 373000  f: +44 1252 371922 e: info@paa-automation. co. uk  w: www. paa-automation. com Overlord3™ User Manual Software Version 3. x Document version 1. 3 Dated: November 2015

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 2 of 202 Table of Contents 1 Getting Started ............................................................................................................................. 6 1. 1 New in this Version ................................................................................................................ 6 1. 2 Quick Start ............................................................................................................................ 6 1. 3 Using the command palette .................................................................................................. 10 1. 4 Saving the procedure ........................................................................................................... 12 1. 5 Running the procedure ......................................................................................................... 14 2 Scheduling ................................................................................................................................. 15 2. 1 Event driven/real-time.......................................................................................................... 15 2. 2 Static/time driven ................................................................................................................ 17 2. 3 Dynamic/time driven ............................................................................................................ 18 3 Configuration ............................................................................................................................. 19 3. 1 Command Setup tab ............................................................................................................ 19 3. 1. 1 Getting instrument commands ....................................................................................... 19 3. 1. 2 Adding Instrument Commands ....................................................................................... 21 3. 1. 3 Removing Commands .................................................................................................... 27 3. 1. 4 Adding a st orage instrument .......................................................................................... 28 3. 1. 5 Positions ....................................................................................................................... 37 3. 2 Labware Setup .................................................................................................................... 40 3. 3 Command Setup .................................................................................................................. 43 3. 4 Options ............................................................................................................................... 45 3. 4. 1 Options, General ........................................................................................................... 45 3. 4. 2 Options-Setup ............................................................................................................. 49 3. 4. 3 Options, Schedule ......................................................................................................... 51 3. 4. 4 Options, Email .............................................................................................................. 52 3. 4. 5 Email on Error ............................................................................................................... 52 3. 4. 6 Options, Script .............................................................................................................. 54 3. 5 Overlord3™ Activation .......................................................................................................... 55 3. 6 Overlord1 Instrument Driver registration ............................................................................... 59 4 Commands ................................................................................................................................. 61 4. 1 Decision .............................................................................................................................. 61 4. 2 Loop................................................................................................................................... 69 4. 2. 1 Running a simple loop ................................................................................................... 69 4. 2. 2 Looping on a condition .................................................................................................. 76 4. 3 Call Procedure ..................................................................................................................... 80

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 3 of 202 4. 4 Exit Procedure ...................................................................................................................... 83 4. 5 Exit Run ............................................................................................................................... 84 4. 6 Initialize Variables ................................................................................................................ 84 4. 7 Set Variables ........................................................................................................................ 85 4. 8 Message Box ........................................................................................................................ 90 4. 9 User Input ........................................................................................................................... 95 4. 10 Scripts .............................................................................................................................. 98 4. 10. 1 Intelli Sense ................................................................................................................. 100 4. 10. 2 Using Overlord variables in Scripts ................................................................................ 101 4. 10. 3 Code Snippets ............................................................................................................. 102 4. 11 Timers............................................................................................................................ 105 4. 11. 1 Duration ...................................................................................................................... 106 4. 11. 2 Description .................................................................................................................. 107 4. 11. 3 Adjust Timer ............................................................................................................... 109 4. 11. 4 Return Time ................................................................................................................ 110 4. 11. 5 Wait for Timer ............................................................................................................. 111 4. 12 Loop.............................................................................................................................. 111 4. 13 Move Command .............................................................................................................. 111 4. 13. 1 Setup .......................................................................................................................... 111 4. 13. 2 Move Type .................................................................................................................. 113 4. 13. 3 Initialize Procedure ...................................................................................................... 114 4. 13. 4 Change Selected Procedure .......................................................................................... 114 4. 13. 5 Direct Moves ............................................................................................................... 114 4. 13. 6 Advanced: Enable variable selection on Move Edit dialog ............................................... 116 4. 14 Move Command Procedures ............................................................................................ 117 4. 14. 1 Get Move Command Procedure .................................................................................... 117 4. 14. 2 Put Move Command Procedure ..................................................................................... 119 4. 15 Adding a Move to a Standard or Schedule Procedure......................................................... 121 4. 15. 1 Process Number .......................................................................................................... 123 4. 15. 2 Return Barcode ........................................................................................................... 123 4. 15. 3 Use Wait Time ............................................................................................................. 125 5 Main Overlord3™ screen............................................................................................................ 127 5. 1 Running Overl ord3™ .......................................................................................................... 127 5. 2 File ribbon options .............................................................................................................. 128 5. 2. 1 File options ................................................................................................................. 128 5. 2. 2 Ribbon options ............................................................................................................ 129

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 4 of 202 5. 3 Top panel-tab and buttons ................................................................................................ 133 5. 3. 1 Design tab ................................................................................................................... 133 5. 3. 2 Runtime tab ................................................................................................................. 143 5. 3. 3 Setup tab .................................................................................................................... 145 5. 3. 4 Environmental controls, main additional options ............................................................. 145 5. 3. 5 Environmental controls, help ......................................................................................... 146 5. 3. 6 Environmental controls, about....................................................................................... 146 5. 4 Right panel ......................................................................................................................... 147 5. 4. 1 Variables ..................................................................................................................... 147 5. 4. 2 Help............................................................................................................................ 151 5. 4. 3 Devices ....................................................................................................................... 155 5. 5 Runtime information/Error list .............................................................................................. 157 5. 6 Command palette ............................................................................................................... 158 5. 7 Favorites area ..................................................................................................................... 160 5. 8 Palette configuration ........................................................................................................... 162 5. 9 Overlord3™ window controls ............................................................................................... 164 5. 9. 1 Environmental controls, thumbtacks .............................................................................. 164 5. 9. 2 Work Area controls, Multiple Document Interface ........................................................... 165 5. 9. 3 Tooltips ....................................................................................................................... 171 5. 9. 4 Getting and changing properties of a procedure step...................................................... 172 5. 9. 5 Cut, Copy, Paste, Delete, Proper ties.............................................................................. 173 6 Creating Procedures .................................................................................................................. 174 6. 1 Opening a new procedure ................................................................................................... 174 6. 2 Standard Procedure ............................................................................................................ 175 6. 3 Move Command Procedure .................................................................................................. 175 6. 4 Schedule Process Procedure ................................................................................................ 177 6. 5 Procedure Flowchart ........................................................................................................... 178 6. 6 Overlord Variables .............................................................................................................. 180 6. 7 Actions ............................................................................................................................... 181 6. 8 Example Procedure ............................................................................................................. 183 6. 9 Advanced Procedure with Incubations and Data Handling ..................................................... 189 7 Running Procedures................................................................................................................... 193 7. 1 Standard (Event-driven) Procedures ..................................................................................... 193 7. 1. 1 Run............................................................................................................................. 193 7. 1. 2 Validation .................................................................................................................... 195 7. 1. 3 Error Handling ............................................................................................................. 195

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 5 of 202 7. 1. 4 Logfile......................................................................................................................... 196 7. 2 Running Schedule Process (time-driven) Procedures ............................................................. 198 8 Frequently Asked Questions ....................................................................................................... 199 9 Troubleshooting ........................................................................................................................ 201 10 External Control ..................................................................................................................... 202 10. 1 Run from Command Line ................................................................................................. 202

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 6 of 202 1 Getting Started Overlord3™ is the latest version of the Overlord range of laboratory automation workcell software packages. Overlord3 is a flowchart-based supervisory software package that allows the control of multiple instruments from one PC in a standard package. Overlord3 utilizes t he native software of ancillary equipment for maximum flexibility. Even the most complex system is easy to put together and the most complex instrumentation is simple to integrate. Overlord3 allows the control of an automated workcell with either: event d riven, real-time scheduling (as implemented in OVERLORD™ Workstation and Overlord2) static, time-resolved scheduling (as implemented in OVERLORD™ Scheduler) dynamic, time-resolved scheduling (new option) 1. 1 New in this Version Features Multiple scheduling opt ions Treat all sample plates idenitically Parallel processing on multiple instruments Advanced run-time error checking and recovery Empowering advanced users Benefits Ease of programming Rapid assay development Increased plate throughput Fully recoverab le from device errors Powerful design environment Support for device pooling 1. 2 Quick Start It is really easy to create an Overlord3 procedure. Follow these steps to familiarize yourself with the basics. Start Overlord3. There should be an entry on the Start Menu under START  All Programs  PAA  Overlord3

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 7 of 202 Figure 1. 1-Start menu Upon starting you will see the splash screen ( Figure 1. 2-Splash screen ). Figure 1. 2-Splash screen The splash screen contains the detail of the loading sequence (yellow) and the Overlord3 version number (red). Then the Overlord3 main screen should appear ( Figure 1. 3-Overlord Main Screen ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 8 of 202 Figure 1. 3-Overlord Main Screen On the left hand-side of the window is the Command Palette and here you will find the Overlord3 Commands, which allow you to build a procedure. 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 use 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 9 of 202 Figure 1. 4-Flow palette Figure 1. 5-Plug-Ins palette Figure 1. 6-Devices palette

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 10 of 202 1. 3 Using the command palette For example the Message Box command (show a message to the user at runtime). From the Plug-Ins palette, drag the Message Box command across onto the empty Action box on the Procedure Flowchart. Figure 1. 7-Message Box icon This is achieved by putting the mouse cursor on the Message Box icon, hold the left hand mouse down, move the cursor over the required Action box in the Overlord3 Procedure work area, and release the mouse button. The move command is represented by the plus icon. Figure 1. 8-using the message box command The Edit properties for this command wi ll then appear. Type in the Empty white text box “Hello” and then click on the OK button ( Figure 1. 9-Message Box Edit).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 11 of 202 Figure 1. 9-Message Box Edit The window will then close and the procedure flowchart should have the first Action in the Overlord3 Procedure ( Figure 1. 10-Simple Procedure ). Figure 1. 10-Simple Procedure

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 12 of 202 1. 4 Saving the procedure Click on the File Functio n Disc in the top left hand corner of the window ( Figure 1. 11-Save As function location ). Figure 1. 11-Save As function location In the drop down menu select Save As (Figure 1. 12-Save As menu ). Figure 1. 12-Save As menu

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 13 of 202 The Save As dialog window will appear ( Figure 1. 13-Save As dialog window ). Figure 1. 13-Save As dialog window Enter the procedure name 'Simple Demo' and select Save. The new procedure name will then appear on the name tab ( Figure 1. 14-procedure name tab ). Figure 1. 14-procedure name tab

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 14 of 202 1. 5 Running the procedure Select the tab ' Runtime' from the toolbar and click on the Run button ( Figure 1. 15-Running a procedure ). Figure 1. 15-Running a procedure A message box saying “Hello” should appear. Click Ok on this message box and the run will complete. Figure 1. 16-Running a Procedure Add another Message Box now between the existing Message box Action and the End Action. When you drag the Message Box across from the Command Palette, the place where you want to insert will be highlighted red. The Message box Edit dialog will appear again. This time enter “Hello again” and then click OK. Save this procedure and click Run. “Hello” should appear and then clicking OK will bring up the next dialog box saying “Hello again”. Click OK and the run will complete. If you have a security key error, contact PAA for support.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 15 of 202 2 Scheduling Scheduling of laboratory equipment into a fully integ rated automated system required integration software. There are three major types: Event driven/real-time Static/time driven Dynamic/time driven 2. 1 Event driven/real-time This type of process is linear. The instructions are processed sequentially, and are b est represented by a flow chart. In its simplest form, the next step of the process is not started until the last step is completed. However, this would be a very slow way of completing a complex process with multiple steps. For example, if there is inc ubation for 1 hour, nothing would happen until that 1 hour waiting time has elapsed. So the process is controlled by a series of events, so the next process does not start until event has been completed. In a simple example, if we wish to process a stack of plates through a dispenser and then a plate reader, the linear process would be... There would be wasted time in this process because the plate reader is unused during the dispensing step, and the dispenser is unused during the plate reading step. As this process is a two stage process, then as the first plate is moved from the dispenser to the plate reader, another plate can be moved from the input stack to the dispenser. Get plate from input stack Put plate in liquid dispenser Wait for dispenser to finish action Put plate in plate reader Wait for plate reader to fi nish action

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 16 of 202 Step 1: 2 plates on input stack Step 2: move first plate to dispenser Step 3: when dispenser completes, move plate 1 to the plate reader Step 4: move plate 2 to the plate reader Step 5: when plate reader completes, move plate 1 to the output stack Step 6: when dispenser completes, move plate 2 to the plate reader Step 7: when plate reader completes, move plate 2 to the output stack input stack Plate 2 Plate 1 dispenser plate reader output stack input stack Plate 2 Plate 1 dispenser plate reader output stack input stack Plate 2 Plate 1 dispenser plate reader output stack Plate 2 Plate 1 input stack dispenser plate reader output stack Plate 2 Plate 1 input stack dispenser plate reader output stack Plate 2 Plate 1 input stack dispenser plate reader output stack input stack Plate 2 Plate 1 dispenser plate reader output stack

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 17 of 202 The process is then run as a loop until all the plates are processed. This technique, known as round robin, allows the plates to be proc essed quickly, but does NOT allow any timings to be taken into account. These types of schedulers are simple algorithms and are very rapid in completing a process. No time is wasted because as soon as one process is completed, the next process starts. Th ese schedulers are very flexible in what process can be modelled, but can get complex to set up because of the flexibility available. Processes that have more than one critical time can be difficult, or impossible, to encode in this type of scheduler. To summarise, when the user presses the go button, the process is defined but the timing isn't. This scheduler is process centric. 2. 2 Static/time driven A static scheduler pre-processes the run and lays out the robot and instrument moves before the process starts. This type of scheduler ensures that all the resources are free to be used when required during the process. Taking the example above, plate 1 would be processed: Plate one 1 Then plate 2: Plate one 2 Represents a robot or stac ker move However when put together Plate one 1 Plate one 2 There would be a clash of resources, so the process has to be scheduler to make sure the resources are available: Plate one 1 Plate one 2 Plate 2 Plate 1 dispenser plate reader dispenser plate reader Plate 1 dispenser plate reader Plate 2 dispenser plate reader Plate 1 dispenser plate reader Plate 2 dispenser

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 18 of 202 The offset is becau se the time requirements are the same, the robot can't start work on the second plate until the first plate is finished. Often the time requirements of the instruments and scheduling becomes more efficient. Plate one 1 Plate one 2 For maximum accuracy, all the moves and instrument processing times have to be measured. The calculation of the processing time requires a sophisticated algorithm. To summarise, when the user presses the go button, the process and timings are is defined. T his scheduler is sample centric. 2. 3 Dynamic/time driven Dynamic schedulers try to combine the best of both event-driven and static schedulers by starting as a static scheduled process and then allowing rescheduling on the fly. These schedulers are very hungr y for computer resources during the run. With a pre-emptive scheduler, the system runs to a planned time schedule, with total control of the time windows for each element in the system. There is resource sharing and there will never be any conflict in the use in the system resource (unless there is an error, when under certain circumstances the time windows will shift). Uses include; cell culture and processing. The strength of this type of schedule is the guarantee of samples being treated in an identica l way. There is little scone for decisions in the schedule. A pre-emptive is TIME driven. Plate 1 plate reader Plate 2 plate reader

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 19 of 202 3 Configuration This section describes the configuration commands found in the:  Command Setup tab.  Labware Setup tab  Options tab 3. 1 Command Setup tab This tab opti on allows the user to configure the attached instruments. 3. 1. 1 Getting instrument commands There is a library of available instrument commands available to users for 1 year after purchase of Overlord3™ and for current service contract holders. The library is held at paa. helpserve. com, and user access will be on product purchase. Goto paa. helpserve. com and login ( Error! Reference source not found. ): Once you have logged in successfully, you will see the options screen. Enter the instrument driver that you require into the Search box.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 20 of 202 The selection of this search will bring up all information relevant to the selected instrument, in this case the Thermo Multidrop ( paa. helpserve. com entry for Thermo Multidro p):

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 21 of 202 paa. helpserve. com entry for Thermo Multidrop From here you are able to download any of the available drivers, help files and support files to run any of the extensive Overlord instrument driver library. Where possible ALW AYS use the Overlord2 (. NET) driver version. When downloading place: Overlord1 drivers in c:\overlord \drivers Overlord1 help files in c:\overlord \help Overlord2 drivers in c:\program files \paa\overlord3 \Commands Overlord2 help files in c:\ program files \paa\overlord3 \help With help files, once this file is installed it will be available from the Help pane on the main screen once the command has been selected in the Command Palette. 3. 1. 2 Adding Instrument Commands To add a new command (instrument or data plug-in) into Overlord3, click on the Setup tab and then the Command Setup button ( Command Setup Options button ):

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 22 of 202 Command Setup Options button This will bring up the Command Setup dialog box which will display Commands that have already been selected. If this is a fresh installation, the display will be empty ( Commands Setup dialog box ): Commands Setup dialog box The text box in the bottom left informs the user how many sockets are used and how many instrument sockets are available for use in the current license.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 23 of 202 The dialog shows a number of properties relating to the instrument command. Command Instrument driver name Version Software version number (use to check you have the lates t version) The version number is included in the paa. helpserve,com download screen for downloading new drivers, please see download section (Section 3. 1. 1 Getting instrument commands ). Type Communication type, Serial, TCP/IP. The port value differs depending upon the communication type of the command. For instance, a command that uses TCP/IP would have the IP address entered in as the port value. Refer to the Readme. txt for ea ch command that is found on the PAA website. Port Connection com port 1-n Simulate Allows the system to be tested Simulate Time (secs) Estimated time for an action when Overlord3™ is being used in ti me resolved mode. Alias The name used in Overlord3™ can be changed. This can be used to reduce the length of the instrument driver name or identify multiple instruments of the same type. The Alias name for each command by default is setup with the name of the Command. This can be changed though and is typically changed if there is more than one of this command on the system. For example if there was two Biotek Washers, the first command would have the Alias “Washer 1”; the second Washer would have the na me “Washer 2”. Positions Allow the supervisor to setup the number of positions on the instrument. Action Time Every time an Action is run in Overlord3™ the time duration (in seconds) is recorded. This information is used when running Schedule Procedures, to calculate the schedule for the run. Add a new instrument in the Command Setup dialog box.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 24 of 202 To add a command, click on the green cross in the top right corner of this window. Overlord3 will then scan for Overlord Drivers in two locations. Command fo lder in the folder the Overlord. Main. exe resides in-(in X:\Program Files \PAA\Overlord3 \Commands, where X is the installation directory, usually C) Overlord1 Driver folder (in X:\Overlord \Drivers where X is the installation directory, usually C) Overlord3 can use Overlord2 Commands, which have been programmed with the. NET Framework. These are known as. NET native commands and will have following name. Overlord. Command. <Device Name>. dll <Device Name> is the name of the device or instrument this command will control. For example, the driver to control the Deerac Latitude is called Overlord. Command. Deerac Latitude. dll. If this file is found in the Commands folder, normally located at C: \Program Files \PAA\Overlord3 \Commands, it will be available to be used in O verlord3. Overlord3 can also use Overlord1 instrument driver. These drivers are known as COM Drivers and will have the following name. ov<Device Name>. dll If this file is found in the Drivers folder in C:\Overlord \Drivers, it will be available to use in Overlord3 provided it has been registered. COM Drivers need to be registered on the PC they are being used on. This can be completed in two ways, both are explained in a later section (Section 3. 6 Overlord1 Instrument Driver registration ). In addition, it is possible that there will be customer specific code modules ( Plug-Ins Commands ) in the command list. When these are selected, the command will be installed in the Plug-Ins pa lette, not the Device palette. These Plug-Ins modules are for specific customer requirements and are not installed on all systems. Once Overlord3 has finished scanning these locations, the Add Commands dialog box will appear listing all the Commands that have been found ( Add Command ): Add Command

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 25 of 202 Select the Command you require by ticking the check box to the left of the Command Name and then click OK (Select the required command ): Select the required command This command will then appear in the Command Setup Dialog. In the example below, the Thermo Multidrop has been added to the instrument list ( Error! Reference source not found. ): If the instrument is added to the system, but has been added and then removed in the past, the user will be offered to restore the command. If the command has been used in Overlord3™ procedures, choose Yes and this will allow the previous procedures to fu nction ( Restore the previous installation of the instrument ):

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 26 of 202 Restore the previous installation of the instrument As the Thermo Multidrop washer uses serial communication, the port of the PC needs to be entered into the Port text box. Enter the port number by clicking the cursor in the Port box and enter the physical connection port number ( Enter port number in Command Setup ): Enter port number in Command Setup After adding all of the co mmands, click OK on the Command Setup dialog to save these settings. The new commands will now be available to add into a procedure. Depending upon the type of command, they will either be in Plug-Ins or Devices section of the Command Palette ( Thermo Multidrop instrument now available to use ):

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 27 of 202 Thermo Multidrop instrument now available to use 3. 1. 3 Removing Commands The Overlord3 licence allows the user to run a number of instruments on the system, without stating which ins truments are being used. Sometimes the user may require to change the instrument command driver. To remove an installed driver, select the red cross at the far right of the instrument description line (Removing a Command for the configuration ). The instrument will be removed from the configuration. To add a new instrument, follow the instructions in the section above (Section 3. 1. 2, Adding Instrument Commands ). DO NOT REMOVE THE DRIVER FILENAME FROM X:\Program Files \PAA\Overlord3 \Commands BEFORE IT HAS BEEN REMOVED FROM THE COMMAND SETUP SCREEN.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 28 of 202 Removing a Command for the configuration 3. 1. 4 Adding a storage instrument Most automated systems have a storage facility, racks, stacks, hotel or incubator. Overlord3 has a special setup procedure for these. Each storage devices can be used as a single coherent unit, i. e. one type of plates in the whole device, or in Zones, where particular types of plate are stored in particular racks in the storage device. Download a Thermo Cytomat incubator 6000 instrument driver from paa. helpserve. com (Section 3. 1. 1, Getting instrument commands ) and save the driver in the Overlord3™ folder structure. Load the instrument driver into Overlord3™ (Section 3. 1. 2, Adding Instrument Commands, Selecting the storage instrument ). The user will be asked to describe the 1st zone in the plate storage device. The first example is whether the entire incubator is one zone, i. e. all plate are the same and are treated the same by the Overlord3™ (The whole s torage device as one zone ). This is represented by the entries in the table. Give the storage device a Name. The storage zone Start position is plate 1 and the No Stacks is 9. Enter the Capacity of the stacks as 21 and Overlord 3™ calculates the End is position as plate 189. The Sequence of the plate stacks is normally 1,2,3,4,5,6,7,8,9. With default system this will apply to all plates ( Add a single zone to a Thermo Cytomat 189 plate store ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 29 of 202 The whole s torage device as one zone Add a single zone to a Thermo Cytomat 189 plate store Selecting OK will give the two instruments installed on the system ( Selecting the storage instrument ): Selecting the storage instrument Both instr uments will be available in the Devices palette ( Storage in Devices palette ). Choose the setup option for the Thermo Cytomat instrument.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 30 of 202 Thermo Cytomat installed If the procedure requires multiple plate types, e. g. 2 stacks of source plates (DW = deep well) and two stacks of assay plates (MTP = standard plates). The first thing to do is assign the new plate types in the Labware setup up tool (Section 3. 2 Labware Setup ). Use the Labware Types Setup to enter the two required plate types. On addition, the Labware type dialog box will have two options ( Required labware types ). Required labware types

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 31 of 202 Select OK, then assign the plate type to the storage device with the Add button. You will need to assign both the DW plates ( Assign Source plates to storage device ) and the MTP plates ( Assign Assay plates to storage device ) to the storage device. Assign Source plates to storage device Assign Assay plates to storage device Both types of plates are defined in the Labware Setup dialog box and are then set up and ready to use (Assigned Labware types ): Assigned Labware types The ph ysical layout of the storage system would be as below ( Two different plate zones in the storage device ):

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 32 of 202 Two different plate zones in the storage device First remove the existing layout of one zone of identical plates. Overlord3 main window followed by Command Setup (top left tool bar option). Select the red hash to edit the existing positions: Redefining the zones in the storage device, select the storage device The current zoning will defined, select Default and click Remo ve (Removing the existing setup ), the user is asked if this is the required activity ( Check if this is the required action ), then if Yes is selected, the current zone setup is cleared ( Clear zone setup for storage device ):

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 33 of 202 Removing the existing setup Check if this is the required action Clear zone setup for storage device To implement the two zone setup, select the Add button for the 1st zone, and enter

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 34 of 202 Start = 1 No Stacks = 2 Capacity =21 Sequence = 1,2 tick the DW plate type ( Set up source plate zone ): Set up source plate zone

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 35 of 202 Select OK and the Add another zone and enter the assay plate zone information: Start = 1 No Stacks = 2 Capacity =21 Sequence = 3,4 Tick the MTP plate type ( Zone 2 for Assay plates ): Zone 2 for Assay plates Initially the Position Setup dialog box only shows the details for zone 1 ( View zone 1 information for Source plates ). Click the-to see the 2nd zone information ( View zone 2 information for Assay plates ). View zone 1 information for Source plates View zone 2 information for Assay plates

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 36 of 202 Storage in Devices palette Setup the Storage instrument The Cytomat Setup dialog box will be displayed, enter then number of stacks installed in the hotel/incubator ( Cytomat Setup dialog box ): Cytomat Setup dialog box Selecting the Stack Setup button allow the setup of the individual stack pitches ( Cytomat Stack Pitch dialog box ). This allows deep well plates and standard plate stacks to co-exist in one storage module:

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 37 of 202 Cytomat Stack Pitch dialog box 3. 1. 5 Positions Most instruments only have one position for a robot to place a microplate. Other instruments do have multiple positions. Viewing the Thermo Multidrop position configuration ( Configuring the number of positions on an instrument ): Configuring the number of positions on an instrument The default configuration is shown ( Defau lt position information for a Thermo Multidrop ). The single plate position can be seen. :

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 38 of 202 Defau lt position information for a Thermo Multidrop By selecting the Add button, the user can enter particular uses of the instrument ( Add a new position on a Thermo Multidrop instrument ): Add a new position on a Thermo Multidrop instrument Select OK to exit, to view all positions on Thermo Multidrop instrument ( All positions on Thermo Multidrop instrument ):

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 39 of 202 All positions on Thermo Multidrop instrument For a storage device, sel ect that positions option ( Position information for storage device ). Position information for storage device

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 40 of 202 3. 2 Labware Setup The location, type and size of labware are a key components to the automated setup o ptions of Overlord3. The Labware Setup command can be accessed from the Setup, Labware Setup tab option (Labware Setup tab option ). This section also allows the user to allocate a plate type to a storage location: Labware Setup tab option This will present the Labware Definition Setup dialog box ( Labware Definition Setup dialog box ).

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 41 of 202 Labware Definition Setup dialog box To setup a new labware setup type, choose the Labware Types Setup button ( Labware Type Setup button ). Labware Type Setup button Then to add a new type, choose Add from the Labware Type Setup dialog box ( Add new labware type).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 42 of 202 Add new labware type The new labware can be named, the type of labware selected ( Add labware type name and number of wells) and any features such as lid or sealed can be selected ( Choose plate type options ). Add labware type name and number of wells Choose plate type options Selecting OK, with display the features of the new plate type ( New plate type add ed to library ):

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 43 of 202 New plate type add ed to library The plate typ can be changes with the Edit button or removed with the Remove button. Once all the new plate types have been added, the user can return to the Labware Definition Setup dialog box by selecting OK (Labware Type Setup button ). The labware can now be allocated to a storage location, select the Add button ( Add the plate type to a storage location ): Add the plate type to a storage location 3. 3 Command Setup Some commands have setup dialogs available for setting parameter specific to that command. Typical parameters are connection timeout values, the location of data files and the location of third party software executables. Setup also brings up the Teach so ftware for robotic arms and diagnostic software.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 44 of 202 To access the Setup section of a command, click on the small arrow to the right of the command in the Devices palette. This will bring up a small context menu and if the Setup is available, it will be liste d as a menu entry ( Instrument command installed in Devices palette ): Instrument command installed in Devices palette Click on this to bring up the Setup dialog box ( Thermo Multidrop setup screen ): Thermo Multidrop setup screen Default instrument settings can be modified in this dialog box. Refer to the Readme. txt file that can be found for each command on the paa. helpserve. com site for more information on what settings can be altered. Information can also be found in the command help file if it has been installed.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 45 of 202 3. 4 Options There are various system settings for Overlord3 that are accessible by clicking on the toolbar and selecting Setup and clicking the Options button Options Button There are five sections in Options:  General  Setup  Schedule  Email  Script 3. 4. 1 Options, General This section allows the user to control the Logfiles, Trace Log and Runtime parameters ( Options, General ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 46 of 202 Options, General 3. 4. 1. 1 Logfiles Each and every time that Overlord3™ is run, a log file is produced. Logfiles are stored in folder X:\Program Files \PAA\Overlord3 \Logfiles (where X is the Overlord3™ installation directory). Over time, these log files can occupy a v ery large amount of PC hard disc space. The user can move, archive or delete these files manually, or Overlord3™ can be setup to automatically delete the logfiles based on the date that the log file was written. Tick the Auto Clean Up Logfiles check box to automatically delete logfiles older than the value in Delete logfiles older than... days every time Overlord3™ is started. The user can delete unwanted logfiles NOW, by selecting the file age in Delete logfiles older than... days data entry box and clicki ng Clean Up Logfiles. Logfile Max Size (MB) specifies the maximum size of an individual logfile. The first logfile for a run will be named by the date and time with __1 appended on the end. If the run generates a logfile that is over the maximum value a ne w logfile is created with same data and time as the first file, but with __2 on the end. 3. 4. 1. 2 Trace Log The Trace Log is usually activated to identify system problems. Selecting Trace Log options write detailed information into a file to assist with problem so lving and error detection. Selecting Trace Overlord writes low level information on internal Overlord3 processes. The information provided by this trace function is only required in exceptional circumstances and should only be turned on if requested by a m ember of the PAA Technical Support Team. Selecting Trace Commands writes the low level communications between Overlord3 and the instrument, this is usually used to determine if Overlord3 is sending the wrong commands to the instrument, or the instrument is replying in an unexpected way. The usual configuration for a system is to have Trace Overlord Off and Trace Commands On

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 47 of 202 The Trace Log can get very large, so a maximum size can be set in the Trace Log Max Size (MB) data entry box. This log can be archives rather than deleted with the Archive when Trace Log exceeds maximum size check box. Or the trace log can be cleared NOW with the Clear Trace button. 3. 4. 1. 3 Runtime Treat Validation Warnings as Errors At the beginning of a run, Overlord3 does a quick check to se e if the procedures to be actioned have any structural errors. If the Treat Validation Warnings as Errors check box is selected, the validation stage will stop displaying the errors, unselected, the warnings are just highlighted. For example, if an initial ise Cytomat command ( Initialise Cytomat instrument dialog bo x) is put in an Overlord3 procedure ( Initialise Cytomat instrument procedure ). Initialise Cytomat instrument dialog bo x Initialise Cytomat instrument procedure If the Treat Validation Warnings as Errors check box is selected, when the procedure is run, the error will be detected in the validation phase of the run ( Error on validation failure ) and the procedure will not be actioned: Error on validation failure If the Treat Validation Warnings as Errors check box is unselected, the error will be detected at runtime ( Runtime error detected (Overlord3 screen, bottom left) and Runtime err or detected, (Overlord3 screen bottom right )). It is necessary to hit the Retry or Ignore to continue:

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 48 of 202 Runtime error detected (Overlord3 screen, bottom left) Runtime err or detected, (Overlord3 screen bottom right ) Disable Runtime Validation Check Checking the Disable Runtime Validation Check box overrides the setting of Treat Validation Warnings as Errors, so errors are only reported at runtime. Open Procedures At Runtim e Checking the Open Procedures At Runtime box, allows all the sub-procedures to opened and seen as the sub procedures run. Cache Procedures At Runtime If the option is selected procedure files are saved in memory at runtime. The standard behaviour is to open the procedure from disk every time. This option should be used on finished or final sytems to improve performance. Cache Scripts At Runtime If the option is selected script files are saved in memory at runtime. The standard behaviour is to open the script from disk every time. This option should be used on finished or final sytems to improve performance. Runtime Output Filter Limits the type of entries displayed in runtime output screen at runtime.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 49 of 202 3. 4. 2 Options-Setup These options effect the setup an d Overlord3™ display features: Options, Setup Hide Enhanced Features Enhanced features refer to the upgrade of an additional runtime engine to upgrade Overlord2 to Overlord3. With this selected, Overlord3 performs at edit and runtime the same as Overlo rd2, i. e. only real-time, event-driven schedules are available. Unselected, the user is able to edit and run dynamic time-resolved schedules. Load Controlled Stop Command The Controlled Stop Command is a special Command used by Assay Manager and third-party integrations that use the Overlord Framework. It is not required by stand-alone Overlord3 installations. Secure Remoting Connection This option is only required when using Overlord Remoting. In most cases Overlord Remoting will run without this option c hecked. However, in rare circumstances, the security settings on the network require this option can be selected. In this case the option must be turned on in both Overlord3 and the Remote Listener. Show Robot, Stacker and Storage Commands in Standard Proc edures (. ovp) By default any Robot, Stacker or Storage devices are hidden in the Command Palette when building Standard Procedures (. ovp). This is to guide users to use the Move Command. Select this option to show hidden device types in the Command Palette when creating Standard Procedures. Get Security Code The activation of Overlord3 is described in a later section (Section 3. 5 Overlord3™ Activation ).

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 50 of 202 Register Commands The regi stration of Overlord1 compatible commands for use with Overlord3™ is described in a later section (Section 3. 6 Overlord1 Instrument Driver registration ). Export Commands The Exp ort Commands button will create a copy of the Command settings and save them to an XML file location that can be specified in the 'Save As' Dialog window that appears ( Export Command dial og box ): Export Command dial og box If there is a problem with the system, it is worth sending this generated file to PAA for technical support. Device Manager Shortcut to the Windows XP Device Manager

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 51 of 202 3. 4. 3 Options, Schedule Tolerance mode and value (seconds or %) The Tolerance options a re used when running a Schedule Procedure in which a Move Command has the Use wait time option selected. The system will compare the actual wait duration with the value set in the Procedure and log any values outside the given tolerance. Options are Time and Percentage. Determines whether the Tolerance value is used as an absolute Time value (e. g. plus 10 seconds) or as a Percentage of the set wait time (e. g. plus 5% on 600 seconds = 30 seconds): Options, Schedule

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 52 of 202 3. 4. 4 Options, Email Options, Email 3. 4. 5 Emai l on Error If the Send email on error check box is selected, an email will be sent to the listed email addresses every time there is an error with a command. The following settings need to be made for this to work. SMTP Client : The SMTP Outgoing mail serv er address (e. g. smtp-1. mail. vi. net) SMTP Port : This number is normally 25 Send from : The name that will appear on the email when it is received (e. g. Overlord3PC) Username : The username for the POP/SMTP account that is being used Password : The username fo r the POP/SMTP account that is being used Send to : A list of the email addresses to send the message to. These must be full email addresses (e. g. yourname@companyname. com ) and are added with the Add Email Ad dress button ( Add Email Address ):

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 53 of 202 Add Email Address This will add the email address to the list of recipients ( Email address added, edit op tion): Email address added, edit op tion

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 54 of 202 To edit the email address, select the email address to edit and click on Edit (Email address added, edit option) to bring up the edit dialog box ( Edit email address ): Edit email address To remove an email address, select the email address and click on Remove. The settings can be tested by clicking on the Test button. This will send an email message to the listed recipients exactly as the system would if there was an error. Any problems with the settings will become apparent at this point. Send an email on complete uses the same parameters as above, except an email message is sent to the email list at the completion of an Overlord3 procedure. 3. 4. 6 Options, Script VB Scripts allo ws the extension of Overlord3™ to allow novel and bespoke software modules to be used: Options, Script If the Script on error check box is selected, the selected script will be run when there is an error with a Command. Typically, the selected script wi ll contain code to report the error to a data store or send a message via a messaging application (e. g. SMS). To create a script, click on the Edit button. This will bring up the Overlord3 Script window ( VB Script editor window ): When an error is generated, these variables will be set with these error values. There is additional information relating to the implementation of VB/C #/VB. NET Scripting in the Editing section.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 55 of 202 VB Script editor window All Overlord3™ variables are available in the scripting environment to report the error. They are [Error Number]-The Error code of the generated error [Error Device]-The Alias of the device that has generated the error [Error Description]-The error description Run script on complete runs the script at the completion of an Overlord3™ procedure. 3. 5 Overlord3™ Activation When you run a procedure (MAJOR LINK), you may see an error dialog box ( No security key found ) or wrong key Incorrect security key ). No security key found

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 56 of 202 Incorrect security key You need to apply to paa for an activation key for running the Overlord3 software. Follow the following instructions for product activation. Run Overlord3 and select the Setup tab, and then the Options tab (Setup Options tab ). Setup Options tab This will bring up the Setup dialog box. Select the Setup side tab and the Get Security Code button (Get Security Code button ):

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 57 of 202 Get Security Code button This will bring up the security code dialog box ( Security Code dialog box ): Security Code dialog box Send the number by email to info@paa. co. uk and you will receive the activation code by return email. The-ve sign IS significant if present. The activation code is usually sent as a text file (e. g. activation. txt ), save it on your desktop ( Text file icon), rename the file as a reg file ( activation. reg ). You will receive a warning-select yes: Text file icon File extension warning You will then see the file icon change ( Registry file icon ). Then double click on the file name (activation. reg ), to run the file. You may receive a security warning ( Security Warning ), which you should answer Run. This is a single user activation key for the comp uter that has been activated only.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 58 of 202 Registry file icon Security Warning You will see an offer to add information to registry ( Add information dialog box ) that you should answer Yes. Add information dialog box This will be followed by an information dialog box ( Information added dialog box ) that the information has been added. Information added dialog box

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 59 of 202 3. 6 Overlord1 Instrument Driver registration To register any new Over lord1 instrument drivers on your Overlord3 installation, run Overlord3 and select the Setup tab, and then the Options tab (Setup Options tab ). Setup Options tab

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 60 of 202 This will bring up the Setup dialog box. Select the Setup side tab and the Get Security Code button (Register (Overlord1) Commands button ). Register (Overlord1) Commands button A dialog box will be displayed showing the progress of the command registration ( Registering (Overlord1) Commands ): Registering (Overlord1) Commands When the window disappears, the process is complete. Sometimes this registration process can be unsuccessful and the instrument driver of interest does n ot appear in the instrument list. When this happens please follow this process: There is a utility in the folder C\:Overlord \Setup \Register DLLs. exe. Running this program will register every Overlord1 Driver in this folder.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 61 of 202 4 Commands All items that are li sted in the Command Palette are known as Commands. 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 wou ld be used within a Procedure. 4. 1 Decision Making a decision allows the user to compare the state of one variable against another. IF condition = TRUE THEN go right ELSE go down Condition FALSE: Do this action Condition TRUE: D o this action 4. 1. 1. 1 Variables The default on the left of the Decision dialog box is Variables. Different types of decision can be achieved with the action (comparison of numbers, comparison of text and determination if a True/False variable is true or false). The Decision dialog box is:

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 62 of 202 Decision Dialog Box For example if the condition is [loop counter] = 1, the variable to make the decision [loop counter] is selected from the drop down list. Then the + is select ed to add the condition. Adding a condition This displays the condition option box:

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 63 of 202 Displaying the condition options The Compare type can be selected from: Equals Does not equal Greater than Less than Greater than or equa l to Less than or equal to Text and Yes/No variables can only be Equals or Does not equal. These can be seen below: Choosing the Compare type In the example [loop counter] = 1, the Equals option should be chosen. Finally, the Compare Value should be entered; this can be a variable or a value. For the example, 1 should be entered.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 64 of 202 Finally, the Compare Value should be entered; this can be a variable or a value. For the example, 1 should be entered. Enter the Compare Value This option can be deleted by selecting the red cross at the end of the Compare line. Selecting the OK button, will give the following procedure steps: The final procedure for this Decision step If the Decision step is TRUE that is [loop variable] = 1, the right hand path will be run. If the Decision is FALSE, the left hand path will be run.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 65 of 202 4. 1. 1. 2 Advanced This statement can also be used to run multiple options, sometimes known as a SELECT CASE statement. If the user wishes to tes t if [loop variable] = 1, 2 or 3, and complete different operations based on the value of [loop counter]. The user should extend the Decision dialog with an additional couple of steps: Multiple options in a Decision procedure step If [loop counter] is not equal to 1, 2 or 3, the left hand path will be run. If [loop counter] is equal to 1 the second path from the left will be run. If [loop counter] is equal to 2 the third path from the left will be run. If [loop counter] is equal to 3 the right hand path will be run.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 66 of 202 4. 1. 1. 3 Status Selecting the Status option on the left of the Decision dialog box, changes the options. Status refers to the runtime state of the instruments installed on the system. In this example, an automate. it SCARA and a Bio Tek EL406. Status options The instrument activity can be in one of three states: Idle Busy Error These options are displayed as below: Instrument states The resulting procedure is:

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 67 of 202 Checking the status of an instrument If the robot is Busy, the right hand path will be followed. If the robot is not Busy the left hand path will be followed. 4. 1. 1. 4 Timers Selecting the Timers option on the left of the Decision dialog box, changes the options. Status refers to the runtime state of the timers used on the system. In this example, there is the system Wait timer (see Wait Timer) and the other variables that may represent a timer. The Timers Decision Dialog Box

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 68 of 202 Choose the Timer that you wish to check, then select th e state of the timer in the lower drop down box, the options are: Running Expired (complete the set time) Timer state selection Selection of the OK button, give the following procedure steps: Decision step for Timers option If the chosen timer is Running the right hand path will be run. If the Timer is not Running, the left hand path will be run.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 69 of 202 4. 2 Loop 4. 2. 1 Running a simple loop The Loop command allows the user to construct a procedure that can repeat a number of actions again and again. Drag a Loop comm and from the Flow palette to the procedure and the Loop dialog box is displayed. Keep the Fixed option selected. Initial Loop Dialog box If you enter a number into the Loop Count text box: Enter a number for the Loop Count Selecting OK will give t he following procedure: Enter number here

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 70 of 202 Result of entering a Loop Count of 5 This action will get the procedure to loop around running any actions inside it 5 times 4. 2. 1. 1 Using a variable to control the number of loops Entering a variable value into the procedure step (doub le left hand click on the Loop icon) gives: Changing to a variable loop Selecting OK gives the same flow chart as above, but with a different runtime profile. Select variable here

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 71 of 202 Result of entering a variable Loop Count of [loop counter] This will run the loop a vari able number of times determined by the value of [loop counter] at that point at runtime. So if [loop counter] is equal to 4, the loop will run 4 times; if [loop counter] is equal to 20, the loop will run 20 times. 4. 2. 1. 2 Accessing the looping variable It is poss ible to know what the current loop number is. Click the Use Variable Counter check box and select the counting variable name form the drop down list. In this example [loop counter] is selected. Loop with named looping variable Select variable here

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 72 of 202 This gives the follow ing flow chart: Loop with accessible counting variable This will allow the user to use the counting variable inside the loop as shown below: FOR [loop counter] = 1 TO [Plates] Do this action Display the value of [loop counter] NEXT Leave loop here

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 73 of 202 An example would be if [Plates] was set to 5 (see setting variable values ), then the value of [loop counter] would be first one, then 2, then 3, then 4 and finally 5. The procedure would then continue out of the bottom of the Loop step. 4. 2. 1. 3 Changing the starting value for the loop and the step In each of the above examples the loop counter starting position and the step value has a default value of 1. This is normal for most examples. However, if the user needs to start from a different value other than one, for example start at a value 2 and finish at 5, the Advanced option needs to be selected. Making the Loop run from a value of 2 to 5 In addition, in very complex cases, the user may wish to go from 1 to 9 in jumps of 3. An example of this would be when plates are removed from a stack 3 at a time. So the first pass of the loop will use plates 1, 2 and 3; the second pass of the loop would use plates 4, 5 and 6, etc. This is shown diagrammatically below:

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 74 of 202 Loop from 1 TO 9 STEP 3, using [Loop_counter] as the loop counter Use plate [loop counter] (1, 4, 7) Use plate [loop counter] +1 (2, 5, 8) Use plate [loop counter] +2 (3, 6, 9) End The Loop flow chart procedure step would be modified as below: Loop from 1 to 9 step 3

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 75 of 202 The procedure would then look like this: Procedure with a stepped loop

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 76 of 202 4. 2. 2 Looping on a condition Looping on a condition allows the user to complete a loop a set number times, but the decision is based on a condition at runtime. This conditional test can be completed at the beginning of a loop: IF condition = TRUE THEN loop right ELSE leave loop Do this action Then do this action Leave loop here

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 77 of 202 Or at the end of the loop: loop Do this action Then do this action IF condition = TRUE THEN loop again ELSE leave loop Leave loop here The key difference is that the test at the top of the loop, the loop may never run; if the test is completed at the end of the loop, that loop will run at least once. Each of the following can be applied to testing at the start or the end of the loop. Test at Start of loop Test at End of loop

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 78 of 202 4. 2. 2. 1 Testing at the top of the loop with “Loop while variable” Drop a Loop step into the procedure and select the Conditional option on the left of the dialog box, and select the Start of loop option button. Select conditional at the start of the loop The loop conditions are set under the Loop while variable. Choose the key looping variable: Select the required looping variable

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 79 of 202 Then the inequ ality from the list: Select the required inequality Then finally the comparison, this can be another variable or number/text value: Set the comparison variable 4. 2. 2. 2 Testing at the top of the loop with “Loop until the following timer is complete” This opt ion allows a timer to be checked to see if it has reached its target time. The user can either choose the wait timer or any of the variables. See Section 0

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 80 of 202 Timers for more information on Timers. Select the timer comparison option 4. 2. 2. 3 Testing at the top of the loop with “Loop while device” This allows the user to test if one of the instruments is Busy or Idle. The drop down list is filled with the instruments installed on the system. Select the Loop while Device option 4. 3 Call Procedure The Call Procedure step allows the user to call a previously written and saved procedure. On dropping on the procedure, the following dialog box will appear:

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 81 of 202 Call Procedure Dialog Box It is possible to type the req uire file name into the text box, however, it is easy to make typographical mistakes and it is recommended that the user select the required procedure name from the list. Click the ... icon to open the File Open dialog so the procedure can be selected. Call Procedure File List Click on the required Procedure file...

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 82 of 202 Call Procedure File List with Procedure File selected ... and the select Open. Call Procedure Dialog Box with file name filled in The user can either select OK, and that file will be u sed in the Call Procedure step or select OK and Open to show both the calling file and the called file.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 83 of 202 In this example, the opened file is blank. Select OK and Open Select OK 4. 4 Exit Procedure The Exit Procedure command allows the user to exit a runnin g procedure when the processing has completed. The Exit Procedure command has no edit screen and can be used anywhere in a procedure. Exit Procedure step added to the procedure In this example, if the decision gives a value of TRUE, the procedure will exit to the calling procedure.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 84 of 202 4. 5 Exit Run The Exit Run command allows the user to exit a running procedure ending the run completely. The Exit Run command has no edit screen and can be used anywhere in a procedure. Exit Run procedure entered in the proced ure In this example, if the decision gives a value of TRUE, the procedure will exit the run completely. 4. 6 Initialize Variables The Initialize Variables command allows the user to initialize all the declared variables. The declared variables are found in th e variables window, usually in the top right hand side of the screen. Set and View Variables window

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 85 of 202 If the initialize command is used in the procedure as below: Initialize Variables procedure step When this procedure is run, the variables are initi alized. Variables Window shows that the variables have been initialized 4. 7 Set Variables The Set Variable command allows the user to set a variable to the required value. When this command is placed in the procedure, the edit screen is displayed.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 86 of 202 Choose the variable to be set The user can then choose the variable to be modified: Select the variable name from the drop down list The orange box indicates the variable type. Numeric Any number

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 87 of 202 Text Any non-numeric piece of data True/False Choice of TRUE or FALSE Enter the value to be assigned to the variable name The choice of number/text/yes-no will affect the acceptable entries for the variable. Multiple variables can be assigned in a single procedure step. Use the Add Equation button for each additional assignment.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 88 of 202 Add an additional set variable line Equations can be entered into the value box. The assignment can be tested. For example, in the example above if [plates] = 3, selecting the Test button will display the new value. Testing the Set Variable option that has been entered Select OK to acknowledge the new value, which will be visible in the variables window.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 89 of 202 Variable window after the Set Variable step has been run Assignment of one variable to another variable is al so possible. Assigning variable to another variable name Any of the assignments can be deleted with the red cross. Additional assignments will lead to the display of a scroll bar.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 90 of 202 Result after multiple Add Equation clicks Selecting the OK button w ill display this command in the procedure. The values of the Set Variables are visible in the flow chart 4. 8 Message Box The Message Box command is user by the person setting up the system to ask the user of the system to complete a task. Such actions coul d be “check a pippetting station waste bottle is empty” or “load the stack with microplates”. The edit screen is as below:

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 91 of 202 The Message Box edit box The user puts the message into the text area: Enter the message into the text window Press OK to ret urn to the procedure.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 92 of 202 The message box contents in the tooltip Save and then run the procedure displays the message: The message at runtime Any of the variables can be incorporated into the message. Place the cursor where you want the variable to be entered, select the variable name from the list: Add a variable to the message If the procedure step is exited, the procedure saved and run, the value of the variable is displayed:

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 93 of 202 Message at runtime The symbol may be changed with the other drop dow n list: Changing the symbol in the message window The symbols are: Information Exclamation

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 94 of 202 Error The final option is the facility to play a wave file at runtime. This is useful to issue ”verbal” messages to the user at runtime, in any langua ge. Use Windows Sound Recorder and a microphone to record the required message/sound. Select the Show Advanced check box. Adding a sound recording to the message Click on the Click load to select sound file and use Load to select the filename of the s ound to play.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 95 of 202 Loading the sound recording file Use Clear to delete the current filename and Play to test the sound. Select the Loop Sound check box to run the sound on a continuous loop. The sound will stop when the OK button is selected. 4. 9 User Input The User Input message box allows the person setting up the system to ask the user to enter information for later use in the run. An example would be to elicit how many plates in a run. The edit box allows the information to be entered:

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 96 of 202 The User Input s creen The user can be asked to enter a value, a yes/no answer or for a filename. For the entry of a variable, enter the question that the user will be asked in the message text box. Enter the message to be displayed at runtime As with a message box, a variable can be requested as part of the message if required using the Add Variable option. The user can also be prompted for a textual value or numeric value with the radio button. In this example we are going to ask the user for the barcode value for the second plate of six plates in the stack. The plate value (2) will be stored in [loop counter] the total number of plates in

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 97 of 202 [plates]. Once the message has been entered, use the add variable button to insert the two variables in the message: Add a variable to the message A barcode is of type Text, the select which variable will be loaded with the input value at runtime. Select the variable to receive the input at runtime A default value can be entered or the user to see at runtime if there is a usual value for the input. If the OK is selected, and the procedure saved and run, the input message will be displayed. As for Message Box, sounds can be entered to be played at runtime. Click the Show Advanced check box and select the AVI file to be pla yed at runtime.

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 98 of 202 Adding a sound recording to the User Input screen 4. 10 Scripts Scripts allow code snippets of VBScript, VB. NET or C# to be run as part of a Procedure. Using scripts allows custom code to be used to perform actions which are very specific to t he application being automated. These actions include Formatting Plate Data so that it can be uploaded to a LIM Running Stored Procedures on an SQL Database and using this data to populate Overlord variables Generating Pipetting Worklists based upon the ba rcode of a plate. Sending status messages via a 3rd Party application (e. g. SMS to a mobile phone). These are just some of the actions Scripts can carry out. The list is endless. Whatever a piece of code can do inside Visual Studio or as part of an Excel m acro, it pretty much can do via a script. The only exception is that it cannot display windows, message and input boxes being the only exceptions. However, there are ways around this which will be described in this section For more information on the code syntax on each language that is supported in Scripts, please take a look at the following resources.

Overlord3 Manual ©Peak Analysi s and Automation Ltd Version 1. 3 (January 2014) Page 99 of 202 Language Title Address C# C# Programming Guide http://msdn2. microsoft. com/ en-us/library/67ef8sbd(VS. 80). aspx C# C# Reference http://msdn2. microsoft. com/en-us/library/618ayhy6(VS. 80). aspx Visual Basic Visual Basic Programming Guide http://msdn2. microsoft. com/en-us/library/y4wf33f0(VS. 80). aspx Visual Basic Visual Basic Reference http://msdn2. micr osoft. com/en-us/library/25kad608(VS. 80). aspx VBScript VBScript Users Guide http://msdn2. microsoft. com/en-gb/library/sx7b3k7y. aspx VBScript VBScript Language Reference http://msdn2. microsoft. com/en-gb/library/d1wf56tt. aspx There is also a set of VBScripts that are commonly used in Overlord, available from the PAA website. Assuming you have logged in, the scripts are available from http://www. paa. co. uk/labauto/knowledgebase/vbscripts. asp The following section assumes you are familiar wi th VBScripts. If not, please look at the resources listed above. When the script command is added to a procedure, the following window will appear. New Script

Overlord3 Manual ©Peak Analysis and Automation Ltd Version 1. 3 (November 2015) Page 100 of 202 The Script Editor, as this window is called, will start up using the language that has been se t as default in the Setup for the Script. Setup for Scripting can be reached by clicking on the small arrow to the right of the Script icon in the command palette. Script Setup The language can also be changed by clicking the New toolbar button in the Script Editor. Before loading up a new code pane, a dialog similar to that in Setup will appear asking what language should be used. Once the language has been set, code can be entered into the pane. The following lines of code would rename a data file. Save this code to a file, in this case a VBS file and then exit. The code will now be part of the procedure, although it is important to note the procedure refers to the file that contains to the code, not the code itself. At runtime, this code would execute a copy the file Data. txt to Result. txt. 4. 10. 1 Intelli Sense The Script Editor supports Intelli Sense, which is the ability to autocomplete a keyword that is being entered. If for example the letter 'C' is typed into the Code pane an d then CTRL-SPACE (the Control and Space button on the keyboard) is then pressed, the Intelli Sense menu will come up with all the keywords that begin with C. Set obj FSO = Create Object (“Scripting. File System Object” ) obj FSO. Copy File "C:\Data. txt", "C:\Result. txt", true Set obj FSO = Nothing