Gemini Software Manual V4.0

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391201 V4.0 Issued March 2002

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1 About This Manual... 1

1.1 Introduction ... 1

1.2 Intended use of this product... 1

1.3 Related documentation ... 2

1.4 Warning, cautions and notes... 2

2 Product Support ... 3

3 System Setup ... 5

3.1 System requirements ... 5

3.2 Supported pipetting instruments ... 6

3.3 Standard and advanced hardlocks... 7

3.4 Installation ... 7

3.5 Upgrading to the latest software version... 8

4 Menus ... 9

4.1 File menu ... 9

4.1.1 New / Open / Close / Save / Save As...9

4.1.2 Print / Print Preview / Print Setup ...9

4.1.3 Backup Data / Recover Data ...10

4.1.4 Data Explorer...10

4.1.5 Recent files list ...12

4.1.6 Quit Gemini...12

4.2 Edit menu ... 13

4.2.1 Cut / Copy / Paste ...13

4.2.2 Edit / Delete / Insert New Command ...13

4.3 Setup menu... 15

4.3.1 Configuration ...15

4.3.2 Liquid Classes ...15

4.3.3 Setup & Service Te-MO...15

4.3.4 Settings...16 4.3.5 Arm initialization ...20 4.3.6 External Devices...21 4.4 Execute menu ... 22 4.4.1 Flush Instrument...22 4.4.2 Drop DITIs ...22 4.4.3 Reset Options...23

4.4.4 Fill System (ActiveTip) ...24

4.4.5 Switch on/off Doorlocks ...24

4.4.6 Send Firmware Command...24

4.4.7 Set DITI Position...24

4.4.8 Loading the Te-MO with racks...25

4.4.9 Validate...26

4.4.10 Start ...26

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4.4.15 Undefined Variables... 27

4.5 View menu... 27

4.5.1 Log window ... 27

4.5.2 Emergency Stop window ... 27

4.5.3 Variables window ... 28 4.5.4 Info window ... 28 4.5.5 Toolbar... 28 4.5.6 Status Bar ... 28 4.5.7 Command Bar... 29 4.6 Window menu... 30 4.6.1 Cascade... 30 4.6.2 Tile ... 30 4.6.3 Arrange Icons... 30 4.7 Help menu ... 31

5 Configuration Editor ...33

5.1 Basic concepts ... 35

5.1.1 Introduction to carriers and racks... 35

5.2 Moving the arms... 37

5.2.1 Moving the LiHa ... 37

5.2.2 Moving the RoMa... 39

5.2.3 Moving the PnP... 40

5.2.4 Moving the Te-MO ... 42

5.2.5 Moving the PosID... 43

5.3 Configuring racks ... 45

5.3.1 Rack coordinates ... 48

5.3.2 Rack types ... 51

5.4 Rack Wizard ... 53

5.5 Configuring carriers ... 62

5.5.1 Carrier dimensions and X/Y offsets ... 64

5.5.2 Z offsets for carriers ... 65

5.5.3 Custom objects ... 65

5.6 Carrier Wizard ... 66

5.7 Defining RoMa vectors ... 69

5.8 RoMa Vector Wizard ... 73

5.9 Defining PNP Vectors... 76

5.10 PnP Vector Wizard ... 79

5.11 Configuring the LiHa... 82

5.12 Configuring the PosID ... 85

5.13 Configuring the MPO/LICOS ... 86

5.14 Configuring the ChemSystem ... 87

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6 Liquid Classes ... 91

6.1 Liquid Classes Editor ... 91

6.1.1 Global parameters ...93

6.1.2 Type parameters ...94

6.1.3 Aspirate parameters ...95

6.1.4 Dispense parameters ...97

6.1.5 Calibration parameters ...100

6.2 Liquid classes for nanopipetting (NPS) ... 101

6.2.1 Global parameters (NPS) ...101

6.2.2 Type parameters (NPS)...101

6.2.3 Aspirate parameters (NPS) ...102

6.2.4 Dispense parameters (NPS)...102

6.2.5 Calibration parameters (NPS) ...103

7 Commands for Gemini Scripts ... 107

7.1 List of Gemini script commands ... 108

8 Creating a Pipetting Script... 117

8.1 The Worktable window... 117

8.1.1 Adding carriers and racks to the worktable ...118

8.1.2 Assigning a label (or name) to the racks ...121

8.2 Specifying script commands ... 122

8.3 Creating a Gemini script... 123

9 Example Script... 129

9.1 Typical application of a Gemini script... 129

10 Validating, Starting and Stopping a Script ... 157

10.1 Validating a script... 157

10.2 Starting a script ... 158

10.3 Pausing a script... 158

10.4 Continuing a script ... 158

10.5 Stopping a script ... 159

10.6 Starting a script at a certain line... 159

10.7 Undefined Variables option ... 159

10.8 Sample scripts... 159

11 Advanced Programming Features ... 161

11.1 Variables ... 161

11.1.1 Defining and setting a variable ...161

11.1.2 Querying the value of a numeric variable during runtime ...164

11.1.3 Pre-defined variables...165

11.1.3.1 CENTRIFUGE_RACK_CNT ...165

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11.1.3.6 REPLICATE_CNT ... 166

11.1.3.7 SAMPLE_CNT... 166

11.1.3.8 TUBE_CNT... 167

11.1.3.9 WELL_OFFSET... 167

11.1.4 Querying the value of a string variable during runtime ... 168

11.1.5 Commands supporting string variables... 168

11.1.6 Expressions ... 170

11.1.7 Commands supporting expressions... 171

11.1.8 Converting variables and expressions to a string ... 172

11.1.9 Commands supporting variables and expressions converted to a string... 174

11.1.10 Validating a script containing variables... 174

11.2 Conditions (Condition command) ... 175

11.3 Sub-routines ... 176

11.3.1 Creating a sub-routine ... 176

11.3.2 Sub-routine command... 176

11.3.3 Exchanging data with sub-routines ... 177

11.3.4 Validating a script with sub-routines ... 177

11.3.5 Log file for a script with sub-routines ... 178

11.4 Loop options... 178

12 Description of selected commands...181

12.1 Copy Plate command ... 181

12.2 Replicates command... 184

12.3 Serial Dilution command ... 187

12.4 Merge Plates command ... 190

12.5 Transfer command ... 193

12.6 Worklist command... 195

12.6.1 Worklist file format ... 196

12.6.2 Worklist using rack labels ... 198

12.6.3 Worklist using rack barcodes ... 199

12.6.4 Worklist using tube barcodes... 199

12.6.5 Advanced worklist features ... 199

12.7 Export Data command... 200

12.7.1 Report file format ... 201

12.8 Worklist Import command... 206

12.9 RoMa vectors ... 208

12.9.1 Defining a RoMa only carrier ... 208

12.9.2 Defining a RoMa vector ... 210

12.9.3 RoMa Vector command ... 211

12.9.4 Move RoMa command... 212

12.9.5 Using a RoMa vector in a script ... 213

12.9.6 Defining the home position for a RoMa... 216

12.10 PnP vectors ... 217

12.10.1 Defining a PnP vector ... 218

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12.11 Move LiHa command ... 226

12.12 Te-Stack command ... 228

12.13 Carousel commands ... 230

12.13.1 Carousel Scan Barcodes command ...230

12.13.2 Carousel Retrieve command ...231

12.13.3 Carousel Return command...232

12.13.4 Carousel Direct Movements command ...233

12.13.5 CAROUSEL settings in Gemini.opt ...234

12.14 Execute VB Script command ... 236

12.14.1 Toolbar buttons for VB Scripts...237

12.15 Set DiTi Position command... 239

12.16 Pick Up DITIs command ... 240

12.17 Pickup ZipTip command... 242

12.18 Detect Liquid command ... 244

12.19 Te-MO Relative Movements command... 246

12.20 PosID command... 248

12.21 Doorlocks command ... 251

12.22 System command ... 252

12.23 MIO command... 253

12.24 Execute Magellan Method command... 255

12.25 Execute WinWash Program command ... 259

12.26 Centrifuge command... 262

12.27 Active WashStation command ... 264

13 Error Handling... 265

13.1 Liquid error ... 265

13.2 Clot error ... 267

13.3 Instrument error... 268

13.4 Diluter error ... 270

13.5 DITI Fetch error... 271

13.6 Lost DITI error ... 272

13.7 Barcode error ... 273

13.8 Grip error... 274

13.9 WRC/Te-MO error... 275

13.10 WRC Empty error... 276

13.11 WRC Overflow error... 277

13.12 Setup port for Magellan... 278

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13.14 Te-Stack errors... 281

14 Appendices ... A-1

14.1 How to create a custom default worktable ...A-1 14.2 Standard options for carriers and racks ...A-1 14.3 How to create additional carriers...A-1 14.4 Error messages ...A-3 14.5 Structure of the log files...A-5 14.5.1 Structure of the Trace file...A-8 14.6 Gemini directory structure and files...A-9 14.7 Backing up your Gemini system and Gemini data ...A-12 14.8 Command line parameters ...A-12 14.9 Glossary of terms ...A-13

List of Figures ... A-27

List of Tables... A-31

Index ... A-33

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1 About This Manual

1.1 Introduction

This manual describes the Gemini pipetting software for the GENESIS series of pipetting instruments. Gemini provides a graphical user interface for controlling the GENESIS instrument that facilitates the liquid handling needs of a wide range of diagnostic and life science applications, including both routine and research activities. Gemini can either be used stand alone for controlling Genesis and Genesis Freedom pipetting instruments or together with the Tecan dynamic scheduling software FACTS. The Gemini software allows the user to develop Gemini programs (which are normally called scripts) and to quickly visualize how a process can be implemented. Script commands are provided for a wide range of Tecan hardware options and the scripting system is designed for maximum flexibility when developing complex custom scripts. When the script is ready, Gemini controls the pipetting run by sending control signals to the GENESIS instrument through a data connection. If operator interaction is

necessary, Gemini can display a dialog box on the display of the workstation which prompts for the information which is needed.

The external programming interface which uses named pipes allows you to integrate Gemini into third party products or custom applications or to use Gemini components within other Tecan products running on the same computer or a different computer in the network.

It is instructive for new users of Gemini to load the sample scripts which are provided and to work through each script by reviewing the on-line help (see also “Glossary of terms” on page A-13).

This manual instructs the user how to: • install the Gemini software,

• set up instrument and configuration data, • define the worktable,

• define the pipetting scheme, • start pipetting runs, and • react to errors during pipetting.

1.2 Intended use of this product

This product and manual is intended for laboratory specialists who need to develop programs (or scripts) for the GENESIS series of pipetting instruments. It is assumed that such specialists are already acquainted with standard laboratory procedures for handling and pipetting liquids as described in standard textbooks on this subject.

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1.3

1.4 Warning, cautions and notes

Three types of informational notices are used in this manual. They highlight important information or warn the user of a potentially dangerous situation. The following notices have the same level of importance throughout this manual.

Warning:

Indicates the possibility of severe personal injury, loss of life, or equipment damage if the instructions are not followed.

Caution:

Indicates the possibility of severe instrument damage or loss of data if instructions are not followed.

Note:

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2 Product Support

How to get help

Tecan and its representatives maintain a fully trained staff of technical specialists around the world. For any technical questions, contact your nearest Tecan representative.

Addresses

TECAN Regional Organizations:

ASIA

AUSTRIA

BELGIUM

FRANCE

GERMANY

TECAN Sales Schweiz AG Seestrasse 103 CH-8708 Männedorf Switzerland Telephone Telefax Helpdesk eMail +41-1-922-8111 +41-1-922-8484 41-1-922-8282 [email protected]

TECAN Asia (Pte) Ltd. 80, Marine Parade, # 13-04 Singapore, 449 269 Telephone Telefax eMail +65-4441-886 +65-4441-836 [email protected] TECAN Austria GmbH Untersbergstrasse 1a A-5082 Grödig / Salzburg

Telephone Telefax Helpdesk eMail +43-6246-8933-0 +43-6246-72770 +43-6246-8933-444 [email protected]

TECAN Benelux B.V.B.A. Vaartdijk 55 B-2800 Mechelen Telephone Telefax eMail +32-15-421319 +32-15-421612 [email protected]

TECAN France S.A.

Parc d’Activités de Pissaloup Bâtiment B - Hermes II 27, Rue Edouard Branly F-78190 Trappes Telephone Telefax Helpdesk eMail +33-1-3068-8150 +33-1-3068-9813 +33-1-3068-8150 [email protected] TECAN Deutschland GmbH Theodor-Storm-Straß e 17 D-74564 Crailsheim Telephone Telefax Helpdesk eMail +49-7951-9417-0 +49-7951-5038 +49-7951-9417-73 [email protected]

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GREAT BRITAIN ITALY JAPAN NETHERLANDS USA TECAN UK Ltd.

Theale Court, 11-13 High Street Theale, Reading Berkshire RG7 5AH Telephone Telefax Helpdesk eMail +44-118-930-0300 +44-118-930-5671 +44-118-930-0300 [email protected] TECAN Italia, S.r.l. Via F.Ili Cervi Palazzo Bernini

Centro Direzionale Milano 2 I-20090 Segrate (MI)

Telephone Telefax Helpdesk eMail +39-02-215-2128 +39-02-215-97441 +39-02-215-2128 [email protected]

TECAN (Japan) Co. Ltd. Meiji Seimei Fuchu Building 10F 1-40 Miyamachi Fuchu City Tokyo 183 Telephone Telefax Helpdesk eMail +81-4-2334-8855 +81-4-2334-0401 +81-4-2334-8855 [email protected]

TECAN Benelux B.V.B.A. Industrieweg 30 NL-4283 Giessen Telephone Telefax eMail +31-183-448174 +31-183-448067 [email protected]

TECAN US, Inc. P.O. Box 13953

Research Triangle Park, NC 27709

Telephone Telefax Helpdesk eMail +1-919-361-5200 +1-919-361-5201 (800) TECAN-US, (800) 832-2687 [email protected]

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3 System Setup

This chapter describes the steps required to install and set up the Gemini software and to set up the Genesis instrument.

3.1 System requirements

The Gemini software has the following minimum hardware and software requirements: • An IBM-compatible computer with Microsoft Windows NT version 4.0, Service

Pack 4 or later or Windows 2000 Service Pack 2 or later; • Pentium 166 MHz or higher; at least 128 MB RAM;

• About 50 MB of hard disk space for the standard Gemini software, optional software components, scripts and log files;

• An SVGA monitor with a minimum resolution of 1024x768 pixels; to ensure correct display of the dialog boxes, we recommend you to configure your display settings in the Control Panel for Small Fonts;

• 100 MB of virtual memory;

• A Gemini hardlock (a copy protection device which is plugged into the parallel interface of the computer). This is often called a dongle;

• 1 parallel interface for the hardlock (you can connect a printer to the back of the hardlock if necessary);

• 1 unused serial interface for the data interface to the GENESIS instrument; • additional serial interfaces are required by some of the instrument options (e.g. the

Mettler balance); • Printer (optional):

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3.2 Supported pipetting instruments

The Gemini software is designed for the following Tecan pipetting instruments: Genesis RSP, Genesis RWS, Genesis NPS and Genesis Freedom

In addition, Gemini supports the following GENESIS options and systems: • 4 or 8 tips

• Disposable Tips (DITIs)

• Monitored Pump Option (MPO) • Liquid Container Supervisor (LICOS) • Low Volume Option

• Lower DITI Eject

• Te-VacS, the Tecan SPE Vacuum System • Te-MagS, the Tecan Magnetic Bead Separator • 6-way valve for different system liquids • Vacuum assisted waste for viscous liquids • NPS System (Nanopipetting System) • Te-Shake (Orbital Shaker)

• Te-MO (Tecan Multipipetting Option)

• MIO (heated incubator with optional shaker hardware) • Carousel

• Te-Stack (Tecan Microplate Stacker) • Hettich Centrifuge

• H+P Variomag

• Connection Box for the Te-Flow option

• Tecan Magellan software (for Tecan Reader and Photometer) • Tecan WinWash Plus software (for Tecan Plate Washers) • Huber Recirculator

• Mettler Balance

• Symbol LS1220 Barcode Scanner

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3.3 Standard and advanced hardlocks

Gemini is available with two different software feature levels. Whereas the software on the CD which is supplied is the same in both cases, the additional features provided by the advanced feature level are enabled by using the Advanced hardlock (sometimes called a dongle). The Standard hardlock does not support the following commands: • Gemini commands Move ROMA, ROMA_VECTOR, Move PnP and PnP_VECTOR. • Named-Pipe commands ROMA_GRIP, ROMA_MOVE, ROMA_RELATIVE,

SET_ROMA_BARCODE, PNP_GRIP, PNP_MOVE, PNP_RELATIVE and SET_PNP_BARCODE.

The hardlock version you are currently using is shown in the Gemini status bar (see “Status Bar” on page 28).

SeeGem_Pipe.pdfin the Gemini program directory for more information on the named pipes programming interface for Gemini.

3.4 Installation

Please proceed as follows to install the Gemini software: • Insert the Gemini CD into your CD-ROM drive. • Click the Start button on your Windows task bar. • Choose Run.

• TypeD:\SETUP, whereD:is the drive letter of your CD-ROM drive. • Click OK.

• After the installation program has started please follow the instructions on the screen.

Note:

Gemini runs in Simulation mode if no hardlock is detected.

Caution:

You must use the Genesis Setup & Service software module to check the reference positions. Otherwise your rack and carrier coordinates might be wrong. See the “Genesis Instrument Software Manual - Doc ID 390791”, “Setup & Service Software Module” for more information.

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3.5 Upgrading to the latest software version

The steps required to upgrade your Gemini software to the latest version are dependent in part on the GENESIS instrument version and system options which you are already using. For this reason upgrading is normally carried out by a Tecan representative. Please see the README.TXT file in the Gemini program directory and the upgrade notes supplied with the product for additional information.

Where applicable, please observe your local regulations for certification of your GENESIS system.

It is strongly recommended to backup up you system and data files before upgrading (see “Backing up your Gemini system and Gemini data” on page A-12).

Gemini version 4.0 can read files created by Gemini version 3.2 or later. Files created with Gemini version 4.0 are generally not compatible with earlier versions of the software.

Gemini configuration files and script files are now protected by checksums (see “Data Explorer” on page 10). When upgrading from an earlier version of Gemini, the Data Explorer will initially show that all files have incorrect checksums since earlier Gemini versions did not support the checksum feature. A warning is shown if an attempt is made to load a file with an missing checksum. A checksum is added automatically when the file is saved.

Choose About Gemini in the Help menu if you want to check which version of Gemini you are using.

Caution:

The setup program overwrites existing Gemini installations. If you specify the same installation path which was used for an older version of Gemini, please back up your data first and copy it back after the installation is finished (see “Backing up your Gemini system and Gemini data” on page A-12 and “Upgrading to the latest software version”, below, for more information).

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4 Menus

This chapter describes the main menu options which are provided by the Gemini software. Each menu will be discussed in more detail in subsequent chapters.

4.1 File menu

This menu allows you to create a new Gemini script, to open an existing script, to print the contents of a script, to select a recent script or to quit Gemini

4.1.1 New / Open / Close / Save / Save As

These menu items allow you to create, open and save Gemini scripts. Please note that Gemini script files have the extension .GEM and are normally stored in the

\Gemini\Data directory.

4.1.2 Print / Print Preview / Print Setup

If you have a printer connected to your computer, these menu items allow you to print Gemini scripts. The following items are printed:

• The script

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• The path and filename of the script file • The worktable layout

• Page number, time and date • Gemini user name

4.1.3 Backup Data / Recover Data

Choose Backup to make backup copies of the Gemini configuration files and script files to your local hard disk.The following files are backed up:

• Carrier.cgf • Gemini.cfg • Gemini.set • Gemini.opt • LClasses.dat

• All script files (*.gem)

Apart from Gemini.set, which is in the Gemini directory, from the Gemini/Data directory Gemini creates a new sub-directory in the Gemini directory for each backup. The name of the new sub-directory is BACKUP_YYYYMMDD_HHMMSS, where YYYYMMDD is the date and HHMMSS is the time of the backup.

Choose Recover to recover previously backed up Gemini configuration files and script flies. This copies all of the backed up files to the Gemini/Data directory. A dialog box is shown to allow you to choose which backup version to recover.

Choose Settings in the Setup menu to configure Gemini to make automatic backups at specified intervals. See “Settings” on page 16.

Both backup and recovery operations are reported in the general trace file.

See “Backing up your Gemini system and Gemini data” on page A-12 if you want to make an external backup of your Gemini installation.

4.1.4 Data Explorer

The following Gemini configuration files and script files are protected by checksums: • Carrier.cfg

• Gemini.cfg • Gemini.set • Gemini.opt • LClasses.dat

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• All script files (*.gem) • Log files

• Export files • The trace file

Choose Data Explorer to check whether these files have valid checksums. An incorrect checksum indicates that the file contents of the file may be corrupted or has been modified outside of Gemini by another program or process.

A warning is shown if an attempt is made to load a file with an incorrect or missing checksum. The user can then choose to load the file or cancel. In the latter case, Gemini aborts with the exception of script files (*.gem). In this case, the file is not loaded but Gemini remains running. The incorrect checksum warning can be disabled in the Settings dialog box by a user with administrator status (see page 20). An entry is written to the log file each time an incorrect or missing checksum is found.

When upgrading from an earlier version of Gemini, the Data Explorer will initially show that all files have incorrect checksums since earlier Gemini versions did not support the checksum feature. A warning is shown if an attempt is made to load a file with an missing checksum. Gemini automatically adds a checksum when the file is saved. If you select a configuration file or script, the Data Explorer also shows the date and time of the last modification to the file alongside the name of the user who modified it and a comment to explain the reason for the change. See Log Reason in the Settings dialog box on page 20 for additional information on this feature.

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4.1.5 Recent files list

Gemini keeps a list of up to 8 of the most recently opened scripts. You can load one of them by choosing it from the list or by opening the File menu and pressing the

corresponding digit on the keyboard.

4.1.6 Quit Gemini

This menu item closes all currently open scripts, de-initializes the instrument and quits Gemini.

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4.2 Edit menu

This menu allows you to edit, insert and delete Gemini commands. The menu items are used when writing a Gemini script (see “Creating a Gemini script” on page 123). If you choose Insert new command, a floating menu appears with additional choices, as shown below:

You also get the floating menu if you click on the script window with the right mouse button.

4.2.1 Cut / Copy / Paste

Gemini allows you to repeat script lines by using Copy & Paste. If you have more than one script opened at the same time, you can copy or move lines from one script to another.

4.2.2 Edit / Delete / Insert New Command

These menu items are used to edit or delete existing commands (i.e. script lines) or to insert new commands. New commands are inserted below the currently selected command, which is highlighted in color (the default color is light yellow). You can select a command by clicking with the mouse or by using the cursor keys. If you select the first

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line of the script, you will be asked whether to insert the new command above or below the current command.

Note:

You can also insert a command in your script by clicking on a button in the Command Bar or one of the commands toolbars, clicking with the right mouse button and choosing the command from the floating menu or by pressing the Insert key.

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4.3 Setup menu

After opening a Gemini script, this menu allows you to configure the pipetting instrument (see “Configuration Editor” on page 33), set up liquid classes (see “Liquid Classes” on page 91) and to configure general settings:

4.3.1 Configuration

See “Configuration Editor” on page 33.

4.3.2 Liquid Classes

See “Liquid Classes” on page 91.

4.3.3 Setup & Service Te-MO

See the “Te-MO Operating Manual - Doc ID 391733“, “Setup & Service” for more information.

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4.3.4 Settings

This menu item lets you configure general settings for the Gemini software. The following dialog box is shown:

Paths panel

Specify where Gemini should store its data files (Data), log files (Log) and output files (Output). Enter the required paths directly or click the Browse buttons and choose the required directories.

Baud rate / COM-Port

Specify the COM (V.24) port that the GENESIS instrument is connected to. You can also set the baud rate used for communication between Gemini and GENESIS. We recommend you to use a baud rate of 38,400 baud. See “External Devices” on page 21 for information on configuring COM ports for external devices such as the carousel or centrifuge.

Simulation

When running in simulation mode, Gemini pauses for a certain time after executing each pipetting command. You can set the duration of the pause here.

Language

Select the required language of the user interface (German (Deutsch) or English).

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Initialising the instrument

Gemini detects automatically whether the instrument needs to be initialized, and carries out initialization if necessary. If your instrument is equipped with a LiHa, during initialization it is moved above the left-most waste and all diluters are

initialized. This can cause some liquid to drip from the tips. If you check the Deep in Waste checkbox, Gemini lowers the tips into the waste to minimize the risk of contamination during initialization. See also “Arm initialization” on page 20.

User management

User management is provided to restrict access to the Gemini software. Users are prompted to enter a user name and password during program start-up. Note that passwords are case-sensitive.

When upgrading from an earlier version of Gemini, when the software is started for the first time you will be forced to create a new user with administrator status (unless one was already created with the earlier software version).

Click Change Password to change the password of the currently logged in user. Click Edit User to create new users or delete existing users. Gemini provides three user levels with the following rights:

Caution:

Please check the coordinates of the waste before activating this option. Otherwise the tips might collide.

User has rights to:

• flush the instrument or drop DITIs • specify the DITI position

• load, close or print a Gemini script • validate or start a script

• handle errors during pipetting

Since user level users are not allowed to create or modify scripts, the Command bar and various other program interface features used to create scripts are hidden or disabled.

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Log off user after ...

Users are automatically logged out of Gemini after a specified time during which no keyboard or mouse-click activities have been detected. Specify the required interval in minutes in this field (range 1 to 1440 minutes).

If the user is logged out while a script is running, the script continues to run. In addition, a dialog box containing a pause button is displayed in case it is necessary to stop the script. The dialog box also allows the user to log in again. All other Gemini functions are disabled until the user logs in again.

Password has to be changed after ...

To maximize security, users can be forced to change their passwords at regular intervals. To activate this feature, check the checkbox and specify the interval in days.

Maintenance panel

Click Maintenance Settings to view the instrument’s internal counters for LiHa, RoMa and PnP movements. Gemini gets this information by interrogating the instrument (the counters are all set to zero in simulation mode).

Check the Active checkbox in the Maintenance panel of the Settings dialog box if you want to activate automatic warnings when predefined limits have been reached. In this case, the user is prompted to perform routine maintenance activities and the instrument will not start the pipetting run. See the specific instrument operating manual for information on the maintenance which is required. After carrying out the maintenance, click the Reset buttons to reset the internal counters to allow pipetting to resume. The predefined limits are specified in the Maximum allowed fields. You need to have Administrator rights to activate the maintenance check and/or set the predefined limits for the counters (see User Management in “Settings” on page 16).

Manager same as User with additional rights to: • create, modify and save Gemini scripts • edit the Configuration

• edit the Liquid Classes • edit the Settings • edit the password

• skip timers during pipetting

Administrator same as Manager with additional rights to: • create or delete users

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After installing Gemini, the maintenance checkbox and button are initially disabled. To activate them, open the file Gemini.opt in the Gemini\data directory with a plain text editor such as Notepad and add the entry DISABLE_MAINTENANCE=0 to the [OPTIONS] section (or edit the existing entry accordingly).

Display panel

If required, you can choose an image such as a company logo to display as

wallpaper in the background of the main Gemini window. Click the Browse button to choose the required file. The supported image file formats are .bmp, .dib, .gif, .jpg and .jpeg.

Choose Center, Tile or Stretch as required to achieve the required effect. In addition, you can choose an image or movie file to display while a script is running. Click the Browse button to choose the required file. The supported image file formats are .bmp, .dib, .gif, .jpg and .jpeg. The supported video file formats are .avi, .mpg and .mpeg.

Color of selected script line

A colored background is used to indicate the script line which is currently selected. The default color is light yellow. If required click on the color and use the color picker to choose another color. When a script line is selected, the same color is used to highlight the associated object in the Worktable window.

Log Files

Gemini can write log files to document the pipetting, to record user inputs, to help you to check scripts in simulation mode and to find errors. You can activate three types of log files with different levels of logging detail, either individually or in combination:

Check the Full checkbox to enable log files of type LOG. Check the Input checkbox to enable log files of type USR. Check the Error checkbox to enable log files of type ERR.

See “Structure of the log files” on page A-5 for Information on each of these log file types.

Even if you have not activated the Log Files option, you can view recent log entries by choosing Log Window in the View menu. The Log Window has the same

structure as the log files and shows the last 1000 log entries when it is first opened.

Caution:

Gemini can write up to 100,000 individual log files, which can use up a lot of storage on your hard disk. Accordingly, it is recommended to delete or archive old or unwanted log files on a regular basis.

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Log Reason

When saving one of the following files after making changes, users are forced to enter a comment to explain the reason for the changes:

• Carrier.cgf • Gemini.cfg • Gemini.set • Gemini.opt • LClasses.dat

• All script files (*.gem)

Uncheck the Log Reason checkbox if you want to disable this feature (you need administrator status to do this). This setting can only be changed by a user with administrator status.

Note: The user comment can be viewed in the Data Explorer (see page 10). Only the most recent comment is saved. Earlier comments are stored with earlier versions of these files, which are automatically backed up to the History sub-directory (see “Gemini directory structure and files” on page A-9).

Evaluate file checksums

Gemini configuration files and script files are protected by checksums, and a warning is shown if an attempt is made to load a file with an incorrect or missing checksum. Uncheck the Evaluate file checksums checkbox if you want to disable the warning (you need administrator status to do this). The validity of the checksums can be viewed in the Data Explorer (see page 10).

Automatic data backup

Check this checkbox and specify the duration in days to automatically back up Gemini configuration files and script files at regular intervals. Gemini creates a new sub-directory in the Gemini directory for each backup. See “Backup Data / Recover Data” on page 10 for more information.

4.3.5 Arm initialization

When Gemini initializes the arms (LiHa, RoMa and PnP), a sequence of movements is carried out to determine the reference (zero) positions along the X, Y and Z axes. During the full initialization sequence which is carried out e.g. when Gemini is started after powering up the instrument, the arms need to move fully to the rear of the instrument to determine the zero position in the Y direction.

Initialization mode: Standard

With the GENESIS Freedom instrument, all arms move to the rear left of the worktable to initialize all axes.

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With the GENESIS RSP instrument, during initialization the LiHa moves to the rear left of the worktable and the (optional) RoMa moves to the rear right of the

worktable.

With all instrument types, after initialization the arms move to their home (parking) positions if they have been defined (see “Defining the home position for a RoMa” on page 216 and “Defining the home position for a PnP” on page 224).

Initialization mode: To the front

If the rear left of the worktable is occupied by other objects, choose To the front to avoid a collision during initialization. In this case you must specify the grid position range in the From grid and To fields to indicate where it is safe to move the arms to the rear. Since the arms move one at a time to the rear in this case and then back to the front, the grid position range only needs to wide enough to accommodate one arm. When initialization is finished, all arms move to a parking position at the front left of the worktable.

The initialization mode To the front is only available for the GENESIS Freedom instrument.

4.3.6 External Devices

This menu item is used to select the COM ports to use for external devices such as the carousel or centrifuge.

Gemini uses the following communication parameters for the serial interfaces:

If Gemini is not able to successfully communicate with an external device, make sure that the device’s serial interface has been correctly configured for the above

communication parameters. Also make sure that you are using the correct serial interface cable.

Device Baud rate

Bits Stop Bits Parity Flow control

Carousel 9600 8 1 Even None

Carousel Scanner 9600 8 1 No None

Waterbath 9600 8 1 No None

Centrifuge 9600 7 1 Even None

Variomag 9600 8 1 No None

Balance 2400 7 1 Even DTR

Barcode Scanner 9600 7 2 Even None

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4.4 Execute menu

This menu allows you to flush the instrument (you must first define the worktable; see “The Worktable window” on page 117), drop DITIs (you must first define the worktable), reset the Genesis options Te-VacS, Te-MagS, Te-Shake, set the DITI position (you must first define the worktable), validate and start a script. You can also start a script at a specified line.

4.4.1 Flush Instrument

This menu item is used to flush the instrument (fill it with system liquid). Gemini prompts you for the volume and the location of the waste and cleaner on the worktable.

4.4.2 Drop DITIs

This menu item is used to drop DITIs directly without running a script. Gemini prompts you for the location of the DITI waste on the worktable.

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4.4.3 Reset Options

This menu item is used to initialize the following hardware options for your GENESIS instrument manually. The hardware options are normally reset automatically at the appropriate time and a manual reset is only necessary under abnormal circumstances. • Te-VacS

• Te-MagS • Te-Shake • Te-MO WRC • Carousel

The GENESIS instrument is interrogated for the presence of these options and the Reset Options menu item will be inactive (gray) if none of the options are detected or if Gemini is running in simulation mode.

The following dialog box is shown if at least one of the options is present (the list of devices will change according to the installed options):

The device number is shown alongside the device name. Notes

Te-VacS

You can initialize the Te-VacS devices individually or all devices.

Te-MagS

You can initialize the Te-MagS devices individually or all devices. In addition, you can initialize the Te-MagS heaters individually.

Te-Shake

You can initialize the Te-Shake devices individually or all devices.

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Te-MO WRC

You can initialize the Te-MO WRC devices individually. This flushes the WRC with washing liquid #1 for 20 s using 50% pump power. This ensures that the tubing and the wash carrier is filled with liquid and free of bubbles.

Carousel

You can initialize the carousels individually.

Click OK to initialize the selected device and close the dialog box. Click Cancel to close the dialog box without initializing.

4.4.4 Fill System (ActiveTip)

If your instrument is fitted with ActiveTips, this menu item is used to fill the liquid system. A special procedure is necessary because of the very small inner diameter of the ActiveTips.

4.4.5 Switch on/off Doorlocks

This menu item is used to open or close the doorlocks manually. This menu item is only available if your instrument is fitted with doorlocks and is not available in simulation mode. The doorlocks are normally opened and closed automatically at the appropriate time and you should only need to operate the doorlocks manually in special situations (e.g. during instrument configuration). See also “Configuring the Doorlocks” on page 90.

4.4.6 Send Firmware Command

This menu item lets you send a firmware command directly to the instrument and is only intended for specialists. See the respective instrument manual for a list of firmware commands.

4.4.7 Set DITI Position

If you are using DITIs, Gemini stores the position of the last fetched DITI. When starting a new run, the Get DiTis command starts picking up DITIs at the next available position. After loading new DITI racks onto the worktable, this menu item can be used to ensure that the next DiTi is fetched from position 1 rather than from the middle of the new rack.

Warning:

Please be careful when using this feature. Sending the wrong commands can damage the instrument or objects in its workspace, hurt yourself or other people.

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You can specify the next location for each of the available DiTi types. You can also specify the next DiTi position during script runtime with the Set DiTi Position command.

DiTi type

Specify the DiTi type for which you want to specify the next location.

Next DiTi position

Specify the rack containing the next available unused DiTi of this type by clicking on the new DiTi tray in the Worktable window. Then specify the rack position (you should normally choose position 1).

4.4.8 Loading the Te-MO with racks

The Te-MO can be loaded with racks during script runtime using the RoMa. You can also load it manually before starting the script. Depending on their position in the TeMO, some of the sites may be difficult to access due to the position of the slides. This command is used to move a specified site to the RoMa exchange position (transfer position) manually to make it easier to exchange the rack. In this position, the LiHa or RoMa can access the specified site without colliding with the Te-MO pipetting head.

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Choose the required slide and site in the Sites panel and click Move in the RoMa Exchange Position panel to move the site to the exchange position.

When the Te-MO reaches the RoMa exchange position and you are using an APC (Active Positioning Carrier), click Open in the APC panel to release the rack. Click Close in the APC panel to lock the rack in position again.

4.4.9 Validate

See “Validating a script” on page 157.

4.4.10 Start

See “Starting a script” on page 158.

4.4.11 Pause

See “Pausing a script” on page 158.

4.4.12 Continue

See “Continuing a script” on page 158.

4.4.13 Abort

See “Stopping a script” on page 159.

4.4.14 Start at line ...

See “Starting a script at a certain line” on page 159.

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4.4.15 Undefined Variables

See “Undefined Variables option” on page 159.

4.5 View menu

This menu allows you to view or hide the Log, Emergency-Stop, Variables and Info windows, to create custom toolbars and to view or hide the Status bar and the Command bar.

4.5.1 Log window

This menu item lets you view or hide the Log window, a troubleshooting tool that tracks every command sent by the computer to the instrument, every response returned from the instrument to the computer and any user input. The content and format of the log corresponds to a Full log file of type LOG (see “Structure of the log files” on page A-5).

4.5.2 Emergency Stop window

This menu item is used to show or hide the Emergency Stop window (a quick access button that immediately stops the script, and thus the pipetting). The Emergency Stop window is always shown in the foreground to ensure that it is always available when

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required. If you click the Emergency Stop button, the script is stopped and Gemini switches to simulation mode. Note: The Emergency Stop button is inactive in simulation mode.

4.5.3 Variables window

This menu item is used to show or hide the Variables window, which shows the value of all defined variables during script runtime. This window is refreshed after every script line; changed variables are shown in red and unchanged variables are shown in black.

4.5.4 Info window

This menu item is only available if you have a Te-VacS, Te-MagS and/or Te-Shake option connected to your instrument. During script runtime, the info window displays information such as pressure or temperature.

4.5.5 Toolbar

This menu item lets you customize the standard toolbars and allows you to create and delete custom toolbars. You can also reset the toolbars to the default settings.

4.5.6 Status Bar

This menu item is used to show or hide the status bar, which displays the following information:

The Dongle Type fields show which Gemini feature level you are using. The feature level is dependent on the hardlock version you are using:

REAL MODE = Real mode (normal operation), SIMULATION = Simulation mode STD = Standard Gemini hardlock, ADV = Advanced Gemini hardlock

GEM = hardlock detected, DEMO = no hardlock detected

See “Standard and advanced hardlocks” on page 7 for more information.

Note:

To rearrange toolbar buttons, press the Alt key and drag them with the mouse. You can remove a button by dragging it off of the toolbar. Select a toolbar in the Toolbars window and click Reset to restore the default button assignments. Double-click a toolbar (or drag the toolbar with the mouse) to switch between floating mode and docking mode. In addition, you can resize or reshape a toolbar by dragging its borders.

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4.5.7 Command Bar

This menu item allows you to display or hide the Command Bar, which lists all of the script commands in the same style as the element bar in Microsoft Outlook:

The Command Bar is an alternative way of selecting script commands to the commands toolbars (see page 108). The commands in the Command Bar are grouped according to their function as follows:

• Pipetting commands (e.g. Aspirate)

• Advanced pipetting commands (e.g. Copy Plate) • Script programming commands (e.g. Start Timer) • Te-MO commands

• Commands for storage devices (e.g. Carousel) • Commands for robotic devices (e.g. RoMa and PnP) • Commands for optional devices or accessories (e.g.

Vacuum Separator)

Click on the group name button in the Command Bar to choose commands from the respective group. Right click on one of the commands to switch between large and small icons.

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4.6 Window menu

This menu allows you to display the currently open windows in cascade or tile style, or to arrange minimized icons. In addition, this menu lists all currently opened scripts and marks the currently active script with a check mark.

4.6.1 Cascade

If several script windows are open, this command arranges the script windows on top of each other.

4.6.2 Tile

If several script windows are open, this command arranges the script windows as non-overlapping tiles.

4.6.3 Arrange Icons

If several script windows are open and minimized, this command arranges the icons along the bottom of the screen.

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4.7 Help menu

This menu opens the online help (Help Topics) and identifies the version of Gemini you are using (About Gemini...).

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5 Configuration Editor

Gemini stores information on fixed and variable parts of the GENESIS pipetting instrument in the two configuration filesCARRIER.CFGandGEMINI.CFGin the Gemini/ data directory, which are collectively called the configuration. The configuration also contains information on the dimensions of the racks and carriers which are available and parameters for optional accessories. The configuration is edited with the Configuration Editor, which is started when you choose Configuration in the Setup menu:

Click the tabs at the top of the dialog box to choose the object type that you want to edit. Gemini then displays a list of the objects which are defined for the selected type. Then choose an item and click one of the following buttons:

Edit

Click this button to edit the properties of the selected item.

Delete

Click this button to delete the selected item.

New

Click this button to create a new item of the selected type, e.g. a new rack.

Copy

Click this button to copy the selected item. You will be prompted for the name of the copy.

Name

Click this button to change the name of the selected item.

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Please proceed as follows when setting up a new GENESIS instrument:

• Use the Genesis Setup & Service software module to check the reference positions. See the “Genesis Instrument Software Manual - Doc ID 390791”, “Setup & Service Software Module” for more information.

• Edit the settings for the LiHa (see “Configuring the LiHa” on page 82)

• If necessary, edit the settings for MPO/LICOS (see “Configuring the MPO/LICOS” on page 86) and ChemSystem (see “Configuring the ChemSystem” on page 87). • Click OK to save the configuration and close the configuration editor.

On delivery, the database of the Genesis software package already includes information on all standard Tecan carriers, racks and containers. I

Caution:

It is recommended not to change the properties of the predefined standard Tecan carriers, racks and containers. Copy the object and save it under a new name if you want to alter any of the properties.

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5.1 Basic concepts

5.1.1 Introduction to carriers and racks

Gemini allows you to define an object (e.g. a microplate rack) once only, and then to assign it to any required position on the worktable grid. This is handled by the Gemini software by storing the coordinates in a hierarchy:

• The rack coordinates are relative to the site on which the rack is placed. • The site coordinates are relative to the carrier.

• The carrier offsets are relative to the grid position on the worktable (see also Figure 5-16 on page 64).

• The grid positions on the worktable have a periodic spacing of 25 mm.

The hierarchy allows you to place a rack at any suitable site, carrier and worktable position without having to redefine its coordinates.

The figure below shows the relationship between racks, carriers and the worktable.

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When you set up the worktable for your Gemini script, you first choose a carrier with the required number of sites (see “Configuring carriers” on page 62). Each of the sites can hold a rack. If you cannot find the carrier you need in the Gemini database, you can define a new carrier (see “Configuring carriers” on page 62).

You then choose the racks you want to use. If you cannot find the rack you need in the Gemini database, you can define a new rack (see “Configuring racks” on page 45). In the third step you position the carriers on the worktable and place the racks onto the carriers (see “Adding carriers and racks to the worktable” on page 118).

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5.2 Moving the arms

Positions in Gemini are measured and verified by moving the LiHa, RoMa, PnP or Te-MO etc. to the required place by pressing keys on the numeric keypad. You can then store the current position coordinates in the dialog box for the object. Positions are defined in instrument steps, i.e. the smallest unit of movement of the servo motors (0.1 mm). The coordinate system of the instrument uses three axes for the LiHa (X, Y, and Z), five axes for the RoMa (X, Y, Z, R, and G), five axes for the PnP (X, Y, Z, R, and G), five axes for the Te-MO (X, Y1, Y2, Y3 and Z) and three axes for the PosID (X, Y and B).

5.2.1 Moving the LiHa

The LiHa (Liquid Handling Arm) is mounted on the X-slide and holds the pipetting tips. In Genesis, the origin of the LiHa coordinate system (X=0, Y=0, Z=0) is the rear left of the worktable with the pipetting tips raised. The three axes of the LiHa are defined as follows:

X from left to right Y from rear to front Z tips from top to bottom

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You can move the LiHa using the numeric keypad (make sure that NUM Lock key is pressed):

Each time you press one of these keys, the arm is moved by a single step. Keep the key pressed to move the arm by two steps per second. If you also press the CONTROL key, the arm is accelerated until it reaches a certain maximum speed.

When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The LIHA tab shows the current position of the LiHa. If your instrument is not fitted with a LiHa, the LIHA tab is not displayed unless you are running in simulation mode.

The Z-movements panel lets you select which tips should be moved in the Z-direction. You can specify the first tip to move and the total number of tips to move.

The Adjust button is only available when editing racks. It is used to adjust the rack position for a specified, single site to compensate for small manufacturing inaccuracies without needing to switch to the carrier definition. To use the Adjust button, move the LiHa to the Z-max position above the first well of the rack while it rests on the required site. Then click the Adjust button to modify the carrier definition to match the current X, Y and Z coordinates.

Figure 5-3: Move LIHA dialog box

7 8 : rear (- Y) 9 : up (- Z) 4 : left (- X) 5 6 : right (+ X)

1 2 : front (+ Y) 3 : down (+ Z)

Table 5-2: Moving the LiHa using the numeric keypad

Note:

You cannot use the cursor keys to move the arm since they have default functions in Windows applications.

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5.2.2 Moving the RoMa

The RoMa (Robotic Manipulator Arm) is a robotic arm with gripper fingers that can grip and move objects such as microplates. In Genesis, the origin of the RoMa coordinate system (X=0, Y=0, Z=0) is the rear left of the worktable with the gripper raised and pointing towards the front of the instrument. The five axes of the RoMa are defined as follows:

X from left to right Y from rear to front Z from top to bottom

R clockwise rotation of the gripper when viewed from above

G from narrow to wide gripper distance

Table 5-3: Movement axes for the RoMa

When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The ROMA tab shows the current position of the RoMa. If your instrument is not fitted with a RoMa, the ROMA tab is not displayed unless you are running in simulation mode.

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You can move the RoMa using the numeric keypad (make sure that NUM Lock key is pressed):

5.2.3 Moving the PnP

The PnP (Pick and Place) is a robotic arm with gripper fingers that can grip and move small objects such as tubes. In Genesis, the origin of the PnP coordinate system (X=0, Y=0, Z=0) is the rear left of the worktable with the gripper raised. The five axes of the PnP are defined as follows:

7 : clockwise (+R) 8 : rear (- Y) 9 : up (- Z) 4 : left (+ X) 5 6 : right (- X) 1 : counterclockwise (-R) 2 : front (+ Y) 3 : down (+ Z) 0 : narrow (-G) , : wide (+ G)

Table 5-4: Moving the RoMa with the keys on the numeric keypad

Note:

X from left to right Y from rear to front Z from top to bottom

R clockwise rotation of the gripper when viewed from above

G from narrow to wide gripper distance

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You can move the PnP using the numeric keypad (make sure that NUM Lock key is pressed):

When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The PnP tab shows the current position of the PnP. If your instrument is not fitted with a PnP, the PnP tab is not displayed unless you are running in simulation mode.

Figure 5-5: Move PnP dialog box

7 : clockwise (+R) 8 : rear (- Y) 9 : up (- Z) 4 : left (+ X) 5 6 : right (- X) 1 : counterclockwise (-R) 2 : front (+ Y) 3 : down (+ Z) 0 : narrow (-G) , : wide (+ G)

Table 5-6: Moving the PnP with the keys on the numeric keypad

Note:

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5.2.4 Moving the Te-MO

Moving the Te-MO (Tecan Multipipetting Option) is similar to moving the LiHa or RoMa. The five axes of the Te-MO are defined as follows:

You can move the Te-MO using the numeric keypad (make sure that NUM Lock key is pressed):

X Head, left to right Y1 Left slide, rear to front Y2 Middle slide, rear to front Y3 Right slide, rear to front Z Head, top to bottom

Table 5-7: Movement axes for the Te-MO

7 : Y1 back 8 : Y2 back 9 : Y3 back - : Z up 4 : X left 5 : 6 : X right + : Z down 1 : Y1 front 2 : Y2 front 3 : Y3 front

Table 5-8: Moving the Te-MO with the keys on the numeric keypad

Note:

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5.2.5 Moving the PosID

The PosID (Positive Identification System) is a barcode scanner device. Moving the PosID is similar to moving the LiHa or RoMa. In Genesis, the origin of the PosID coordinate system (X=0, Y=0, B=0) is the rear left of the worktable with the carrier gripper near the front. The three axes of the PosID are defined as follows:

You can move the PosID using the numeric keypad (make sure that NUM Lock key is pressed):

When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The Te-MO tab shows the current position of the MO. If your instrument is not fitted with a Te-MO, the Te-MO tab is not displayed unless you are running in simulation mode.

To move the Te-MO to the transfer position, for example to test a RoMa vector, select a slide and site from the pop-up list and click Move to Transfer Position. In this position, the LiHa or RoMa can access the specified site without colliding with the Te-MO pipetting head. When the Te-MO reaches the transfer position and you are using an APC (Active Positioning Carrier), click Open APC to release the rack. Click Close APC to lock the rack in position again.

Figure 5-6: Move Te-MO dialog box

X PosID, from left to right

Y PosID carrier gripper, rear to front B PosID scanner head, top to bottom

Table 5-9: Movement axes for the PosID

7 : 8 : back 9 : B counterclockwise 4 : X left 5 : 6 : X right

1 : 2 : front 3 : B clockwise

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Note:

When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The PosID tab shows the current position of the PosID. If your instrument is not fitted with a PosID, the PosID tab is not displayed.

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5.3 Configuring racks

A rack is an object such as a microplate which has one or more containers (wells) which are available for liquids or samples. Racks are placed on carriers. Carriers can be located at various positions on the worktable (see Figure 5-2 on page 35).

The following explains the options in the Edit Rack dialog box. See “Rack Wizard” on page 53 for information on creating new racks.

Position panel

This specifies the X, Y and Z coordinates of the wells in the rack (see Table 5-11 on page 48 for more information). The coordinates are normally set by manually moving the LiHa above the first and last positions on the rack and clicking the < buttons (see “Teaching the rack coordinates” on page 49).

Figure 5-8: Edit Rack dialog box

Caution:

On delivery, the database of the Genesis software package already includes information on all standard Tecan carriers, racks and containers. It is

recommended not to change the properties of the predefined standard Tecan objects. Copy the object to a new name if you want to alter any of the properties.

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Type panel

Choose the rack type. See “Rack types” on page 51 for more information on this topic. Rack panel

This specifies the well geometry:

Wells (X): Specify the total number of wells in the X-direction (max. 128). Wells (Y): Specify the total number of wells in the Y-direction (max. 128).

Color panel

You can choose a unique color here to make it easier for you to identify this rack type in the Worktable window. The default rack colors are as follows:

• Microplate racks: blue • Tube racks: green • DiTi racks: red

• Washstation racks: yellow

• Default for all other rack types: blue Y-distance of wells

Check that the Y-distance (the spacing between adjacent wells) which is shown graphically by the vertical bar lies within the green area (see “Y-distance of wells” on page 52). If the vertical bar lies within the red area, you may have specified the coordinates incorrectly or inaccurately.

Well panel

Tip-Touching Distance or X offset while pipetting

This parameter is used when you activate tip touching for the liquid class in the pipetting script. When tip touching is activated, Gemini dispenses to the destination container in the normal way, but then moves the tips to the side of the well and back before retracting them. This helps to remove any drops which may be adhering to the tip.

Gemini also uses this parameter if you select an offset (non-center) x-position for aspiration. This is done on the Aspiration tab of the liquid class and is mainly used for the Te-MagS.

Tips per well

This is used to enter the number of tips which can access the well at the same time. Specify “1” for normal wells. Specify the appropriate number for troughs (e.g. “8” for a Trough 100ml).

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flat / round / v-shaped

Select the shape of the bottom of the well.

Depth of bottom

For a well with a v-shaped bottom, specify the vertical distance in mm from the lowest point of the v (Z-max) to the beginning of the cylindrical part of the well.

Area

Specify the area of the well in mm². Click to display a dialog box which helps you to calculate the area from the diameter or from the length and the width.

Position during definition

Specify the carrier, grid and site that you want to use to define the rack:

Choose the carrier from the list, specify the grid position and the site. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden).

Allowed Carriers and Sites

For each of the carriers which can be used with the rack, check the checkboxes alongside the allowed sites.

Piercing panel

If you activate this option, Gemini executes special movements for septum piercing when accessing the rack. It will pierce from Travel to Start and then retract from Z-Start to Z-Travel. Liquid level detection is not available with this option activated.

Pierce with

Specify the piercing speed in mm/s.

Retract with

Specify the retract speed after piercing in mm/s.

Note:

Troughs are normally specified with length and width. To do this, click

and press the Delete key to delete the diameter value. The length and width fields will then become active.

Caution:

Please choose the correct site before specifying any coordinates. Otherwise the tips might move to the wrong position on the worktable.

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Precise Positioning panel

If you activate this option, Gemini executes a special movement to increase positioning accuracy, e.g. for 1536 well plates. When accessing a rack for the first time in a sequence of pipetting commands, it makes a normal move to X-Start/Y-Start. It then makes a high resolution move to the actual pipetting position. This sequence of movements eliminates mechanical backlash and ensures the highest possible accuracy. X-Start should be set to ca. 0.4 cm to the left of the first well in the rack. Y-Start should be set to ca. 0.4 cm behind the first well in the rack. Note: The first well is at the rear left of the rack.

X-Start

Specify the required X-Start position for the precise X movement. Besides typing the position manually, you can teach the position with the < and M buttons.

Y-Start

Specify the required Y-Start position for the precise Y movement. Besides typing the position manually, you can teach the position with the < and M buttons.

Move with

Specify the speed for the precise positioning movement in mm/s.

5.3.1 Rack coordinates

The following table describes the X, Y and Z coordinates for racks:

Coordinate Position / Function

X,Y At this position, the tip is situated above the well/tube of the first/last position on the rack. See Table 5-12 on page 51 for additional information on racks with offsets.

Z-Travel Height at which the tip moves from one X/Y position to another. At this position, the tip should be above the highest point of the well/tube of the rack. Movements that cross different racks always use the highest Z-Travel value which is defined.

Z-Dispense Tip height at which liquid is dispensed. Gemini dispenses liquid into the rack at this position. It should be low enough to ensure that liquid cannot drop into the adjacent wells/tubes.

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The figure below illustrates the different Z positions:

Teaching the rack coordinates

Teaching is the process of showing Gemini the required positions on the worktable by physically moving the LiHa (see the table “Moving the LiHa using the numeric keypad” on page 38) and then clicking the appropriate buttons in the dialog boxes.

Z-Start Tip height at which the liquid detection (ILID) is switched on during a search for liquid operation. It is usually slightly above the rim of the liquid container.

On the one hand, Z-Start should be chosen as low as possible for fast detection; on the other hand, Z-Start must be above the highest liquid level in the well/tube or the liquid will not be detected.

Z-Max This position is the lowest point of the well/tube of the rack and is the lowest possible position the tip is allowed to reach. During a search for liquid operation, the instrument will search for liquid from Z-Start down to Z-Max.

Figure 5-9: Z positions for a tube

Coordinate Position / Function