Thermo Scientific BindIt Software For KingFisher Instruments

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Thermo ScientificBindIt Software forKingFisher InstrumentsUser ManualSoftware Version 4.0N07974Rev 1.02016

2016 Thermo Fisher Scientific Inc. All rights reserved.Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in theproduct operation. This document is copyright protected and any reproduction of the whole or any part of thisdocument is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.The contents of this document are subject to change without notice. All technical information in thisdocument is for reference purposes only. System configurations and specifications in this document supersedeall previous information received by the purchaser.Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss thatmight result from any use of this document, even if the information in the document is followedproperly.This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. Thisdocument shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions ofSale shall govern all conflicting information between the two documents.Release history:For Research Use Only. Not for use in diagnostic procedures.

WEEE ComplianceThis product is required to comply with the European Union’s Waste Electrical & ElectronicEquipment (WEEE) Directive 2002/96/EC. It is marked with the following symbol:Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in eachEuropean Union (EU) Member State, and these companies should dispose of or recycle this product.See www.thermoscientific.com/rohsweee for further information on Thermo Fisher Scientific’scompliance with these Directives and the recyclers in your country.WEEE KonformitätDieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen. Das Produkt ist durch folgendes Symbol gekennzeichnet:Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EUMitgliedsstaaten getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgtwerden kann. Mehr Information über die Einhaltung dieser Anweisungen durch Thermo FisherScientific, über die Verwerter, und weitere Hinweise, die nützlich sind, um die Produkte zuidentifizieren, die unter diese RoHS Anweisung fallen, finden sie unter www.thermoscientific.com/rohsweee.

Conformité DEEECe produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'EquipementsElectriques et Electroniques (DEEE). Il est marqué par le symbole suivant:Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque étatmembre de l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantaged'informations sur la conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votrepays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la détection dessubstances sujettes à la directive RoHS sont disponibles sur www.thermoscientific.com/rohsweee.

PPrefaceAbout This ManualThis guide explains how to install and use Thermo Scientific BindIt Software for KingFisher instruments version 4.0. You can find information on the software features and operations. Thesoftware is used with different types of instruments, and there may be information that may not berelevant to the instrument you are using.Thermo Scientific BindIt Software for KingFisher instruments is used with: Thermo Scientific KingFisher Thermo Scientific KingFisher Duo Thermo Scientific KingFisher Duo Prime Thermo Scientific KingFisher Flex Thermo Scientific KingFisher mL Thermo Scientific KingFisher Presto Thermo Scientific KingFisher 96 Applied Biosystems MagMAX Express Applied Biosystems MagMAX Express-96 Dynal BeadRetriever Read the manual in its entirety before using the software.Related DocumentationIn addition to this manual, Thermo Fisher Scientific provides the following instrument-relateddocuments: Thermo Scientific KingFisher User Manual (Cat. no. 1507730) Thermo Scientific KingFisher Duo User Manual (Cat. no. N12420) Thermo Scientific KingFisher Duo Prime User Manual (Cat. no. N16621) Thermo Scientific KingFisher Flex User Manual (Cat. no. N07669) Thermo Scientific KingFisher mL User Manual (Cat. no. 1508260)Thermo ScientificThermo Scientific BindIt Software for KingFisher Instruments User Manuali

PrefaceSafety and Special Notices Thermo Scientific KingFisher Presto User Manual (Cat. no. N17413) Thermo Scientific KingFisher 96 User Manual (Cat. no. 15018890)The Thermo Scientific BindIt Software user manual can be found in PDF format in theDocumentation directory of the installation CD.In an effort to produce useful and appropriate documentation, we appreciate your comments on thisuser manual to your local Thermo Fisher Scientific representative.Software HelpThe software Help includes the same information as this manual. To open Help, click the Help buttonor press F1 on your keyboard.Use the Help search to find information on specific topics. Write the keyword of the topic you aresearching for, click List Topics, or press Enter.Safety and Special NoticesMake sure you follow the precautionary statements presented in this guide. The safety and otherspecial notices appear in boxes.Safety and special notices include the following:WARNING Risk of injury to the user or users.CAUTION Risk of damage to the instrument, other equipment or loss of performance or functionin a specific application.Note Marks a hint, important information that is useful for the optimum operation of the system,or an item of interest.Tip Highlights helpful information that can make a task easier.Contacting UsFor the latest information on products and services, visit our website at:www.thermofisher.com/kingfisher.iiThermo Scientific BindIt Software for KingFisher Instruments User ManualThermo Scientific

CContentsPreface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iAbout This Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iRelated Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iSoftware Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iiSafety and Special Notices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iiContacting Us. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iiThermo ScientificChapter 1Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1BindIt Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1Thermo Scientific KingFisher System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1Chapter 2Installing BindIt Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5Installation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6Connect the Instrument to the PC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Define a New Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8Remove an Instrument from the PC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Uninstall BindIt Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Chapter 3Main Elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Application Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Navigation Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12Action Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12Chapter 4Basic Concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Plate Layout. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Protocols and Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Protocol View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Protocol Types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Protocol Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Run Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Chapter 5Tip Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Tip Combs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Tip Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22Tip Positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22Thermo Scientific BindIt Software for KingFisher Instruments User Manualiii

ContentsTip Speeds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Tip Speed Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24ivChapter 6Using BindIt Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25Start the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25Open a Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26Define a Plate Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26Plate Layout Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Duplicate a Well . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Duplicate a Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Swap Reagent Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Move Reagent Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Delete a Plate or Strip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Add Protocol Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Modify Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Disable or Enable Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Calculate the Duration of a Step or Protocol . . . . . . . . . . . . . . . . . . . . . . . . . 36Save Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Lock Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Delete Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Execute the Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Add Run Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Add Sample IDs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Add Lot Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Lock Run Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40View the Run Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Export Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Chapter 7Transfer Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Upload Protocols to the Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Download Protocols from the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Backups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Chapter 8Protocol Steps and Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Tip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Pick-Up and Leave. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Collect Beads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Release Beads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Mix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Beginning of Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Step Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Mixing/Pause Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Mixing/Heating Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52End of Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Dry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Pause . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54Thermo Scientific BindIt Software for KingFisher Instruments User ManualThermo Scientific

ContentsChapter 9Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55Colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56Laboratory Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56Instrument Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56General. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57Communications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58Automation Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Chapter 10Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61Chapter 11Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63Appendix A Example Protocol: KingFisher Duo Prime/Duo . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65Appendix B Example Protocol: KingFisher Flex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73Appendix C Effective Use of Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83Thermo ScientificThermo Scientific BindIt Software for KingFisher Instruments User Manualv

ContentsviThermo Scientific BindIt Software for KingFisher Instruments User ManualThermo Scientific

1IntroductionBindIt SoftwareWith BindIt Software you can: Create a plate layout. Create new and modify existing protocols. Transfer protocols to the KingFisher instrument. Delete protocols from the KingFisher instrument. Execute a protocol directly from the software without sending it to the instrument. View protocol status reports.The protocols and run report files are stored in the file system of the PC. Once a protocol has beencreated, you can either transfer it to the KingFisher instrument or execute it directly from the software.Protocols run directly from the software are not stored in the instrument memory.The instrument can store several protocols at the same time. The protocols stored in the instrumentcan be launched from the KingFisher instrument.The PC and the instrument must be connected when protocols are transferred to or removed from theinstrument. The connection is required also if protocols are executed directly from the software. Youcan create and edit protocols without an instrument connection.Thermo Scientific KingFisher SystemKingFisher is an automated system for purifying DNA, RNA, proteins and cells from a variety ofsample materials, such as blood, cells and tissue samples. It utilizes a patented technology in whichmagnetic rods move paramagnetic particles through processing steps to purify nucleic acids andproteins, and isolate cells.The KingFisher purification technology enables high-speed, high-quality processing with nocross-contamination between the samples or reagent carry-over. The KingFisher system provides acomplete solution, including instruments, reagents, software and disposable plastics as well asoptimized protocols.Thermo ScientificThermo Scientific BindIt Software for KingFisher Instruments User Manual1

1IntroductionThermo Scientific KingFisher SystemThe following automated instrument platforms are available for different processing requirements: KingFisher Presto Purification of 24 or 96 samples per run, maximum capacity thousands of samples per day. A processing volume of 50–5,000 μl with the following three plate formats: 96 KF plate 96 deep well plate 24 deep well plate KingFisher Flex Purification of 24 or 96 samples in one run, maximum capacity hundreds or thousands ofsamples per day. A processing volume of 20–5,000 μl with the following four plate formats: 96 KF plate 96 PCR plate, skirted (for example, ABgene SuperPlate #AB-2800) 96 deep well plate 24 deep well plate KingFisher Duo Prime and KingFisher Duo Purification of 6 or 12 samples in one run. Possibility to run two purification methodssequentially without interruption, raising the throughput to 24 samples. Maximum capacityhundreds of samples per day. A processing volume of 30–5,000 μl with the following formats: 96 deep well Plate 24 deep well Plate KingFisher Duo elution strip KingFisher and MagMAX Express Purification of up to 24 samples in one run, maximum capac

Preface Safety and Special Notices ii Thermo Scientific BindIt Software for KingFisher Instruments User Manual Thermo Scientific Thermo Scientific KingFisher Presto User Manual (Cat. no. N17413) Thermo Scientific KingFisher 96 User Manual (Cat. no. 15018890) The Thermo Scientific BindIt Software user manual can be found in PDF format in the

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