Thermo Fisher Scientific RapidMAX Software User guide

USER GUIDE

RapidMAX™ Software

DATA ANALYSIS SOFTWARE FOR PCR ASSAYS

Publication Part Number 4469874

Revision Date September 2011 (Rev. A)

Not intended for any human therapeutic or diagnostic use.

Information in this document is subject to change without notice.

APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF

MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE, WHETHER

IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES

IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT

APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

NOTICE TO PURCHASER: DISCLAIMER OF LICENSE

Purchase of this software product alone does not imply any license under any process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims

owned or otherwise controlled by Life Technologies Corporation, either expressly, or by estoppel

NOTICE TO PURCHASER: LIMITED USE LABEL LICENSE:

Subject to the terms and conditions of this Agreement, Life Technologies grants the purchaser of this product a non-exclusive license only to install and use the Software on a single

computer (or a single network, if your Software is designated as a network version). You may transfer the Software to another single computer (or network, if a network version),

but the software may never be installed on more than one computer (or more than one network, if a network version) at any one time.

If the Software uses registration codes, access to the number of licensed copies of Software is controlled by a registration code. For example, if you have a registration code that

enables you to use three copies of Software simultaneously, you cannot install the Software on more than three separate computers.

You may make one copy of the Software in machine-readable form solely for backup or archival purposes. You must reproduce on any such copy all copyright notices and any other

proprietary legends found on the original. You may not make any other copies of the Software. For information on obtaining additional rights, please contact outlicensing@lifetech.com

or Out Licensing, Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008.

RESTRICTIONS

You may not copy, transfer, rent, modify, use or merge the Software, or the associated documentation, in whole or in part, except as expressly permitted in this Agreement.

You may not reverse assemble, decompile, or otherwise reverse engineer the Software.

You may not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation.

You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export

or reexport, directly or indirectly, the Software into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United

States law.

You may not modify, sell, rent, transfer (except temporarily in the event of a computer malfunction), resell for profit, or distribute this license or the Software, or create derivative

works based on the Software, or any part thereof or any interest therein.

WARRANTY AND LIABILITY

PATENTS AND LICENSING NOTIFICATIONS

TRADEMARKS

The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners.

Excel and Microsoft are registered trademarks of Microsoft Corporation.

Agilent Technologies, Stratagene, Mx3000P, and Mx3005P are registered trademarks of Agilent Technologies.

Part Number 4469874

September 2011 (Rev. A)

Contents

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RapidMAX™ Software User Guide

About This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

User attention words . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

PART I Install, Configure, and Manage RapidMAX™ Software . . . 11

■CHAPTER 1 Install RapidMAX™ Software . . . . . . . . . . . . . . . . . . . . . . . . 13

Required user role . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

System requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Hardware requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Software requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Download RapidMAX™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Install RapidMAX™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Apply the license file to RapidMAX™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Apply the license file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Install license offline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Request additional licenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Log in as Administrator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Verify RapidMAX™ Software installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Uninstall RapidMAX™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

■CHAPTER 2 Manage User Accounts and Roles . . . . . . . . . . . . . . . . . . . 19

Required user role . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

User roles and tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Manage user accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Create user accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Edit user accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

(Optional) Import and export user accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

(Optional) View a report on user accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Manage user roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

4RapidMAX™ Software User Guide

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Create user roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Edit user roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

(Optional) Import and export user roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Delete user roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

(Optional) View a report on user roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

PART II Set Up and Run RapidMAX™ Software . . . . . . . . . . . . . . . . . 29

■CHAPTER 3 Log In and Configure Preferences . . . . . . . . . . . . . . . . . . . 31

Required user role . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Log in to RapidMAX™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Change your password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

When to change your password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Install assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

About failed login attempts and expired sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Failed login attempts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Expired sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

(Optional) Configure preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Configure preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Configure target colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Secure your data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

■CHAPTER 4 Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

■CHAPTER 5 Manage Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Required user role . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Assay definition files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Assay types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Manage assays and view assay definition files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Open the Assay Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Install purchased assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Close the Assay Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

View assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Edit parameter values of user-defined assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Uninstall assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Set parameter values for a user-defined assay definition file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Delete assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

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■CHAPTER 6 Import a File and Set Up a Plate for Analysis . . . . . . . . . 45

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Analysis rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Import a file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Import a file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

(Optional) Enter supplementary information about plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Import data from an Agilent Stratagene® Mx3000P® or Mx3005P® QPCR instrument . . . 48

View and edit reagent information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Save RapidMAX™ files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

(Optional) Delete imported files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Set up a plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Edit well attribute values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Other well tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

(Optional) Set Up a Plate from a Plate Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

About plate templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Create a plate template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Set up a plate from a plate template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

(Optional) Set up a plate template outside of RapidMAX™ Software . . . . . . . . . . . . . . . . . . . . . 53

About modifying existing plate templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

■CHAPTER 7 Analyze a RapidMAX™ file and view analysis results . . . 55

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Analyze a file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

View analysis results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

View plate results and override calls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

View sample results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

View amplification results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Save analysis results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Open a previously created RapidMAX™ file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

■CHAPTER 8 Export RapidMAX™ File Data . . . . . . . . . . . . . . . . . . . . . . . . 69

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Export analysis results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Export analysis results as an image file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Export all results as a text file or spreadsheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Export plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

View exported results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

How to view exported results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

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Read exported results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Export a plate report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Plate report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Plate report by assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Sample report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

How to export a plate report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Read exported reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

■CHAPTER 9 Manage Security Settings . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Required user role . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Acknowledge security events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Software security specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

User names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Passwords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Password expiration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Failed login attempts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Session expiration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

(Optional) Edit system security settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Edit account setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Edit security policies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

(Optional) Export system security settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Save system security settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Exit security settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

■CHAPTER 10 Audits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

About audits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Types of audits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Local audits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

System audits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

View RapidMAX™ file audit records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

View an audit record of an RapidMAX™ file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Read an audit record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

View audit details in the Assay Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

View audit details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

(Optional) View the system configuration history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

View the system configuration history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

(Optional) View system action records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Filter system action records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Change audit settings in Security Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Save audit settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

(Optional) Export audit settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Purge system audit records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

7

RapidMAX™ Software User Guide

Contents

■CHAPTER 11 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

PART III Supplemental Information . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

■APPENDIX A Supplemental Information . . . . . . . . . . . . . . . . . . . . . . . . . 97

About RapidMAX™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

Compatible real-time PCR systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

Compatible files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

■APPENDIX B Supplemental Procedures . . . . . . . . . . . . . . . . . . . . . . . . . 99

Use Microsoft® Excel® software to modify well attribute values . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

Good laboratory practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

Documentation and Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Obtaining support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

8RapidMAX™ Software User Guide

Contents

9

RapidMAX™ Software User Guide

About This Guide

Purpose

Usethisguidetoinstall,configure,andlearntouseRapidMAX™Softwaretoanalyze

yourPCRdata.Useittohelpyou:

•Installandsetupthesoftware.

• CreateandanalyzeaRapidMAX™file.

•Reviewresultsandthedataunderlyingresults.

•Saveandreportresults.

• Troubleshootproblems.

•Performadditionalpost‐analysisprocedures.

Prerequisites

Thisguideassumesthatyouhaveworkingknowledgeof:

•ProceduresforperformingPCRassays.

•Microsoft

®Windows®7andWindows®XPoperatingsystem.

•InstrumentoperationandsystemsoftwareforyourReal‐TimePCRSystem.

•TheInternetandInternet‐basedbrowsers.

User attention words

Fiveuserattentionwordsmayappearinthisdocument.Eachwordimpliesa

particularlevelofobservationoractionasdescribedbelow:

Note: Providesinformationthatmaybeofinterestorhelpbutisnotcriticaltotheuse

oftheproduct.

IMPORTANT! Providesinformationthatisnecessaryforproperinstrumentoperation

oraccuratechemistrykituse.

CAUTION! Indicatesapotentiallyhazardoussituationthat,ifnotavoided,may

resultinminorormoderateinjury.Itmayalsobeusedtoalertagainstunsafe

practices.

WARNING! Indicatesapotentiallyhazardoussituationthat,ifnotavoided,

couldresultindeathorseriousinjury.

10 RapidMAX™ Software User Guide

About This Guide

User attention words

DANGER! Indicatesanimminentlyhazardoussituationthat,ifnotavoided,

willresultindeathorseriousinjury.

PART I

Install, Configure, and Manage

RapidMAX™ Software

13

RapidMAX™ Software User Guide

1 Install RapidMAX™ Software

Thischaptercovers:

■Requireduserrole ....................................................13

■Workflow ............................................................13

■Systemrequirements..................................................14

■DownloadRapidMAX™Software .......................................14

■InstallRapidMAX™Software ...........................................15

■ApplythelicensefiletoRapidMAX™Software ...........................15

■LoginasAdministrator................................................16

■VerifyRapidMAX™Softwareinstallation ................................16

■UninstallRapidMAX™Software........................................17

Required user role

Toperformtheproceduresinthischapter,youruserrolemustbeAdministrator.

Workflow

Download RapidMAX™ Software

Install RapidMAX™ Software

Apply the license file to RapidMAX™ Software

Log in as Administrator

Verify RapidMAX™ Software installation

14 RapidMAX™ Software User Guide

Install RapidMAX™ Software

System requirements

1

System requirements

Hardware

requirements

RapidMAX™Softwarehasnotbeenverifiedonsystemconfigurationsotherthanthe

twolistedinthefollowingtable:

IMPORTANT! Tominimizetheriskoffaulty,inaccurateanalyses,makesurethatthe

instrumentyouusetorunexperimentsiscalibrated.Followthecalibrationprocedures

intheinstrumentuserguide.

IMPORTANT! OntheAppliedBiosystems7500/7500FastSystems,runningdiagnostics

longerthan2000hoursdecreasesthecurrentofthehalogenlamp.Decreasedlamp

currentcanresultinadropinfluorescenceandincorrectanalysisresults.Refertothe

AppliedBiosystems7500/7500FastReal‐TimePCRSystemsSystemMaintenanceGuide

(PN 4387777)forinstructionsonmonitoringandreplacingthelamp.

Software

requirements

•OperatingSystem:Windows®XP32‐bit(recommendedServicePack3)or

Windows®7

•Adobe

®Acrobat®Reader®softwarev9.0orlaterinstalled

•Microsoft

®Excel®oranyspreadsheetapplication

Download RapidMAX™ Software

TodownloadRapidMAX™SoftwarefromLifeTechnologiesCorporationtoyour

desktop:

1. Gotowww.lifetechnologies.com,clickonAppliedBiosystemsintheViewOur

Productssection,searchforRapidMAX™Softwareandfollowthepromptsfor

downloadingthesoftware.

2. FollowthepromptstoinstalltheRapidMAX™Software.

AlicensekeyandinstructionsfordownloadingRapidMAX™Softwareare

emailedtoyou.

Minimum hardware configuration Recommended hardware configuration

Intel CPU, 1.6 GHz

Available hard disk space: 1 GB

Memory: 1 GB

Screen resolution: 1024 ✕768 pixels

Intel CPU, 3 GHz

Available hard disk space: 20 GB

Memory: 2 GB

Screen resolution: 1024 ✕768 pixels

15

RapidMAX™ Software User Guide

Chapter1

Install RapidMAX™ Software

1

Install RapidMAX™ Software

IMPORTANT! Inordertoinstallthesoftware,youmusthaveComputerAdministrator

privilegesintheWindowsXPProfessionaloperatingsystem.

1. Navigatetothefoldercontainingthedownloadedinstaller,anddouble‐click

setup.exetostarttheinstallation.

2. FollowthepromptsintheInstallationWizardtoinstallRapidMAX™Softwarein

thepreferredlocation.

Apply the license file to RapidMAX™ Software

Prerequisites Beforeapplyingthelicensefile,pleaseensurethatyouhavedownloadedandinstalled

RapidMAX™SoftwareoncomputerhardwarethatmeetstheRapidMAX™minimum

hardwarerequirements.

Apply the license

file

AfterRapidMAX™Softwarehasbeensuccessfullyinstalled,applythelicensefileto

yourcopyofRapidMAX™Software:

1. RunRapidMAX™Software.

2. IntheRapidMAX™SoftwareActivationwindow:

a. Enterthelicensekey(intheemailmessagethatwassenttoyouafteryou

placedyourorder).

b. Enteryouremailaddress.

c. Ifyouareconnectedtotheinternet,completethelicenseregistrationform

andsubmitittoactivateyourlicense.

Fillintheremaininginformation,thenclickSubmittoactivateyourlicense.

Note: Yourlicensebeginsthemomentyouactivateyourlicensekey.

d. IntheRapidMAX™SoftwareActivationwindow,findandloadthelicense

file(.lic)thatwasemailedtoyou.

IMPORTANT! Keepabackupcopyofyourlicensefileinasafeplace.

e. ClickInstallandValidateLicense.

3. Inthewindownotifyingyouthatinstallationwassuccessful,clickOK,thenclose

theRapidMAX™SoftwareActivationwindow.

Install license

offline

FollowthisprocedureifthecomputeronwhichRapidMAX™Softwarethatyouwant

toinstallthesoftwareisnotconnectedtotheInternet.

IMPORTANT! Keepabackupcopyofyourlicensefileinasafeplace.

1. UseacomputerconnectedtotheInternettoaccesstheRapidMAXLicense

RegistrationandLicenseActivationpageanddownloadthelicensefile(.lic).

16 RapidMAX™ Software User Guide

Install RapidMAX™ Software

Log in as Administrator

1

2. TransferthelicensefiletoaportablestoragedevicesuchasaFlashdrive,CD,or

memorystick.

3. Transferthelicensefilefromtheportablestoragedevicetothecomputerthathas

RapidMax1.0installed.

4. IntheRapidMAXSoftwareActivationwindow,findandloadthelicensefile(.lic).

5. ClickInstallandValidateLicense.

6. Inthewindownotifyingyouthatinstallationwassuccessful,clickOK,thenclose

theRapidMAX™SoftwareActivationwindow.

Request additional

licenses

Torequestadditionallicenses:

1. RunRapidMAX™Software.

2. Inthetoptoolbar,clickTools,thenLicenseCentral.

3. FollowtheinstructionsintheLicenseCentralwindow.

Log in as Administrator

Note: LifeTechnologiesCorporationisnotresponsibleforpasswordsandaccess

rightsgrantedtolaboratorystaff.Followlaboratoryprotocolsfortrainingstaffabout

passwordsecurity,privacy,andprotection.

1. RunRapidMAX™Software.

2. Loginwiththedefaultusernameandpassword:

•UserName:Administrator

• Password:Administrator

3. Attheprompt,changeyourpassword,clickOK,thenclickOKagain.

Note: ThisisadefaultpasswordruleanditcanbechangedbytheAdministrator

afterloggingin.

4. IntheLoginwindow,enteryournewpassword,thenclickLogIn.

5. ReadandaccepttheEULA.IfyouwantahardcopyoranAdobe®Acrobat®PDF

fileoftheagreement,clickPrint.

Verify RapidMAX™ Software installation

SeveralfileswithexampleinputandoutputdataareincludedwithRapidMAX™

Software.Examplefilesincludeassaysanddata.Usethesefilestotestthat

RapidMAX™iscompletelyinstalledandthatitisfunctional.Examplefilesarein

C:\AppliedBiosystems\RapidMaxSoftware\UserFiles\examplesv1.0.

Your password must: Be between 8 and 32 characters

17

RapidMAX™ Software User Guide

Chapter1

Uninstall RapidMAX™ Software

1

Uninstall RapidMAX™ Software

UsetheWindowsmethoddescribedinthissectiontouninstallRapidMAX™Software

onyourcomputerbeforeupdatingthesoftwaretoanewversion.

DuringtheuninstallationofRapidMAX™Software,youruserfileswillremaininyour

computer.However,usersettings,suchassecuritysettingsandpreferenceswillbe

removedunlessyouchoosetopreservethesettings.

TouninstallRapidMAX™Software:

1. ClickStart(intheWindowstaskbar)AllProgramsAppliedBiosystems

RapidMaxSoftwareUninstallRapidMaxSoftware.

2. InthePreserveSettingFileswindow,selectYesifyouwanttopreservefilesfor

useinsubsequentreinstallations.

18 RapidMAX™ Software User Guide

Install RapidMAX™ Software

Uninstall RapidMAX™ Software

1

19

RapidMAX™ Software User Guide

2 Manage User Accounts and Roles

Thischaptercovers.

■Requireduserrole ....................................................19

■Workflow ............................................................19

■Userrolesandtasks...................................................20

■Manageuseraccounts.................................................22

■Manageuserroles.....................................................25

Required user role

Toperformtheproceduresinthischapter,youruserrolemustbeAdministrator.

Workflow

Manage user accounts

Create user accounts

Edit user accounts

(Optional) Import and export user accounts

(Optional) View a report on user accounts

20 RapidMAX™ Software User Guide

Manage User Accounts and Roles

User roles and tasks

2

User roles and tasks

TheSecurity,Auditing,ande‐Signature(SAE)featureinRapidMAX™Software

enablesrole‐basedaccesscontroltoenforcedataintegrityandauthenticationofusers

loggingintothesystem,tostrengthensystemsecurity.SAEtracksactionsperformed

byusers,andittrackschangestotheSAEsettings.Formoreinformation,see

Chapter10,“A u d i t s ” onpage 81.

ThedefaultuserrolesinRapidMAX™SoftwareareAdministrator,Technician,and

LabManager.Thetaskseachuserisallowedtoperformarelistedinthetablebelow.

Tasksthatarenotlistedinthetablecanbeperformedbyalluserroles(forexample,all

userscanviewdata).

IMPORTANT! TheAdministratorrolesandtasksaresetinthesoftwareandshouldnot

bechanged.

Manage user roles

Create user roles

Edit user roles

(Optional) Import and export user roles

(Optional) View a report on user roles

Delete user roles

(Optional) View a report on user roles

Task User Role

Administrator Technician Lab Manager

Assay Manager

Install assays (assay definition files, *.tdd) X X

Edit user-defined assays X X

Uninstall assays X X

Setup

Import a file (*.eds, *.sds, *.txt) X X X

Add a plate X X X

Delete a plate X X X

Edit plate properties X X X

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Thermo Fisher Scientific RapidMAX Software User guide

Thermo Fisher Scientific RapidMAX Software User guide

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