QuantStudio 6 and 7 Flex System Softwaretools.thermofisher.com/content/sfs/manuals/4489825.pdf · 2013-11-18 · QuantStudio™ 6 and 7 Flex System Software Programming Supplement

USER GUIDE

QuantStudio™ 6 and 7 Flex System Software Programming Supplementfor use with:

QuantStudio™ 6 and 7 Flex Real-Time PCR Systems

Publication Number 4489825Revision A

For Research Use Only. Not for use in diagnostic procedures.The information in this guide is subject to change without notice.

DISCLAIMER

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LIMITED USE LABEL LICENSE No. 477: Real-Time PCR System

Notice to Purchaser: This product is licensed for use under certain patent claims owned by the University of Utah Research Foundation and licensed to BioFire Diagnostics, Inc. No right is conveyed, expressly, by implication or by estoppel under any other patent claim.

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Contents

3QuantStudio™ 6 and 7 Flex System Software Programming Supplement

About This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Revision history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

About this guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Assumptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

■ CHAPTER 1 Application Programming Interface . . . . . . . . . . . . . . . . . . 9

Custom application design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10Recommended deployment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10Example workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12API interaction with the QuantStudio™ 6 and 7 Flex System Software . . . . . . . . . . . . . . . . . . . . 13Barcode verification and mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Programmatic interfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Automation Server and web services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Invoking the Automation Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Accessing web services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Web services workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16Abstract interface and semantics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Automation notifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Web services files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Automation notification API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Enable/disable the automation notification API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Connection information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

■ CHAPTER 2 Command-line Application . . . . . . . . . . . . . . . . . . . . . . . . . 39

About the command-line application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Command-line workflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Supporting files for experiment creation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Precedence rules for experiment file generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Running the command-line application from a command prompt . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Running the application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Viewing the command-line help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Command syntax and arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

4 QuantStudio™ 6 and 7 Flex System Software Programming Supplement

Contents

Example commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Batch file creation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Results export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

■ CHAPTER 3 Import File Formats and Specifications . . . . . . . . . . . . . 47

About the importable files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48About the import file formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Plate setup file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49File structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Plate setup file header . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Plate setup file body . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Plate setup data columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Sample file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54File structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Barcode file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55File structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Assay information file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

■ CHAPTER 4 Export File Formats and Specifications . . . . . . . . . . . . . . 57

About the exportable files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58Export formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

QuantStudio™ and ViiA™ 7 export formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59File structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59File header . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Sample setup data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62Raw data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64Amplification data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65Multicomponent data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65Results data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

7900 export format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78Exportable files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78Setup file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79Multicomponent file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80Results file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

RDML export format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84For more information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84


Contents

Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Obtaining support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Limited product warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87


Contents


About This Guide

Revision history

About this guide

Purpose This guide provides technical information for engineering software that can be used to integrate the QuantStudio™ 6 and 7 Flex Real-Time PCR Systems into a laboratory information system (LIS).

The document describes the:

• Application programming interface (API), which provides programmatic access to specific routines and protocols that control instrument and software operation.

• Command-line interface, which can be used to automate the creation of new experiment files and the export of data from existing files.

• Specifications of importable and exportable file formats, which are compatible with and generated by the QuantStudio™ 6 and 7 Flex System Software.

Assumptions This guide assumes that:

• All software elements (QuantStudio™ 6 and 7 Flex System Software and other applications) reside and execute on the same local area network (LAN), and possibly on the same physical computer.

• The computer on which the QuantStudio™ 6 and 7 Flex System Software is installed has LAN access to all QuantStudio™ 6 and 7 Flex Systems that will be controlled or monitored through the API.

• The QuantStudio™ 6 and 7 Flex System Software has been correctly installed and configured, including the separately licensed security, auditing, and electronic signature (SAE) module.

• The security requirement of the third-party application matches that of the QuantStudio™ 6 and 7 Flex System Software. For example, the QuantStudio™ 6 and 7 Flex System Software requires authentication, therefore a third-party application that must also require it.

Revision Date Description

A October 2013 Initial release


About This Guide About this guide

• The run methods executed within the third-party application involve synchronous calls from the application to the API for each QuantStudio™ 6 and 7 Flex System controlled by the application instance.

• The QuantStudio™ 6 and 7 Flex System Software and the API, when running in headless mode, do not present user interface elements, relying on the invoking application to do so.

1


Application Programming Interface

This chapter covers:

■ Custom application design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

■ Programmatic interfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

■ Automation Server and web services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

■ Automation notification API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Note: (QuantStudio™ 7 Flex System only) If you have an Applied Biosystems® Twister® Robot, refer to the Applied Biosystems® Twister® Robot Automation Accessory User Guide for instructions on using the automation application programming interface.


Chapter 1 Application Programming InterfaceCustom application design1

Custom application design

The QuantStudio™ 6 and 7 Flex System Software application programming interface (API) can support a variety of custom application designs. This section describes the recommended deployment, the deployment components, and the abstract interfaces accessible via the interface.

Recommended deployment

The QuantStudio™ 6 and 7 Flex System Software API supports both single-computer and distributed deployment models to provide flexibility in the distribution of software and hardware components in potential solutions. In the simplest deployment, both the custom application and the QuantStudio™ 6 and 7 Flex System Software are installed to the same computer, which drives the QuantStudio™ 6 and 7 Flex System(s). In an advanced deployment, the custom application and the QuantStudio™ 6 and 7 Flex System Software are installed to different computers on the same LAN that incorporates one or more networked QuantStudio™ 6 and 7 Flex Systems.

Deployment components

The following figure illustrates the software and hardware components of a possible custom application deployment that involves: one control computer, one or more QuantStudio™ 6 and 7 Flex Systems, and a barcode reader.

The elements in the example deployment are described below:

Automation API

Enables communication between the custom application and the QuantStudio™ 6 and 7 Flex System Software elements (such as instrument control and security and auditing) to execute a specified workflow. The API can process synchronous requests to and from up to four QuantStudio™ 6 and 7 Flex Systems in parallel.

QuantStudio™ 6 and 7 Flex Systems

(networked)BarcodeReader

BarcodeReader Driver

RemoteNotification

Listener

AutomationAPI

CustomApplication

Custom Application QuantStudio™ 6 and 7 Flex System Software

UserInterface

RemoteNotification

Sender

AutomationService

QuantStudio™ 6 and 7 Flex

System Software

Barcode-to-Experiment File Mapping

NotificationServer

WebServices


Chapter 1 Application Programming InterfaceCustom application design 1

Automation Service

Receives commands from the API and, based on the command and target instrument, dispatches commands to the appropriate components on the appropriate threads. The service can support up to four QuantStudio™ 6 and 7 Flex Systems in parallel, including synchronous behavior (relative to the invoking custom application), error handling, and reporting.

Barcode Reader Driver

The API used to communicate with the barcode reader.

Barcode-to-Experiment-File-Mapping

A data store element used by the custom application to map barcodes and the associated experiments (.eds) or template (.edt) files.

Note: The workflow logic can either run plates by associating an experiment (.eds) file with each barcode, or by using a template (.edt) file to create the required experiment file for each barcode.

Custom application

Executes methods that control the barcode reader and the QuantStudio™ 6 and 7 Flex System Software via the API.

Notification Server

(Optional) Conveys remote notification messages between the QuantStudio™ 6 and 7 Flex System Software and any application that can receive them, such as the custom application.

QuantStudio™ 6 and 7 Flex System Software

Responsible for the QuantStudio™ 6 and 7 Flex System user interface, business logic, and data management. When invoked by the custom application, the QuantStudio™ 6 and 7 Flex System Software opens in headless mode, without the user interface. After a session is initiated, the custom application makes API calls to invoke the components of the QuantStudio™ 6 and 7 Flex System Software to generate experiment files, run loaded consumables, perform data collection, and export results data.

Remote Notification Listener

(Optional) Listens for and processes remote notification messages. The Remote Notification Listener is necessary only if you require additional details about the ongoing workflow events and/or real-time monitoring.

Remote Notification Sender

Publishes messages that are configured to be broadcast, including run start, run complete, analysis complete, export complete, run status, and instrument status.

Web Services

Provides language binding for the components of the QuantStudio™ 6 and 7 Flex System Software through the API.


Chapter 1 Application Programming InterfaceCustom application design1

Example workflow The following table provides an overview of an example workflow as executed by a custom application designed to alert a user to the status of QuantStudio™ 6 and 7 Flex Systems on a LAN. For each row, the step appears underneath the application that performs the action; blank cells indicate that the application in the column header does not perform the action. The automation data column lists the data element affected by the process.

Note: See “Barcode verification and mapping” on page 13 for more information about barcode mapping.

� Security/auditing configuration [optional]

� Experiment (.eds) file� EDS workflow configuration� EDS analysis results

� Barcode-to-Experiment- File-Mapping file� Experiment (.eds) file

Sends “end session” to stop the QuantStudio™ 6 and 7 Flex System

Software.

Start the QuantStudio™ 6 and 7 Flex System Software session and

authenticate (if security is enabled).

Signal the user that the instrument is ready.

Prompt the user to scan the barcode of the plate.

Prompt the user to load the plate into the instrument.

Validate the barcode by finding theassociated experiment file (.eds).

Read the barcode of the plate.

Get the instrument state.

Open the instrument tray.

Run the experiment1. Run data collection: a. Start the run and publish the “Run Started” message. b. Finish the run and publish the“Run Completed” message.2. Analyze the experiment and publish the “Analysis Completed” message.3. Export the results and publish the “Analysis Results Exported” message.

Retract the plate adapter.

QuantStudio™ 6 and 7 Flex System SoftwareCustom application Data

End the session.

Repeat for all plates.


Chapter 1 Application Programming InterfaceCustom application design 1

API interaction with the QuantStudio™ 6 and 7 Flex System Software

In the example deployment, the API establishes a connection with a single instance of the QuantStudio™ 6 and 7 Flex System Software, running in headless mode, for the duration of the workflow method executed by the custom application. The state of the QuantStudio™ 6 and 7 Flex System Software is referred to as “headless” because the user interface is inactive during the session. When the custom application executes a workflow, the application establishes a one-to-one relationship with a single instance of an executing QuantStudio™ 6 and 7 Flex System Software process. The relationship continues until the workflow ends and the QuantStudio™ 6 and 7 Flex System Software instance terminates.

Once invoked to run a specific experiment (.eds) file, the API connects to the QuantStudio™ 6 and 7 Flex System Software Workflow Manager, which extracts the experiment workflow from the specified experiment (.eds) file. Based on the experiment workflow, the QuantStudio™ 6 and 7 Flex System Software then invokes the necessary protocols and data elements required to perform the instrument run, analysis, and export. An experiment workflow has at least one data collection stage and optional analysis and results export stages. Progression to each successive stage in the workflow is gated by the success or failure of the previous one.

Barcode verification and mapping

In the example deployment, the custom application performs barcode verification using a user-provided barcode-to-EDS-file path mapping function. The custom application uses the mapping to verify that the QuantStudio™ 6 and 7 Flex System Software can access the experiment (.eds) associated with the barcode of a loaded plate. Failure to locate the correct experiment (.eds) file should cause the associated plate to be skipped, because none of the accessible QuantStudio™ 6 and 7 Flex Systems can run it.

As an alternative to barcode-to-EDS-file path mapping, a workflow can instead specify a barcode-to-EDT-file (experiment template) mapping and call the runExperimentFromTemplate() method (see page 21). This method uses the specified template file to produce an experiment (.eds) file specifically for that barcode, embedding the barcode in the experiment (.eds) file, then performing the run using the generated experiment (.eds) file at the specified location.


Chapter 1 Application Programming InterfaceProgrammatic interfaces1

Programmatic interfaces

The QuantStudio™ 6 and 7 Flex System Software provides several programmatic interfaces that a custom application can access for instrument control, process notification, and experiment file generation. The interfaces were designed to provide optimal access to QuantStudio™ 6 and 7 Flex System functions and services, regardless of operating system or programming language. The following table summarizes the available interfaces.

Interface Used for… Description See…

Automation Server and web services

Instrument control

The Automation Server exposes the API as a web services that can be used to invoke the following elements of the QuantStudio™ 6 and 7 Flex System Software:• Security/auditing module • Main application• Workflow manager• Internal components

Note: The Automation Server and web services provide the only language binding for instrument control.

page 15

Automation notification API

Process notification

The Automation Notification API provides a publish/subscribe delivery model that allows multiple clients to receive notification of workflow and instrument maintenance events. The API can be configured to publish status messages of varying types, which can be received by any application which listens for the published messages.

page 36

QuantStudio™ 6 and 7 Flex System Software command-line application

Experiment generation

Results exportation

The API command-line interface supports a set of commands that can be used to automate the creation of experiment (.eds) files and the export of results from existing experiments.

page 40


Chapter 1 Application Programming InterfaceAutomation Server and web services 1

Automation Server and web services

The Automation Server exposes the API as web services that allows a variety of applications to control the QuantStudio™ 6 and 7 Flex System Software, regardless of operating system or programming language. This section describes how to invoke the Automation Server and use the web services interface to control the API.

Invoking the Automation Server

The Automation Server is invoked by an executable installed with the QuantStudio™ 6 and 7 Flex System Software (automation.exe). When the Automation Server executable is invoked with arguments, the application performs the specified operations, then exits. The path to the executable within the QuantStudio™ 6 and 7 Flex System Software is as follows:

C:\Program Files\Applied Biosystems\QuantStudio 6 and 7 Flex Software\bin\automation.exe

Accessing web services

The Automation Server web services interface is enabled by default, and it can be accessed using the following information. All of the following parameters are required for access except for the Java Client Service Interface, which is the interface class for web services client access via the Java API for XML Web Services (JAX-WS).

WSDL Document URL

http://hostname:9999/AutomationService?WSDLwhere <hostname> is the name of the computer running the Automation Server.

Name Space URI

http://ws.automation.paragon.sds.apldbio.com/

Service Name

AutomationService

Port Name

AutomationServiceWSPort


Chapter 1 Application Programming InterfaceAutomation Server and web services1

Web services workflow

The following figure illustrates an example workflow executed by a custom application via the API Web Services interface. When applicable, the flowchart displays the method or command passed between the elements of the system.

Note: InstrumentName (instrID) is unique for all instruments accessible from a given instance of the custom application.

Get userID and password

ReadBarcode

Map BarcodeTo Filepath

Get Mapping Filepath

LaunchApplication(userID, password)

Run plate

Analyze data

Export results

Iter

ate

over

all

pla

tes

Authenticate

GetInstrumentState(instrID)

OpenTray(instrID)

GetInstrumentState(instrID)

OpenTray(instrID)

GetNextPlate

LoadPlateOnInstrument(instrID)

CloseTray(instrID)

RunExperiment(instrID, filepath)

PublishEventStatusMessages


(returncode)

OpenTray(instrID)

CloseTray(instrID)

RemovetPlateFromInstr(instrID)

EndSession()

CloseTray(instrID)

RunExperiment(instrID, filepath)



ExperimentComplete

OpenTray(instrID)

CloseTray(instrID)

EndSession()

StartMethod

BarcodeReaderDriver

Applicationprogramming

interface

Userinterface

Customapplication

QuantStudio™6 and 7 Flex System Software

BarcodeReaderDriver

Applicationprogramming

interface

Userinterface

Customapplication

QuantStudio™6 and 7 Flex System Software



Abstract interface and semantics

The API methods are documented in alphabetical order where each entry includes the input parameters, return values, and a description of the method.

■ closeTray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

■ endSession . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

■ getBlockType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

■ getInstrumentState . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

■ isTrayIn. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

■ Launch application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

■ openTray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

■ runExperiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

■ runExperimentAsync . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

■ runExperimentFromTemplate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

■ runExperimentFromTemplateAsync . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

■ startSession . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

■ stopCurrentExperiment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Return codes

All API calls return either a success/error status code or an explicit result value. If possible, errors also return human-meaningful strings that can be presented to the user. The API methods result code is an enumeration; however some methods return an integer value that is the ordinal of the enumeration constant. The following table maps the enumeration constant to its integer value.

Enumeration constant Integer value Enumeration constant Integer

value

UNINITIALIZED 0 INSTRUMENT_PAUSED 10

SESSION_INVALID 1 INSTRUMENT_IN_ERROR 11

SESSION_EXISTING 2 INSTRUMENT_FAIL_TO_START 12

AUTHENTICATION_FAILURE 3 INSTRUMENT_TRAY_OPENED 13

USER_ACCOUNT_DISABLED 4 INSTRUMENT_TRAY_CLOSED 14

PASSWORD_EXPIRED 5 EXPERIMENT_NOT_FOUND 15

INSTRUMENT_UNKNOWN 6 EXPERIMENT_READ_ERROR 16

INSTRUMENT_NOT_CONNECTED 7 EXPERIMENT_WRITE_ERROR 17

INSTRUMENT_READY 8 EXPERIMENT_VALIDATION_ERROR

18

INSTRUMENT_RUNNING 9



closeTray (sessionID, instrumentID)

Instructs the QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID) to retract the tray arm and close the door, either in preparation for a new run or for system idle.

Note: If the QuantStudio™ 6 and 7 Flex System tray arm is retracted, the closeTray() method is noop (no operation) rather than an error.

endSession (sessionID)

Ends the execution of the instance of QuantStudio™ 6 and 7 Flex System Software running in headless mode and the existing Application Session (sessionID), including any contained User Session.

getBlockType( sessionId, instrumentID )

Queries the QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID) for the block type currently installed to the instrument.

Arguments • sessionID – (string; required) The session ID of the open session.• instrumentID – (string; required) The name of the instrument of interest.

Returns None

Errors Possible errorCode of AutomationException in fault message:• 1 (SESSION_INVALID)• 6 (INSTRUMENT_UNKNOWN) if the instrument cannot be found or if

communication cannot be established• 11 (INSTRUMENT_IN_ERROR)

Arguments sessionID – (string; required) The session ID of the open session.

Returns None

Errors Possible errorCode of AutomationException in fault message:

1 (SESSION_INVALID)


Returns An integer which indicates block type, where possible value are:• 7 – Array card sample block• 8 – 384-well reaction plate (20-µL) sample block• 9 – 96-well reaction plate (100-µL) sample block• 10 – 96-well reaction plate (200-µL) sample block





getInstrumentState (sessionID, instrumentID)

Confirms the state of the specified QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID). The method is used to ensure that an instrument is in an idle state and ready to perform a run.

isTrayIn (sessionID, instrumentID)

Checks the status of the instrument tray (open or closed) of the QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID).

Launch application

Starts a new instance of the QuantStudio™ 6 and 7 Flex System Software in headless mode by launching the Automation executable (automation.exe). See “Invoking the Automation Server” on page 15 for more information.


Returns The type of return value is integer, possible return values are:• 0 (UNINITIALIZED) if the Automation Server not initialized• 1 (SESSION_INVALID)• 8 (INSTRUMENT_READY)• 7 (INSTRUMENT_NOT_CONNECTED)• 10 (INSTRUMENT_PAUSED)• 11 (INSTRUMENT_IN_ERROR)• 12 (INSTRUMENT_FAIL_TO_START)


communication cannot be established


Returns The type of return value is boolean, where possible return values are:• True if the instrument arm is closed (inside the instrument).• False if the instrument arm is open (outside the instrument).





openTray ( sessionID, instrumentID )

Instructs the QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID) to open the door and extend the tray arm.

Note: If the tray arm is extended, the method is noop (no operation) and does not return an error.

runExperiment ( sessionID, instrumentID, edsPath, barcode )

Instructs the QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID) to execute the workflow contained in the specified experiment (.eds) file (edsPath). In addition to data collection, the workflow can also include analysis and results export. If the workflow includes analysis, the software automatically persists the results to the associated experiment (.eds) file. If security is enabled, the software creates and persists all audit records to the appropriate locations.

Note: If used in a script, runExperiment performs a blocking call in which subsequent calls are not executed until the QuantStudio™ 6 and 7 Flex System has completed the experiment. To perform a non-blocking call, use runExperimentAsync instead.

Note: Errors encountered during processing are propagated through the invoking API, then to the custom application to be reported to the user.

Note: The RunExperiment() method automatically performs experiment (.eds) file verification.


Returns None



Arguments • sessionID – (string; required) The session ID of the open session.• instrumentID – (string; required) The name of the instrument of interest.• edsPath – (string; required) The path to the target experiment (.eds) file.• barcode – (string; required) The barcode of the experiment consumable.

Returns None



runExperimentAsync ( sessionID, instrumentID, edsPath, barcode )

Performs an operation identical to the runExperiment method except that subsequent calls are not blocked.

Note: Use runExperiment if you want to perform a blocking call in which subsequent calls are executed only after designated QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID) runs the specified experiment (.eds) file (edsPath).

runExperimentFromTemplate ( sessionID, instrumentID, edtPath, barcode, outputPath )

Instructs the QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID) to copy the input template file (edtPath) to the output folder (outputPath) as an experiment file (.eds), adding the specified barcode (barcode) to the experiment (.eds) file name for uniqueness, then runs that experiment. The experiment workflow contains data collection, and it can include experiment analysis and results export. If the experiment workflow includes analysis, the QuantStudio™ 6 and 7 Flex System Software automatically persists the results back into the associated experiment file (.eds), regardless of whether they are exported. If security is enabled, the QuantStudio™ 6 and 7 Flex System Software creates and persists all audit records to the appropriate location (mainly to the .eds file).

Note: Errors encountered during processing are propagated through the invoking API, then to the custom application to be reported to the user.


communication cannot be established• 7 (INSTRUMENT_NOT_CONNECTED) – if the instrument was

disconnected during the run• 12 (INSTRUMENT_FAIL_TO_START) – if the instrument failed to start

the run• 15 (EXPERIMENT_NOT_FOUND)• 16 (EXPERIMENT_READ_ERROR)• 17 (EXPERIMENT_WRITE_ERROR)

Arguments • sessionID – (string; required) The session ID of the open session.• instrumentID – (string; required) The name of the instrument of interest.• edtPath – (string; required) The path to the target template (.edt) file.• barcode – (string; required) The barcode of the experiment consumable.• outputPath – (string; required) The path of the directory to which the

QuantStudio™ 6 and 7 Flex System Software will save the experiment (.eds) file.

Returns None



runExperimentFromTemplateAsync ( sessionID, instrumentID, edtPath, barcode, outputPath )

Performs an operation identical to the runExperimentFromTemplate method except that subsequent calls are not blocked.

Note: The runExperimentFromTemplateAsync method can be useful when a single client script is used to control more than one QuantStudio™ 6 and 7 Flex System. The script can invoke calls to run experiments on several QuantStudio™ 6 and 7 Flex Systems without waiting for each individual call to complete.

Note: Use the runExperimentFromTemplate method to perform a blocking call in which subsequent calls are executed only after the designated QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID) runs the plate or array card associated with the specified barcode (barcode).

startSession ( userName, password )

Called after Launch Application to start a new Application Session. If QuantStudio™ 6 and 7 Flex System Software security is enabled, the method authenticates the specified user name (userName) and password (password) against the security module and starts a new user session. If security is not enabled, the software ignores the username and password parameters, which can be null.

Once the session is started, the headless process accepts subsequent connections for additional commands until End Session () is called. Because a single instance of the QuantStudio™ 6 and 7 Flex System Software manages all QuantStudio™ 6 and 7 Flex Systems associated with the custom application instance, all subsequent interactions with the instruments are within the scope of the single application/user session until End Session () is called.

The method returns the sessionID to be used in all subsequent calls during the workflow. You must use the sessionID returned by the startSession() method for all subsequent instrument communication until the session is ended.


communication cannot be established• 7 (INSTRUMENT_NOT_CONNECTED) if the instrument was disconnected

during the run• 12 (INSTRUMENT_FAIL_TO_START) if the instrument failed to start the

run• 15 (EXPERIMENT_NOT_FOUND)• 16 (EXPERIMENT_READ_ERROR)• 17 (EXPERIMENT_WRITE_ERROR)

Arguments • userName – (string; required if security is enabled) The user account used to initiate the session.

• password – (string; required if security is enabled) The password for the user account used to initiate the session.



stopCurrentExperiment ( sessionID, instrumentID )

Instructs the QuantStudio™ 6 and 7 Flex System (instrumentID) associated with the active session (sessionID) to abort the experiment currently in progress.

Note: If the tray arm is extended, the method is noop (no operation) and does not return an error.

Returns • sessionID (string) of the new session.• An error if an existing instance of the QuantStudio™ 6 and 7 Flex System

Software is running, where an application session is still in progress and the QuantStudio™ 6 and 7 Flex System is in an indeterminate state.

Note: The method could return an error if the custom application terminated abnormally.

• Null/empty if the user name and password combination provided fail authentication.

Errors Possible errorCode of AutomationException in fault message:• 3 (AUTHENTICATION_FAILURE)


Returns None


communication cannot be established



Automation notifications

The messages are documented in alphabetical order where each entry includes a description and the message values:

Analysis completed {barcode, edsPath, hostName, dateTime, status}

Broadcast upon the completion of the analysis of an experiment (.eds) file (edsPath) with an experiment workflow that includes autoanalysis. If known, the message includes the barcode (barcode) of the related reaction consumable; otherwise, it is blank.

Analysis results exported {barcode, edsPath, hostName, resultsPath, dateTime}

Broadcast upon the completion of the export of an experiment (.eds) file (edsPath) with an experiment workflow that includes autoanalysis and autoexport. If known, the message includes the barcode (barcode) of the related reaction consumable, otherwise it is blank.

Run completed {barcode, edsPath, instrumentName, dateTime, status}

Broadcast upon the completion of a run. The message includes the consumable barcode (barcode), the path to the experiment (.eds) file (edsPath), the name of the QuantStudio™ 6 and 7 Flex System (instrumentName) that performed the run, the date and time (dateTime) of the run, and the run status (status).

Returns • barcode – (string or blank) The barcode of the reaction consumable run to generate the analyzed data.

• edsPath – (string) The path to the analyzed experiment (.eds) file.• hostName – (string) The name of the host computer.• dateTime – (string) The date and time that the host computer completed the

analysis.• status – (string) The status of the run (ANALYSIS_COMPLETED).

Returns • barcode – (string or blank) The barcode of the reaction consumable run to generate the analyzed data.

• edsPath – (string) The path to the analyzed experiment (.eds) file.• hostName – (string) The name of the host computer that received the exported

data.• resultsPath – (string) The path and file name of the exported file.• dateTime – (string) The date and time that the host computer completed the

export.

Returns • barcode – (string) The barcode of the related reaction consumable.• edsPath – (string) The path to the experiment (.eds) file used to perform the

run.• instrumentName – (string) The name of the QuantStudio™ 6 and 7 Flex System

that performed the run.• dateTime – (string) The date and time that the run was completed.• status – (string) The status of the analysis (RUN_COMPLETED).



Run started {barcode, edsPath, instrumentName, hostName, dateTime}

Broadcast upon the successful start of a run. The message includes the consumable barcode (barcode), the path to the experiment (.eds) file (edsPath), the name of the QuantStudio™ 6 and 7 Flex System (instrumentName) running the consumable, and the date and time (dateTime) that the run was started.

Note: The hostName and edsPath are included so that a listener of a custom application, which automatically generates experiments from templates, can retrieve the experiment (.eds) files after processing is complete.

Returns • barcode – (string or blank) The barcode of the related reaction consumable (may be empty if not specified or known).

• edsPath – (string) The path to the experiment (.eds) file used to perform the run.

• instrumentName – (string) The name of the QuantStudio™ 6 and 7 Flex System that performed the run.

• hostName – (string) The name of the computer host that contains the experiment (.eds) file.

• dateTime – (string) The date and time that the run was started.



Web services files The supporting files for the Automation Server web services are provided on the following pages for reference.

■ WSDL file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

■ Web Services schema file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Note: You can retrieve both the WSDL and schema files when the Automation Server is running.

WSDL file

The following figure lists the contents of the Web Services Description Language (WSDL) file for the Automation Server Web Services. The file defines the collections of network ports for the Automation Server using the WSDL 1.1 standard markup defined in the standard maintained by the World Wide Web Consortium (W3C). For more information on WSDL, refer to www.w3.org/TR/wsdl.

<?xml version="1.0" encoding="UTF-8" standalone="yes"?><definitions targetNamespace="http://ws.automation.paragon.sds.apldbio.com/" name="AutomationService" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:tns="http://ws.automation.paragon.sds.apldbio.com/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/">

<types><xsd:schema><xsd:import namespace="http://ws.automation.paragon.sds.apldbio.com/"

schemaLocation="AutomationService_schema1.xsd"/></xsd:schema></types>

<message name="closeTray"><part name="parameters" element="tns:closeTray"/></message>

<message name="closeTrayResponse"><part name="parameters" element="tns:closeTrayResponse"/></message>

<message name="AutomationException"><part name="fault" element="tns:AutomationException"/></message>

<message name="endSession"><part name="parameters" element="tns:endSession"/></message>

<message name="endSessionResponse"><part name="parameters" element="tns:endSessionResponse"/></message>

<message name="getInstrumentState"><part name="parameters" element="tns:getInstrumentState"/></message>

<message name="getInstrumentStateResponse"><part name="parameters" element="tns:getInstrumentStateResponse"/></message>

<message name="openTray"><part name="parameters" element="tns:openTray"/></message>



WSDL file (continued):

<message name="openTrayResponse"><part name="parameters" element="tns:openTrayResponse"/></message>

<message name="runExperiment"><part name="parameters" element="tns:runExperiment"/></message>

<message name="runExperimentResponse"><part name="parameters" element="tns:runExperimentResponse"/></message>

<message name="runExperimentFromTemplate"><part name="parameters" element="tns:runExperimentFromTemplate"/></message>

<message name="runExperimentFromTemplateResponse"><part name="parameters" element="tns:runExperimentFromTemplateResponse"/></message>

<message name="startSession"><part name="parameters" element="tns:startSession"/></message>

<message name="startSessionResponse"><part name="parameters" element="tns:startSessionResponse"/></message>

<message name="isTrayIn"><part name="parameters" element="tns:isTrayIn"/></message>

<message name="isTrayInResponse"><part name="parameters" element="tns:isTrayInResponse"/></message>

<message name="runExperimentAsync"><part name="parameters" element="tns:runExperimentAsync"/></message>

<message name="runExperimentAsyncResponse"><part name="parameters" element="tns:runExperimentAsyncResponse"/></message>

<message name="stopCurrentExperiment"><part name="parameters" element="tns:stopCurrentExperiment"/></message>

<message name="stopCurrentExperimentResponse"><part name="parameters" element="tns:stopCurrentExperimentResponse"/></message>

<message name="runExperimentFromTemplateAsync"><part name="parameters" element="tns:runExperimentFromTemplateAsync"/></message>

<message name="runExperimentFromTemplateAsyncResponse"><part name="parameters" element="tns:runExperimentFromTemplateAsyncResponse"/></message>




<portType name="AutomationServiceWS"><operation name="closeTray"><input message="tns:closeTray"/><output message="tns:closeTrayResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="endSession"><input message="tns:endSession"/><output message="tns:endSessionResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="getInstrumentState"><input message="tns:getInstrumentState"/><output message="tns:getInstrumentStateResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="openTray"><input message="tns:openTray"/><output message="tns:openTrayResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="runExperiment"><input message="tns:runExperiment"/><output message="tns:runExperimentResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="runExperimentFromTemplate"><input message="tns:runExperimentFromTemplate"/><output message="tns:runExperimentFromTemplateResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="startSession"><input message="tns:startSession"/><output message="tns:startSessionResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="isTrayIn"><input message="tns:isTrayIn"/><output message="tns:isTrayInResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="runExperimentAsync"><input message="tns:runExperimentAsync"/><output message="tns:runExperimentAsyncResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="stopCurrentExperiment"><input message="tns:stopCurrentExperiment"/><output message="tns:stopCurrentExperimentResponse"/>




<fault message="tns:AutomationException" name="AutomationException"/></operation>

<operation name="runExperimentFromTemplateAsync"><input message="tns:runExperimentFromTemplateAsync"/><output message="tns:runExperimentFromTemplateAsyncResponse"/><fault message="tns:AutomationException" name="AutomationException"/></operation>

</portType>

<binding name="AutomationServiceWSPortBinding" type="tns:AutomationServiceWS"><soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>

<operation name="closeTray"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="endSession"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="getInstrumentState"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="openTray"><soap:operation soapAction=""/><input><soap:body use="literal"/></input>




<output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="runExperiment"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="runExperimentFromTemplate"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="startSession"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="isTrayIn"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output>




<fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="runExperimentAsync"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="stopCurrentExperiment"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation>

<operation name="runExperimentFromTemplateAsync"><soap:operation soapAction=""/><input><soap:body use="literal"/></input><output><soap:body use="literal"/></output><fault name="AutomationException"><soap:fault name="AutomationException" use="literal"/></fault></operation></binding>

<service name="AutomationService"><port name="AutomationServiceWSPort" binding="tns:AutomationServiceWSPortBinding"><soap:address location="http://localhost:9999/AutomationService"/></port></service>

</definitions>



Web Services schema file

The following figure lists the contents of the XML schema file for the Automation Server Web Services, which defines the specialized data types it uses.

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>

<xs:schema version="1.0" targetNamespace="http://ws.automation.paragon.sds.apldbio.com/" xmlns:tns="http://ws.automation.paragon.sds.apldbio.com/" xmlns:xs="http://www.w3.org/2001/XMLSchema">

<xs:element name="AutomationException" type="tns:AutomationException"/><xs:element name="closeTray" type="tns:closeTray"/><xs:element name="closeTrayResponse" type="tns:closeTrayResponse"/><xs:element name="endSession" type="tns:endSession"/><xs:element name="endSessionResponse" type="tns:endSessionResponse"/><xs:element name="getInstrumentState" type="tns:getInstrumentState"/><xs:element name="getInstrumentStateResponse" type="tns:getInstrumentStateResponse"/><xs:element name="isTrayIn" type="tns:isTrayIn"/><xs:element name="isTrayInResponse" type="tns:isTrayInResponse"/><xs:element name="openTray" type="tns:openTray"/><xs:element name="openTrayResponse" type="tns:openTrayResponse"/><xs:element name="runExperiment" type="tns:runExperiment"/><xs:element name="runExperimentAsync" type="tns:runExperimentAsync"/><xs:element name="runExperimentAsyncResponse" type="tns:runExperimentAsyncResponse"/><xs:element name="runExperimentFromTemplate" type="tns:runExperimentFromTemplate"/><xs:element name="runExperimentFromTemplateAsync" type="tns:runExperimentFromTemplateAsync"/><xs:element name="runExperimentFromTemplateAsyncResponse"

type="tns:runExperimentFromTemplateAsyncResponse"/><xs:element name="runExperimentFromTemplateResponse" type="tns:runExperimentFromTemplateResponse"/><xs:element name="runExperimentResponse" type="tns:runExperimentResponse"/><xs:element name="startSession" type="tns:startSession"/><xs:element name="startSessionResponse" type="tns:startSessionResponse"/><xs:element name="stopCurrentExperiment" type="tns:stopCurrentExperiment"/><xs:element name="stopCurrentExperimentResponse" type="tns:stopCurrentExperimentResponse"/>

<xs:complexType name="runExperimentAsync"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/><xs:element name="arg2" type="xs:string" minOccurs="0"/><xs:element name="arg3" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="runExperimentAsyncResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:complexType name="AutomationException"><xs:sequence><xs:element name="errorCode" type="tns:automationResultCode" minOccurs="0"/><xs:element name="message" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="isTrayIn"><xs:sequence>



Web Services schema file (continued):

<xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="isTrayInResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:complexType name="startSession"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="startSessionResponse"><xs:sequence><xs:element name="return" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="closeTray"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="closeTrayResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:complexType name="runExperimentFromTemplateAsync"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/><xs:element name="arg2" type="xs:string" minOccurs="0"/><xs:element name="arg3" type="xs:string" minOccurs="0"/><xs:element name="arg4" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="runExperimentFromTemplateAsyncResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:complexType name="endSession"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>




<xs:complexType name="endSessionResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:complexType name="stopCurrentExperiment"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="stopCurrentExperimentResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:complexType name="runExperiment"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/><xs:element name="arg2" type="xs:string" minOccurs="0"/><xs:element name="arg3" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="runExperimentResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:complexType name="runExperimentFromTemplate"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/><xs:element name="arg2" type="xs:string" minOccurs="0"/><xs:element name="arg3" type="xs:string" minOccurs="0"/><xs:element name="arg4" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="runExperimentFromTemplateResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:complexType name="getInstrumentState"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>




<xs:complexType name="getInstrumentStateResponse"><xs:sequence><xs:element name="return" type="xs:int"/></xs:sequence></xs:complexType>

<xs:complexType name="openTray"><xs:sequence><xs:element name="arg0" type="xs:string" minOccurs="0"/><xs:element name="arg1" type="xs:string" minOccurs="0"/></xs:sequence></xs:complexType>

<xs:complexType name="openTrayResponse"><xs:sequence><xs:element name="return" type="xs:boolean"/></xs:sequence></xs:complexType>

<xs:simpleType name="automationResultCode"><xs:restriction base="xs:string"><xs:enumeration value="UNINITIALIZED"/><xs:enumeration value="SESSION_INVALID"/><xs:enumeration value="SESSION_EXISTING"/><xs:enumeration value="AUTHENTICATION_FAILURE"/><xs:enumeration value="USER_ACCOUNT_DISABLED"/><xs:enumeration value="PASSWORD_EXPIRED"/><xs:enumeration value="INSTRUMENT_UNKNOWN"/><xs:enumeration value="INSTRUMENT_NOT_CONNECTED"/><xs:enumeration value="INSTRUMENT_READY"/><xs:enumeration value="INSTRUMENT_RUNNING"/><xs:enumeration value="INSTRUMENT_PAUSED"/><xs:enumeration value="INSTRUMENT_IN_ERROR"/><xs:enumeration value="INSTRUMENT_FAIL_TO_START"/><xs:enumeration value="INSTRUMENT_TRAY_OPENED"/><xs:enumeration value="INSTRUMENT_TRAY_CLOSED"/><xs:enumeration value="EXPERIMENT_NOT_FOUND"/><xs:enumeration value="EXPERIMENT_READ_ERROR"/><xs:enumeration value="EXPERIMENT_WRITE_ERROR"/><xs:enumeration value="EXPERIMENT_VALIDATION_ERROR"/></xs:restriction></xs:simpleType>

</xs:schema>


Chapter 1 Application Programming InterfaceAutomation notification API1

Automation notification API

The QuantStudio™ 6 and 7 Flex System Software Automation Notification API allows custom applications to receive events from the QuantStudio™ 6 and 7 Flex System Software regarding experiment workflow and instrument maintenance. The API delivers event notifications via an Apache™ ActiveMQ® Java Message Service (JMS), a message standard that provides a flexible service for data asynchronous exchange. The Automation Notification API uses a publish/subscribe delivery model to allow multiple clients to receive events. The message topic name is MBS.EVENTS.

Note: The Automation Notification API, when enabled, is active whenever the QuantStudio™ 6 and 7 Flex System Software is running, whether in headless mode (with a custom application) or in normal mode with a GUI.

Note: Apache™ ActiveMQ® supports the following language clients: Adobe® Flash® (ActionScript), Ajax, C, C++, C# and .Net, Delphi™ and Delphi™/FreePascal™, Erlang™, Haskell, Java®, JavaScript®, Perl™, PHP, Pike, Python, Ruby™ and Ruby on Rails™ support via ActiveMessaging, and Smalltalk. The libraries are available at: http://activemq.apache.org/cross-language-clients.html

Note: Apache™ ActiveMQ® is released under the Apache 2.0 License.

Enable/disable the automation notification API

To enable or disable the Automation Notification API:

1. Use a text editor to open the preferences.properties file at:C:\Applied Biosystems\AppData\QuantStudio 6 and 7 Flex Software\UserData\prefs\system\notification\ preferences.properties

2. Change the value of the enabled key, where true enables the Automation Notification API and false disables it.

3. Save the file.

Connection information

The following information is required for connecting to the Apache™ ActiveMQ® broker:

Broker URItcp://<hostname>:61616

orfailover://tcp://localhost:61616

userName

guest

password

guest


Chapter 1 Application Programming InterfaceAutomation notification API 1

Messages The Automation Notification API delivers each message as a MapMessage object that contains the set of name-value pairs shown in the following table. Both the name and value are strings and a value with empty string indicates no value.

Note: <value> denotes any value of string type. <path> denotes a file path as a string.

Name Description Value

event-type Type of event

This entry always exists. It determines what set of name-value pairs is contained in the message. It is recommended that API client checks the value of event-type first.

Five supported values:• RUN_STARTED

• RUN_COMPLETED

• REALTIME_NOTIFICATION

• RUN_STATUS_CHANGED

• ANALYSIS_COMPLETED

• EXPORT_COMPLETED

• CALIBRATION_MAINTENANCE_REMINDER

instrument-id Serial number of the QuantStudio™ 6 and 7 Flex System

<value>

instrument-name Name of the QuantStudio™ 6 and 7 Flex System <value>

hostname Hostname of the computer running the QuantStudio™ 6 and 7 Flex System Software

<value>

eds-file-path Experiment (.eds) file path <path>

barcode Plate barcode <value>

status Status SUCCESS or FAILURE

sample-temperature Temperature of sample during a run <value> in degrees Celsius

cover-temperature Temperature of heated cover during a run <value> in degrees Celsius

remaining-time The time remaining of a run to complete <value> in seconds

stage The current stage of a run <value>

cycle The current cycle of a run <value>

step The current step of a run <value>

experiment-name Experiment name <value>

date-time Timestamp when the message was published Date time in the following format:”yyyy-mm-dd hh:mm:ss"

use-one-file Whether to export data to one file true or false

combined-export-file-path File path of combined export file <path>

plate-setup-file-path File path of plate setup export <path>

raw-data-file-path File path of raw data export <path>

multicomponent-data-file-path File path of multicomponent data export <path>

analysis-results-file-path File path of analysis results export <path>

calibration-type The type of calibration required <value>

expiration-date Calibration expiration date time Date time in the following format:”yyyy-mm-dd hh:mm:ss"


Chapter 1 Application Programming InterfaceAutomation notification API1

Event type name-value pairs

The following table shows the available name-value pairs for a particular event type in the message.

Event type Set of name-value pairs

RUN_STARTED • barcode• date-time• eds-file-path• event-type• experiment name

• hostname• instrument-id• instrument-name• status

RUN_COMPLETED

REALTIME_NOTIFICATION • barcode• cover-temperature• event-type• experiment name

• instrument-id• instrument-name• remaining-time• sample-temperature

RUN_STATUS_CHANGED • barcode• cycle• event-type• experiment-name

• instrument-id• instrument-name• stage• step

ANALYSIS_COMPLETED • date-time• eds-file-path• event-type

• experiment name• hostname• status

EXPORT_COMPLETED If use-one-file is true:• combined-export-file-path• date-time• eds-file-path• event-type• experiment name • hostname• status• use-one-file

If use-one-file is false:• analysis-results-file-path• date-time• eds-file-path• event-type• experiment name• hostname• multicomponent-data-file-path• plate-setup-file-path• raw-data-file-path• status• use-one-file

CALIBRATION_MAINTENANCE_REMINDER • event-type• instrument-id• instrument-name

• calibration-type• expiration-date• date-time

2


Command-line Application


■ About the command-line application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

■ Supporting files for experiment creation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

■ Precedence rules for experiment file generation . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

■ Running the command-line application from a command prompt . . . . . . . . . . . 43

■ Example commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46


Chapter 2 Command-line ApplicationAbout the command-line application2

About the command-line application

The QuantStudio™ 6 and 7 Flex System Software includes a command-line application that allows you to generate and export batches of experiment files from an MS DOS prompt or a batch file. The application is intended for advanced users who choose to create or export experiments using a scripting language.

IMPORTANT! After you use the command-line application to generate experiment files, validate the contents of the files by opening them in the QuantStudio™ 6 and 7 Flex System Software.

Command-line workflows

The command-line interface supports the workflows in the following figure. For each workflow, the figure shows both the required and optional supporting files.

Experiment DocumentTemplate (.edt)

Plate SetupFile (.txt)

SampleFile (.txt)

AIF/X File(.txt/.xml)

Barcode

Single Experiment File Creation Workflow

EDSQuantStudio™ 6 and 7 Flex System Software

Command-lineInput

ResultsFile

Experiment DocumentSingle (.eds)

Export Workflow

QuantStudio™ 6 and 7 Flex System Software

Command-lineInput

Required


Chapter 2 Command-line ApplicationSupporting files for experiment creation 2

Supporting files for experiment creation

The file generation function (cmdlineutil.exe –expgen) can use the files shown below. The command does not require all input files.

File Description

assay information file (.aif or .aix)

A tab-delimited or XML data file that is shipped on a CD with each assay ordered from Life Technologies. (For some products, assay information files are available for download from the Life Technologies website following delivery.) The file, which contains data describing the assay, can be imported into the QuantStudio™ 6 and 7 Flex System Software for use in related experiments.

See “Assay information file” on page 55 for more information.

barcode file (.txt) A user-created, line-separated text file that contains the barcode of each consumable for which you want to create an experiment file.

See “Barcode file format” on page 55 for more information.

experiment document single file (.eds)

A QuantStudio™ 6 and 7 Flex System Software file that contains all information about a particular plate or array card consumable, including metadata (name, barcode, comments), plate setup (well contents, assay definitions), run method (thermal cycling protocol), run results, analysis protocol, analysis results, audit records, and other plate-specific data.

experiment document template file (.edt)

A QuantStudio™ 6 and 7 Flex System Software file used as a template to create experiment files. The file can contain plate setup (well contents, assay definitions), run method (thermal cycling protocol), run results, analysis protocol, and other plate-specific data.

plate setup file (.txt)

A user-created, tab-delimited text file that describes the layout of a consumable for an experiment to be run on the QuantStudio™ 6 and 7 Flex System. The file defines the arrangement of assays and samples on the consumable.

See “Plate setup file format” on page 49 for more information.

sample file (.txt) A user-created, tab-delimited text file containing sample data that can be imported into the QuantStudio™ 6 and 7 Flex System Software for use in related experiments.

See “Sample file format” on page 54 for more information.


Chapter 2 Command-line ApplicationPrecedence rules for experiment file generation2

Precedence rules for experiment file generation

When generating experiment files (.eds), the QuantStudio™ 6 and 7 Flex System Software command-line interface relies on a set of precedence rules to resolve conflicts that arise from the data supplied by the input files. Assay information files (.aif or .aix), plate setup files (.txt), and template files (.edt) can contain data used to populate the same fields of new experiment files. For example, both template and plate setup files can contain location data for samples and assays. The following table describes the precedence rules for the data supplied by each input file.

Files used for experiment file (.eds) creation

Precedence rule

Template file (.edt) The values in the template take precedence except for:• Experiment Name – Determined by the File Name Convention preference.• Bar Code – Determined by the barcode, if present. Otherwise, the value is null.• Experiment File Name – Determined by the File Name Convention preference.

• Template file (.edt) • Assay information

file (.aif/.aix)

All values in the template file take precedence, except for:• Gene Expression Targets/Assay Definition• Genotyping Assay/SNP Definition• Passive Reference

If any conflicts exist between the assay information file and the template for the attributes above, then the assay information file values always take precedence.

• Template file (.edt) • Plate setup file

(.txt)

All values in the template file take precedence, except for:

• Target/Assay/SNP to Well Assignment• Sample to Well Assignment• Task to Well Assignment• Biological Group to Well Assignment• Well Quantity to Well Assignment• Sample Color

• Biological Group Color• Target Color• Gene Expression Targets Definition• Genotyping Assay Definition• Passive Reference

• Template file (.edt) • Plate setup file

(.txt)• Assay information

file (.aif/.aix)

All values in the template take precedence, except for the following.

The following assay information file values take precedence over Plate Setup and Template:• Gene Expression Targets/Detectors Definition• GT Assay/Marker Definition• Passive Reference

The following Plate Setup values take precedence over the template:

• Block Type• Target/Assay/Marker to Well Assignment• Sample to Well Assignment• Task to Well Assignment• Biological Group to Well Assignment

• Well Quantity to Well Assignment• Sample Color • Biological Group Color• Target Color


Chapter 2 Command-line ApplicationRunning the command-line application from a command prompt 2

Running the command-line application from a command prompt

Running the application

1. In the desktop, select StartRun.

2. In the Run dialog box, enter cmd in the Open field, then click OK.

3. In the DOS prompt, change to the installation directory and enter the command:

a. Enter cd C:\Program Files\Applied Biosystems\QuantStudio 6 and 7 Flex Software\bin\, then press Enter.

b. Enter cmdlineutil.exe, followed by -expgen or -export, then all applicable parameters and arguments. See “Command syntax and arguments” on page 43 for a complete list of command-line parameters.

Viewing the command-line help

The command-line application includes a help function that provides the information in this chapter. To view help for:

• The entire application, enter cmdlineutil.exe –help• A particular function, enter cmdlineutil.exe –expgen -help to view the file

generation help, or cmdlineutil.exe –export -help to view the file export help.

Command syntax and arguments

Syntax and arguments used for batch file creation

The command used to create batches of files uses the following syntax:

cmdlineutil.exe -expgen [ parameters ]

The following is a list of the acceptable parameters that can be included in any order. See “Example commands” on page 46 for an example of the experiment creation command.

IMPORTANT! Enclose file paths in double quotes to allow spaces in the string.

-a <filepath>

(Optional) Specifies the path and name (<filepath>) of the assay information file (.aif or .aix) that the software uses to create new experiment files. Example: -a “C:\assayfiles\assayfile.aif”

-b <filepath>

(Optional) Specifies the path and name (<filepath>) of the barcode file that the software uses to create new files. If the -b parameter is not used, then the software creates the number of experiments specified by the -n parameter. Example: -b “C:\barcodefiles\barcodefile.txt”

-c <string>

(Optional) When the -f parameter is included, specifies the alphanumeric string that the software includes in the file names of the new experiments. If no value is supplied, “custom” is used as the default value.Example: -c “Batch001_”


Chapter 2 Command-line ApplicationRunning the command-line application from a command prompt2

-f <option>

(Optional) Specifies the convention that the software uses to name the new files. The convention can consist of all or some of the following interchangeable arguments, in any order:Custom Name Field – The alphanumeric string specified by the -c parameter.ID – The barcode of the plate specified in the barcode file specified by the -b parameter.Example: -f “Custom Name Field_ID”If the -f parameter is used without arguments, then the software names files according to the following convention: “Custom Name Field_ID”

-l <dirpath>

(Required) Specifies the path of the directory (<dirpath>) to which the software saves the new files.Example: -l “C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments”

Before creating experiment files, the software confirms whether the export location exists and aborts if the location does not exist.

-m <filepath>

(Optional) Specifies the path and name (<filepath>) of the sample file that the software uses to create new files. Example: -m “C:\samplefiles\samplefile.txt”

-n <integer>

(Optional) If the -b parameter is not included, specifies number of experiments (<integer>) that the software will create. If no value is supplied, the software creates 25 experiments by default.Example: -n 31

-s <filepath>

(Optional) Specifies the path and name (<filepath>) of the setup file that the software uses to create new files. Example: -s “C:\setupfiles\setupfile.txt”

-t <filepath>

(Required) Specifies the path and name (<filepath>) of the QuantStudio™ 6 and 7 Flex System Software template file that the software uses to create new files.Example: -t “C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments”

-v

(Optional) Configures the software to operate in verbose mode, where the software displays each operation as it is performed.


Chapter 2 Command-line ApplicationRunning the command-line application from a command prompt 2

Syntax and arguments used for results export

The command used to export the results from experiment files uses the following syntax:

cmdlineutil.exe -export [ parameters ]

The following is a list of the acceptable parameters that can be included in any order. See “Example commands” on page 46 for examples of the experiment export command.

IMPORTANT! Enclose file paths in double quotes to allow spaces in the string.

-e <dirpath>

(Required) Specifies the path to the directory (<dirpath>) that contains the experiment files (.eds) for which the software exports data.Example: -e “C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments”

-f <option>

(Required) Specifies the format of the exported data (see page 58 for the export file specifications): ViiA7 – Exports data in a native format compatible with the QuantStudio™ 6 and 7 Flex Real-Time PCR Systems, or in a legacy format compatible with the QuantStudio™ Dx Real-Time PCR System and ViiA™ 7 Real-TIme PCR System.SDS23 – Exports data in a format compatible with the 7900HT Real-Time PCR System. RDML – Exports data in the real-time data markup language (RDML) format.Example: -f “ViiA7”

-l <path>

(Optional) Specifies the path (<path>) of the directory to which the software saves the exported files.Example: -l “C:\exports\”

-s <option>

(Optional) Specifies the data spanning option (<option>) that determines how the software exports data from multiple experiments:single – Exports data for all experiments into one contiguous data file.multiple – Exports data for each experiment to a separate data file.Example: -s “multiple”

-x <filepath>

(Required) Specifies the file format of the exported file: ViiA7 export format – .txt, .xls, or .xlsxSDS23 export format – .txtRDML export format – .rdmlExample: -x “xlsx”


Chapter 2 Command-line ApplicationExample commands2

Example commands

Batch file creation The following example uses all parameters described in “Command syntax and arguments” on page 43 (required and optional) to generate a set of experiment files.

For this example, the command-line application:

• Imports assay definitions from the AIF_820629.txt assay information file.• Imports sample names from the SampleFileNames.txt sample file.• Generates an experiment for each barcode in the barcodes - v12.txt barcode

file, where each new experiment uses the settings found in the standard_curve.edt template file and the SDS_820629.txt setup file.

Note: The setup file links the information from the AIF_820629.txt and SampleFileNames.txt to each new experiment file.

• Saves all generated files using the following naming convention:<barcode>_alloptionsused

• Saves all generated files to:C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments\<date\time>

Note: The command-line application automatically creates a time-stamped folder at the export location for each batch operation. For example, the folder created for files generated on April 7, 2010 at 12:48:35 would be: 2010-04-07 124835

Results export The following example performs a real-time data markup language (RDML) export of experiments in the QuantStudio™ 6 and 7 Flex System Software experiments directory to the exports directory of the C drive. The software generates an RDML file for each individual experiment file.

cmdlineutil.exe -expgen -t "C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments\templates\standard_curve.edt" -s "C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments\examples\Plate SetupFiles\SDS_820629.txt" -m "C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments\examples\SampleNames\ SampleFileNames.txt" -c "alloptionsused" -f "Plate Barcode_Custom NameField" -b "C:\barcodes - v12.txt" -l "C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments"

cmdlineutil.exe -export -e “C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\experiments\” -f “SDS23” -l “C:\exports\” -s “single” -x “rdml”

cmdlineutil.exe -export -e “C:\Applied Biosystems\QuantStudio 6 and 7 Flex Software\User Files\Tests\” -f “SDS23” -l “C:\exports\” -s “single” -x “rdml”

3


Import File Formats andSpecifications


■ About the importable files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

■ Plate setup file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

■ Sample file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

■ Barcode file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

■ Assay information file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55


Chapter 3 Import File Formats and SpecificationsAbout the importable files3

About the importable files

The QuantStudio™ 6 and 7 Flex System Software supports several import file formats that can be used to automate experiment creation and assay and sample data import. The files can be used with the command-line application (see page 39) or the QuantStudio™ 6 and 7 Flex System Software application programming interface (API) to integrate the QuantStudio™ 6 and 7 Flex System into a laboratory information system (LIS).

Note: The file specifications listed in this appendix are subject to change. For updated information, review the QuantStudio™ 6 and 7 Flex System Software Release Notes.

About the import file formats

Conventions The following conventions are used in the rest of this section:

• normal – Normal text must be entered exactly as it appears.• <italic> – Italicized text between brackets must be substituted with custom values.• [ required text ] – Text appearing between brackets is required

information. All information inside the brackets must be present for the QuantStudio™ 6 and 7 Flex System Software to import it.

• { optional text } – Text appearing between braces is optional.• Unless noted otherwise, separate all fields in a row using a tab character (U+0009).• Unless noted otherwise, end all rows using a carriage-return character (U+000D).

File format Description See…

Plate setup file (.txt)

A user-created, tab-delimited text file that describes the layout of a consumable for an experiment to be run on the QuantStudio™ 6 and 7 Flex System. The file defines the arrangement of assays and samples on the consumable, and provides other experiment data, such as the thermal profile and data collection settings.

page 49

Sample file (.txt) A user-created, tab-delimited text file containing sample data that can be imported into the QuantStudio™ 6 and 7 Flex System Software for use in related experiments.

page 54

Assay information file (.aif or .aix)

A tab-delimited or XML data file that is shipped on a CD with each assay ordered from Life Technologies. The file, which contains data describing the assay, can be imported into the QuantStudio™ 6 and 7 Flex System Software for use in related experiments.

page 55

Barcode file (.txt) A user-created, text file containing the barcodes of consumables for which you want to create experiment files using the command-line utility.

page 55


Chapter 3 Import File Formats and SpecificationsPlate setup file format 3

Plate setup file format

You can use plate setup files to automatically populate setup information into an open experiment in the QuantStudio™ 6 and 7 Flex System Software or into new experiments created by the command-line application (see page 39). A plate setup file is a tab-delimited ASCII text file (.txt) that contains data that describes the location experiment data information. The files can be created manually using a text processor or generated automatically by third-party applications.

IMPORTANT! To guarantee successful import of the plate setup file into an experiment, the file must contain all the elements described in the following section and in the order that they appear.

File structure The plate setup file consists of a header, which specifies the instrument model for which the experiment is designed, and a sample setup section.

Plate setup file header

The plate setup file begins with a header that consists of two lines. Each line starts with an asterisk (*) and ends with a carriage return in the following pattern:

* <field name> = <field value>

The header must contain the lines shown in the following table.

Note: The QuantStudio™ 6 and 7 Flex System Software automatically removes any leading and trailing white space around the field name and field value.

Example:

Section Description See…

Plate setup file header Defines the instrument model for which the experiment is designed and the dye used as the passive reference.

page 49

Plate setup file body Defines the contents of an instrument consumable, including target, SNP assay, sample, and task assignments.

page 50

Field Description Valid Values

Instrument Type

The model of QuantStudio™ 6 and 7 Flex System for which the experiment is designed.

QuantStudio 6 or QuantStudio 7

Passive Reference

The dye that the experiment will use as a passive reference.

• The name of a dye in the Dye Library of the QuantStudio™ 6 and 7 Flex System Software†, or

• <blank> if the consumable does not contain a passive reference.

† Custom dyes are allowed as long as they are in the Dye Library.

* Instrument Type = QuantStudio 7* Passive Reference = ROX


Chapter 3 Import File Formats and SpecificationsPlate setup file format3

Plate setup file body

The body of a plate setup file contains either target information, which can be imported into all experiments except genotyping, or SNP assay information. This information can be imported into genotyping experiments only. The body consists of three required elements (the header, the column header, and the body) that describe the contents of an instrument consumable. The sample setup column header and body can appear in any order.

IMPORTANT! Observe the following guidelines when creating a plate setup file:· Do not insert blank lines between the sample setup header and the column header.· Do not use illegal characters, including backslash (\), tab, asterisk (*), hard return,

soft return, brackets([ or ]), or comma (,).

Sample setup header

The header contains the label that defines the beginning of the sample setup data.

Example:

Sample setup column header

The column header contains the headings that define the positions of the data columns in the sample setup body. The headings are separated by tab characters. See “Plate setup data columns” on page 51 for a list of the data column headers.

Example:

Sample setup body

Contains the sample setup data where each row defines the contents of a single well on the consumable, including the: well contents (sample, target, or SNP assay added to the well), task assignments, and comments. If a well contains multiple assays (multiplex PCR), the data for the additional assays are defined on separate lines by repeating the well designation. See “Plate setup data columns” on page 51 for a list of the data column headers.

Note: The sample setup data rows can occur in any order.

Example:

[Sample Setup]

Well Sample Name Sample Color Biogroup Name Biogroup Color Target Name…

Well Sample Name Sample Color Biogroup Name Biogroup Color Target Name…1 Liver cDNA "RGB(25,0,0)"2 Liver cDNA "RGB(25,0,0)"3 Liver cDNA "RGB(25,0,0)"4 Heart cDNA "RGB(0,25,0)"5 Heart cDNA "RGB(0,25,0)"…


Chapter 3 Import File Formats and SpecificationsPlate setup file format 3

Plate setup data columns

The following table lists the headings and columns that are present in the plate setup file body of all experiment types followed by the columns that are specific to genotyping experiments and non-genotyping experiments.

Column name Description Valid values

All

expe

rim

ents

Well The number of the well on the consumable, where the well numbers start at 1 for well A1 (upper-left corner) and increase from left to right and from top to bottom.

<Positive integer (1 to 96/384)>‡

‡ Cannot be blank.

Sample Name The name of the sample contained by the associated well. <100-character string>

Sample Color (Optional) The RGB color of the associated sample. "RGB(<r>,<g>,<b>)"§

§ Contains (r)ed, (b)lue, and (g)reen color values between 0 to 255. The field must be set within double quotes with no spaces between the values.

Biogroup Name (Optional) The name of the associated biological group. <100-character string>

Biogroup Color (Optional) The RGB color of the biological group. "RGB(<r>,<g>,<b>)"§

Comments (Optional) Additional text that describes the well. “<1024-character string>”

All

exc

ept

geno

typi

ng

Target Name The name of the target detected or amplified by the assay in the associated well.

<100-character string>††

††Can be empty if the Task field is empty. Otherwise, the field must contain a value.

Target Color (Optional) The RGB color of the target. "RGB(<r>,<g>,<b>)"§

Task The task assignment of the target assay at the well.†

† See the QuantStudio™ 6 and 7 Flex System Software Getting Started Guide to determine the tasks applicable to your experiment.

<UNKNOWN | STANDARD | NTC | ENDOGENOUS | IPC | BlockedIPC>

Reporter The reporter dye used by the associated target assay. <dye name>††‡‡

‡‡The dye must already exist in the QuantStudio™ 6 and 7 Flex System Software Dye Library. The dye name must be 100 characters or less.

Quencher The quencher dye used by the associated target assay. <dye name>‡‡

Quantity (Optional) The quantity of standard present in the given well expressed as a float or integer. If the associated well is not assigned the STANDARD task, then the field is blank.

<float or Integer>

Geno

typi

ng o

nly

SNP Assay Name The name of the SNP assay detected or amplified by the assay in the associated well.

<100-character string>††

SNP Assay Color (Optional) SNP assay color in RGB "RGB(<r>,<g>,<b>)”§

Task The task assignment of the SNP assay at the well.† <UNKNOWN | NTC | PC_ALLELE_1 | PC_ALLELE_2 |

PC_ALLELE_BOTH>

Allele1 Name The name of the first allele detected by the SNP assay. <100-character string>††

Allele1 Color The RGB color used to represent data for the first allele. "RGB(<r>,<g>,<b>)"§

Allele1 Reporter The reporter dye used to label the probe for the first allele. <dye name>††‡‡

Allele1 Quencher The quencher dye used to label the probe for the first allele. <dye name>‡‡

Allele2 Name The name of the second allele detected by the SNP assay. <100-character string>††

Allele2 Color The RGB color used to represent data for the second allele. "RGB(<r>,<g>,<b>)"§

Allele2 Reporter The reporter dye used to label the probe for the second allele. <dye name>††‡‡

Allele2 Quencher The quencher dye used to label the probe for the second allele. <dye name>‡‡

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Chapter 3 Import File Form

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at3Examples Quantitative PCR experiments

The following example shows a plate setup file created for a quantitative PCR experiment to be run on a QuantStudio™ 7 Flex System. The experiment evaluates the expression of two targets (CCKAR and GH1) in three samples (cDNA from the liver, heart, and brain). For both assays, the probes are labeled with the FAM™ reporter dye and the non-fluorescent quencher (NFQ-MGB). Biological groups are not used in this experiment.

The following example shows a plate setup file for a multiplex version of the experiment above, where the assays for the two targets (CCKAR and GH1 targets) are added to the same well. For both assays, the probes are labeled with the FAM™ reporter dye and the non-fluorescent quencher (NFQ-MGB).

* Instrument Type = QuantStudio 7* Passive Reference = ROX[Sample Setup]Well Sample Name Sample Color Biogroup Name Biogroup Color Target Name Target Color Task Reporter Quencher Quantity Comments1 Liver cDNA "RGB(25,0,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB2 Liver cDNA "RGB(25,0,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB3 Liver cDNA "RGB(25,0,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB4 Heart cDNA "RGB(0,25,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB5 Heart cDNA "RGB(0,25,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB6 Heart cDNA "RGB(0,25,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB7 Brain cDNA "RGB(0,0,25)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB8 Brain cDNA "RGB(0,0,25)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB9 Brain cDNA "RGB(0,0,25)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB…376 Liver cDNA "RGB(25,0,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB377 Liver cDNA "RGB(25,0,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB378 Liver cDNA "RGB(25,0,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB379 Heart cDNA "RGB(0,25,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB380 Heart cDNA "RGB(0,25,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB381 Heart cDNA "RGB(0,25,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB382 Brain cDNA "RGB(0,0,25)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB383 Brain cDNA "RGB(0,0,25)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB384 Brain cDNA "RGB(0,0,25)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB

* Instrument Type = QuantStudio 7* Passive Reference = ROX[Sample Setup]Well Sample Name Sample Color Biogroup Name Biogroup Color Target Name Target Color Task Reporter Quencher Quantity Comments1 Liver cDNA "RGB(25,0,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB1 Liver cDNA "RGB(25,0,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB2 Liver cDNA "RGB(25,0,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB2 Liver cDNA "RGB(25,0,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB3 Liver cDNA "RGB(25,0,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB3 Liver cDNA "RGB(25,0,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB4 Heart cDNA "RGB(0,25,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB4 Heart cDNA "RGB(0,25,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB5 Heart cDNA "RGB(0,25,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB5 Heart cDNA "RGB(0,25,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB6 Heart cDNA "RGB(0,25,0)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB6 Heart cDNA "RGB(0,25,0)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB7 Brain cDNA "RGB(0,0,25)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB7 Brain cDNA "RGB(0,0,25)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB8 Brain cDNA "RGB(0,0,25)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB8 Brain cDNA "RGB(0,0,25)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB9 Brain cDNA "RGB(0,0,25)" CCKAR "RGB(98,25,0)" ENDOGENOUS FAM NFQ-MGB9 Brain cDNA "RGB(0,0,25)" GH1 "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB…

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Presence/absence experiments

The following example shows a plate setup file created for a presence/absence experiment to be run on a QuantStudio™ 7 Flex System. The experiment screens samples for the presence of a pathogen (E. coli O157:H7). The detection assay uses FAM™ and VIC® dye-labeled probes to amplify a unique genomic sequence and an internal positive control (IPC).

Genotyping experiments

The following example shows a plate setup file created for a genotyping experiment to be run on a QuantStudio™ 7 Flex System. The experiment screens samples for one SNP targets (rs15934), using a set of allele-specific probes labeled with the FAM™ and VIC® reporter dyes and the non-fluorescent quencher (NFQ-MGB).

* Instrument Type = QuantStudio 7* Passive Reference = ROX[Sample Setup]Well Sample Name Sample Color Biogroup Name Biogroup Color Target Name Target Color Task Reporter Quencher Quantity Comments1 Control "RGB(25,0,0)" E.coli "RGB(98,25,0)" NTC FAM NFQ-MGB1 Control "RGB(25,0,0)" IPC "RGB(98,25,0)" NTC VIC NFQ-MGB2 Control "RGB(25,0,0)" E.coli "RGB(98,25,0)" NTC FAM NFQ-MGB2 Control "RGB(25,0,0)" IPC "RGB(98,25,0)" NTC VIC NFQ-MGB3 Control "RGB(25,0,0)" E.coli "RGB(98,25,0)" NTC FAM NFQ-MGB3 Control "RGB(25,0,0)" IPC "RGB(98,25,0)" NTC VIC NFQ-MGB4 Pos Control "RGB(0,25,0)" E.coli "RGB(98,25,0)" IPC FAM NFQ-MGB4 Pos Control "RGB(0,25,0)" IPC "RGB(98,25,0)" IPC VIC NFQ-MGB5 Pos Control "RGB(0,25,0)" E.coli "RGB(98,25,0)" IPC FAM NFQ-MGB5 Pos Control "RGB(0,25,0)" IPC "RGB(98,25,0)" IPC VIC NFQ-MGB6 Pos Control "RGB(0,25,0)" E.coli "RGB(98,25,0)" IPC FAM NFQ-MGB6 Pos Control "RGB(0,25,0)" IPC "RGB(98,25,0)" IPC VIC NFQ-MGB7 Blocked IPC "RGB(0,0,25)" E.coli "RGB(98,25,0)" BlockedIPC FAM NFQ-MGB7 Blocked IPC "RGB(0,0,25)" IPC "RGB(0,0,105)" BlockedIPC VIC NFQ-MGB8 Blocked IPC "RGB(0,0,25)" E.coli "RGB(0,0,105)" BlockedIPC FAM NFQ-MGB8 Blocked IPC "RGB(0,0,25)" IPC "RGB(0,0,105)" BlockedIPC VIC NFQ-MGB9 Blocked IPC "RGB(0,0,25)" E.coli "RGB(0,0,105)" BlockedIPC FAM NFQ-MGB9 Blocked IPC "RGB(0,0,25)" IPC "RGB(0,0,105)" BlockedIPC VIC NFQ-MGB10 Sample01 "RGB(90,0,0)" E.coli "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB10 Sample01 "RGB(90,0,0)" IPC "RGB(0,0,105)" UNKNOWN VIC NFQ-MGB11 Sample01 "RGB(90,0,0)" E.coli "RGB(0,0,105)" UNKNOWN FAM NFQ-MGB11 Sample01 "RGB(90,0,0)" IPC "RGB(0,0,105)" UNKNOWN VIC NFQ-MGB…

* Instrument Type = QuantStudio 7* Passive Reference = ROX[Sample Setup]Well Sample Name Sample Color SNP Assay Name SNP Assay Color Task Allele1 Name Allele1 Color Allele1 Reporter Allele1 Quencher Allele2 Name Allele2 Color Allele2 Reporter Allele2 Quencher Comments1 Neg Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" NTC G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB2 Neg Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" NTC G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB3 Neg Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" NTC G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB4 Al1 Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" PC_ALLELE_1 G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB5 Al1 Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" PC_ALLELE_1 G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB6 Al1 Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" PC_ALLELE_1 G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB7 Al2 Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" PC_ALLELE_2 G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB8 Al2 Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" PC_ALLELE_2 G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB9 Al2 Control "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" PC_ALLELE_2 G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB10 Sample01 "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" UNKNOWN G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB11 Sample01 "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" UNKNOWN G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB12 Sample01 "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" UNKNOWN G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB13 Sample02 "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" UNKNOWN G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB14 Sample02 "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" UNKNOWN G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB15 Sample02 "RGB(25,0,0)" SNP rs15934 "RGB(0,75,0)" UNKNOWN G "RGB(0,0,50)" VIC NFQ-MGB A "RGB(0,50,0)" FAM NFQ-MGB…


Chapter 3 Import File Formats and SpecificationsSample file format3

Sample file format

The QuantStudio™ 6 and 7 Flex System Software can import sample files to populate sample information into an open experiment. A sample file is a tab-delimited ASCII text file (.txt) that contains sample/well designations, and custom sample properties. The files can be created manually using a text processor or generated automatically by third-party applications.

IMPORTANT! To guarantee successful import, the file must contain all the elements described in the following section and in the order that they appear.

Note: The command-line application (see page 39) does not import sample files. If you are using the application to create experiments, use plate setup files to import sample information into the new experiments (see “Plate setup file format” on page 49).

File structure Sample file header row

The sample file begins with an optional header row that contains column headers for well number (“Well”), sample name (“Sample Name”), and optional custom properties names. The order of the columns is important and cannot be changed.

Sample file body

A body of rows, containing the sample data, follows the optional header row. Each body row defines the sample information for a single well on the consumable, including: well number, sample name, and any applicable custom fields. The body can contain data for a subset of wells on the consumable, so the rows for empty wells can be omitted from the file. The sample body rows can occur in any order.

Example

Column name Description Valid values

Well The number of the well on the consumable, where the well numbers start at 1 for well A1 (upper-left corner) and increase from left to right and from top to bottom.

<Positive integer (1 to 96/384)>

Sample Name

The name of the sample contained by the associated well.

<100-character string>

Custom1… Custom6

(Optional) Additional text that describes the sample in the well.


Well Sample Name Custom1 Custom2 Custom3 Custom4 Custom5 Custom621 Sample 1 test1 test2 test3 test4 test5 test622 Sample 2 test1 test2 test3 test4 test5 test623 Sample 3 test1 test3 test4 test5 test61 Sample 5 test1 test2 test3 test4 test5 test62 Sample 6 test1 test2 test3 test4 test5 test63 Sample 7 test1 test2 test3 test4 test5 test64 Sample 8 test1 test2 test3 test4 test5 test6…


Chapter 3 Import File Formats and SpecificationsBarcode file format 3

Barcode file format

The QuantStudio™ 6 and 7 Flex System Software command-line application can import barcode files to populate experiment files (.eds) it generates with barcode information. A barcode file is a tab-delimited ASCII text file (.txt) that contains a list of barcodes. The files can be created manually using a text processor or generated automatically by third-party applications.

IMPORTANT! To guarantee successful import, the file must contain all the elements described in the following section and in the order that they appear.

File structure The barcode file contains a list of barcodes, where each line defines a single barcode terminated by a carriage return. The barcodes can occur in any order and cannot contain starting or trailing white space.

Note: The QuantStudio™ 6 and 7 Flex System Software command-line application does not validate the barcodes.

Example

Assay information file

The QuantStudio™ 6 and 7 Flex System Software command-line application can import data for Life Technologies assays from assay information files (.aif), which are shipped on a CD with each assay order. The .aif contains technical details about all assays in the shipment. It includes information about assay concentrations; reporters and quenchers used; part and lot numbers; and assay, vial, and plate ID numbers. The file name includes the number from the barcode on the plate.

HA996346102IB894812348DD834814679EK209825848AF092387348FF225676243


Chapter 3 Import File Formats and SpecificationsAssay information file3

4


Export File Formats andSpecifications


■ About the exportable files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

■ QuantStudio™ and ViiA™ 7 export formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

■ 7900 export format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

■ RDML export format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84


Chapter 4 Export File Formats and SpecificationsAbout the exportable files4

About the exportable files

This chapter describes the export formats supported by the QuantStudio™ 6 and 7 Flex System Software. The information provided is intended for users who want to integrate the QuantStudio™ 6 and 7 Flex System Software with third-party applications, including downstream analysis software and laboratory information system (LIS) tools.

Note: The file specifications listed in this appendix are subject to change. For updated information, review the QuantStudio™ 6 and 7 Flex System Software Release Notes.

Export formats The QuantStudio™ 6 and 7 Flex System Software can export setup and results data from experiment files (.eds) in several file formats that allow further downstream analysis. The export formats feature standardized data structures and markup to maximize accessibility by downstream applications.

The QuantStudio™ 6 and 7 Flex System Software supports the following export formats:

File format Description See…

QuantStudio™ 6 and 7 export file

A QuantStudio™ 6 and 7 Flex-formatted text file that contains setup and/or results data exported from an experiment file (.eds).

page 59

QuantStudio™ Dx / ViiA™ 7 export file

A legacy QuantStudio™ Dx and ViiA™ 7-formatted text file that contains setup and/or results data exported from an experiment file (.eds).

page 59

7900 export file A legacy 7900-formatted text file that contains setup and/or results data exported from an experiment file (.eds).

page 78

RDML export file A compressed XML file that contains setup and/or results data exported from an experiment file (.eds) and parsed in Real-time PCR Data Markup Language (RDML). The file is stored as a compressed file using the PKZIP archive format.

page 84


Chapter 4 Export File Formats and SpecificationsQuantStudio™ and ViiA™ 7 export formats 4

QuantStudio™ and ViiA™ 7 export formats

The QuantStudio™ 6 and 7 Flex System Software can export setup and results data from experiment files (.eds) to tab-delimited text files (.txt) in a native QuantStudio™ 6 and 7 Flex System export format (QuantStudio™ 6 and 7) and a legacy QuantStudio™ Dx System and ViiA™ 7 System format (QuantStudio™ Dx / ViiA 7). Data exported in the QuantStudio™ and ViiA™ 7 export formats can be opened by common spreadsheet applications, such as Microsoft® Excel®, or imported by laboratory information management system (LIS) applications or databases that have been configured to parse the file format.

File structure The following table shows the data structure common to data exported in the QuantStudio™ and ViiA™ 7 export formats, regardless of experiment type. Each row represents one or more lines of data in the exported file corresponding to a common functional group. The QuantStudio™ and ViiA™ 7 export formats allow the user to customize and/or omit columns. The columns and orders described below are the default configuration (all columns in their natural order). Actual files may contain fewer columns if the user modified the configuration.

Section Description See…

File header Describes the qualities of the QuantStudio™ 6 and 7 Flex System used to run the experiment and several general experiment properties, such as the date and time of the run and the dye used as the passive reference.

page 60

Sample setup data

Describes the configuration of samples on the experiment consumable, including sample location, target or SNP assay properties, and task assignments.

page 62

Raw data Contains the raw data collected by the QuantStudio™ 6 and 7 Flex System during the experiment run.

page 64

Amplification data

Contains the normalized data collected during the cycling stage of PCR amplification, which the QuantStudio™ 6 and 7 Flex System Software uses to generate the amplification plot.

Note: Not applicable for presence/absence, genotyping, or melting curve experiments that are run without a PCR (cycling) stage.

page 65

Multicomponent data

Contains the spectral data used by the QuantStudio™ 6 and 7 Flex System Software to generate the multicomponent plot that displays the contribution of each dye over the duration of the PCR run.

page 65

Results data Contains the normalized, processed, and analyzed data generated by the QuantStudio™ 6 and 7 Flex System Software.

page 66


Chapter 4 Export File Formats and SpecificationsQuantStudio™ and ViiA™ 7 export formats4

File header The plate setup file begins with a header that describes the qualities of the QuantStudio™ 6 and 7 Flex System used to run the experiment and several other general experiment properties. Each line starts with an asterisk (*) and ends with a carriage return in the following pattern:

* <field name> = <field value>

Note: The QuantStudio™ 6 and 7 Flex System Software automatically removes any leading and trailing white space around the field name and field value.

The header contains the lines listed in the following table.

Field Description Output

Block Type The model of the sample block installed to the QuantStudio™ 6 and 7 Flex System at the time the experiment was run.

96-well, 384-well, or array card (QuantStudio™ 7

Flex System only)

Calibration Date† The date and time that the current background, ROI, uniformity, normalization, or dye calibration was performed and when it will expire.

<date and time>

Calibration Expiration Date†

Calibration Expired† Expiration status of the calibration. Indicates whether the calibration of the QuantStudio™ 6 and 7 Flex System was current at the time that the experiment was run.

Yes or No

Chemistry The chemistry of the experiment. <100-character string>

Date Created The date and time that the QuantStudio™ 6 and 7 Flex System started exporting the experiment.

<date and time>

Experiment Barcode The barcode of the PCR reaction plate or array card entered into the optional Plate Barcode field.


Experiment Comment The comment to associate with the experiment entered into the optional Comment field.


Experiment File Name The path to the experiment file on the local computer hard drive.

<filepath>

Experiment Name The name of experiment entered into the Experiment Name field.


Experiment Run End Time†

The date and time that the QuantStudio™ 6 and 7 Flex System finished running the experiment.

<date and time>

Experiment Type The type of chemistry application for which the experiment is designed.

Standard Curve, Presence/Absence,

Relative Standard Curve, or DDCt Quantification

Instrument Name† The name of the QuantStudio™ 6 and 7 Flex System that ran the experiment.


Instrument Serial Number†

The serial number of the QuantStudio™ 6 and 7 Flex System that ran the experiment.


Instrument Type The model of the QuantStudio™ 6 and 7 Flex System that ran the experiment.

QuantStudio 6 or QuantStudio 7

Passive Reference The dye used as a passive reference (or blank if the consumable did not contain one).


Quantification cycle method

The method of quantification for the associated experiment. <100-character string>



Signal Smoothing On The smoothing setting status for the experiment. Indicates whether smoothing is turned on for the experiment.

true or false

Stage\Cycle where Analysis is performed

The stage and cycle during the thermal cycling protocol when the QuantStudio™ 6 and 7 Flex System collected data.

Stage <integer>, Step <integer>

User Name Name of the user entered into the User Name field. <100-character string>

† This field present only after the experiment has been run.




Sample setup data When selected as an export option, the QuantStudio™ 6 and 7 Flex System Software exports sample setup data after the file header. The sample setup data describes the sample configuration on the experiment consumable, including positions, sample names, task assignments, assay information, and color coding.

The data consists of a column header followed by the sample data fields, where each row contains the data for a single well separated by tab characters. If a well contains more than one assay (target), the QuantStudio™ 6 and 7 Flex System Software lists the data for each additional assay on separate rows, repeating the well number and sample information. The data included in the sample setup data export varies depending on experiment type.

This section describes the following sample setup data formats:

■ Quantification and presence/absence experiments . . . . . . . . . . . . . . . . . . . . . . . . . 62

■ Genotyping experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Quantification and presence/absence experiments

The table below describes the sample setup data that can be exported from absolute quantification, relative quantification, or presence/absence experiments. The body can contain all or some of the data columns below depending on the export configuration.

Note: For genotyping experiments, see “Genotyping experiments” on page 63.

Column Description Output

Well The number of the well on the consumable. Integer (1 to 96/384)†

† Well numbers start at 1 for well A1 (upper-left corner) and increase from left to right and from top to bottom.

Sample Name The name of the sample contained by the well.

100-character string

Sample Color The RGB color of the associated sample. "RGB(<r>,<g>,<b>)"‡

‡ Contains (r)ed, (b)lue, and (g)reen color values, each between 0 to 255. The field is enclosed in double quotes with no spaces between the values.

Target Name The name of one target in the well, if applicable. If a well contains multiple targets one row is used per target.


Target Color The RGB color of the associated assay. "RGB(<r>,<g>,<b>)"‡

Task The task the target is used for in this well. UNKNOWN, STANDARD, IPC, NTC, or BlockedIPC

Reporter The reporter dye that labels the probe for the target assay.


Quencher The quencher dye that labels the probe for the target assay.


Quantity Standard quantity (if applicable). This column only appears for standard curve experiments.

Float or Integer

Comments Additional text that describes the well. 1024-character string




The table below describes the sample setup data that can be exported from a genotyping experiment. The body can contain all or some of the data columns below depending on the export configuration.

Note: For all other experiments, see “Quantification and presence/absence experiments” on page 62.






Sample Color The RGB color of the associated sample. "RGB(<r>,<g>,<b>)"‡

‡ Contains (r)ed, (b)lue, and (g)reen color values, each between 0 to 255. The field is enclosed in double quotes with no spaces between the values.

SNP Assay Name

The name of the SNP assay applied to the well. If the well contains multiple assays, the data for each SNP assay are exported in an additional row.


SNP Assay Color The RGB color of the associated SNP assay. "RGB(<r>,<g>,<b>)"‡

Task The task assignment of the SNP assay at the well.

UNKNOWN or NTC

Allele1 Name The name of the first allele for the associated SNP assay.


Allele1 Color The RGB color of the first allele for the associated SNP assay.

"RGB(<r>,<g>,<b>)"‡

Allele1 Reporter The reporter dye that labels the probe for the first allele.


Allele1 Quencher

The quencher dye that labels the probe for the first allele.


Allele2 Name The name of the second allele for the associated SNP assay.


Allele2 Color The RGB color of the second allele for the associated SNP assay.

"RGB(<r>,<g>,<b>)"‡

Allele2 Reporter The reporter dye that labels the probe for the second allele.


Allele2 Quencher

The quencher dye that labels the probe for the second allele.


Comments Additional text that describes the well 1024-character string



Raw data The QuantStudio™ 6 and 7 Flex System Software can export the unprocessed raw data (R) collected by the QuantStudio™ 6 and 7 Flex System during the experiment run. The raw data consists of fluorescence readings collected by the QuantStudio™ 6 and 7 Flex System that have not been normalized to the passive reference.

The section begins with a column header followed by the raw data, where each row contains the data for a single well separated by tab characters. Each line of raw data consists of readings sorted by bin, where each bin represents an excitation/emission filter pair that was selected during experiment setup. The bins are named for the corresponding filter combination according to the following convention:

<excitation filter name>-<emission filter name>

HRM raw

Note: High resolution melting curve experiments and data are available only through the purchase and installation of the HRM Software Module for the QuantStudio™ 6 and 7 Flex System Software.

The following table describes the raw data exported from high resolution melting curve experiment. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.




Cycle The cycle of the run during which the QuantStudio™ 6 and 7 Flex System recorded the fluorescence.

Integer

<Bin #> The raw fluorescence for the well measured by the QuantStudio™ 6 and 7 Flex System for the associated bin at the designated cycle.

Float




Reading 1-based index of the reading Integer

Temperature Temperature in degrees Celsius Float

Fluorescence Fluorescence value Float

Derivative Value of the fluorescence curve derivative for this reading point

Float



Amplification data The QuantStudio™ 6 and 7 Flex System Software can export the processed amplification data used to generate the amplification plot of a real-time PCR experiment. The amplification data (Rn) are the raw fluorescence readings collected by the QuantStudio™ 6 and 7 Flex System normalized to the fluorescence from the passive reference. If available, the exported amplification data also exports the baseline-compensated normalized fluorescence data (ΔRn) calculated by the software.

The section begins with a column header followed by the amplification data, where each row contains the data for a single well separated by tab characters. If a well contains more than one assay (target), the QuantStudio™ 6 and 7 Flex System Software lists the data for each additional assay on separate rows, repeating the well number and sample information.

Multicomponent data

The QuantStudio™ 6 and 7 Flex System Software can export the data used to generate the multicomponent plot of a real-time PCR experiment. The multicomponent data tracks the raw fluorescence of all reporter dyes present on the reaction consumable throughout the duration of the experiment run.

The section begins with a column header followed by the multicomponent data, where each row contains the data for a single well separated by tab characters. The multicomponent data contains a dye column for each dye present on the reaction consumable, including reporter dyes, quencher dyes (except non-fluorescent dyes), and the passive reference.




Cycle The cycle of the run during which the instrument recorded the fluorescence.

Integer

Target Name

For genotyping experiments, the name of the SNP assay assigned to the well and the allele name.

<SNP assay name>-<allele name>

For all other experiments, the name of the target assigned to the well.

Name of the target

Rn The raw fluorescence for the associated well normalized to the fluorescence of the passive reference dye (reporter signal or passive reference signal).

Float

Delta Rn The baseline compensated Rn value for the associated well

Float




Cycle The cycle of the run during which the QuantStudio™ 6 and 7 Flex System recorded the fluorescence data.

Integer

<Dye name> The raw fluorescence for the designated dye measured by the QuantStudio™ 6 and 7 Flex System at the specified well and cycle.

Float



Results data The QuantStudio™ 6 and 7 Flex System Software can export the results data from an analyzed experiment file. The format and content of the results data depends on the experiment type and the analysis settings.

The section begins with a column header followed by the results data, where each row contains the data for a single well separated by tab characters. If a well contains more than one assay (target), the QuantStudio™ 6 and 7 Flex System Software lists the data for each additional assay on separate rows, repeating the well number and sample information.

This section describes the following results data formats:

■ BioGroup analysis results (study) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

■ Biological replicate results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

■ Genotyping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

■ Melting curve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

■ High resolution melting curve (HRM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

■ HRM aligned . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

■ HRM difference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

■ Presence/absence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

■ Standard curve and comparative CT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

■ Study data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

■ Technical analysis result (study) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

■ Technical replicate results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77



BioGroup analysis results (study)

The following table describes the biological replicate data exported from a study of relative quantification experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.


Biogroup Name

The name of the biological replicate group. 100-character string

Target The name of the target assay assigned to the well.


Task The task assigned to the target in the well. UNKNOWN or NTC

Omitted Indicates whether the well was omitted from the analysis (true) or included (false).

true or false

# Tech Replicates

The number of technical replicates in the associated biological replicate group.

Integer

RQ The relative quantity calculated for the replicate wells of the target/sample combination.

Float

RQ Min The minimum relative quantity calculated for the replicate wells of the target/sample combination. The lower limit of the confidence interval.

Float

RQ Max The maximum relative quantity calculated for the replicate wells of the target/sample combination. The upper limit of the confidence interval.

Float

Ct Mean The average CT of the replicate wells for the specified target/sample combination.

Float

Delta Ct Mean The average ΔCT of the replicate wells for the specified target/sample combination.

Float

Delta Ct SD The standard deviation of the ΔCT for the replicate well. Depending on the analysis settings, this column may by replaced with “Delta Ct SE” (the standard error of the ΔCT).

Float

Delta Delta Ct The ΔΔCT value of the replicate wells for the specified target/sample combination.

Float



Biological replicate results

The following table describes the biological replicate data exported from an experiment. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.


Biogroup Name

The name of the biological replicate group. 100-character string

Target Name The name of the target assay assigned to the well.




Float


Float


Float


Float


Float


Float


Float



Genotyping

The following table describes the results data exported from genotyping experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.






SNP Assay Name The name of the SNP assay added to the well.



Allele1 Rn The raw fluorescence associated with the allele 1 probe of the SNP assay at the well normalized to the fluorescence of the passive reference dye.

Float


Float

Pass. Ref The raw fluorescence of the passive reference at the well.

Float

Quality(%) The confidence of the automatic allele call. Float (1 to 100)

Call The allele call assigned to the sample at the specified well.

Homozygous <allele x/allele x>, Heterozygous

<allele x/allele y>, or Negative Control

(NC)

Method The method used to call alleles. Auto or Manual

Allele1 Automatic Ct Threshold

Whether the allele 1 threshold was determined automatically (true) or manually (false).

true or false

Allele1 Baseline Start

The start cycle used to calculate the baseline section of allele 1.

Float

Allele1 Baseline End

The end cycle used to calculate the baseline section of allele 1.

Float

Allele2 Automatic Ct Threshold

Whether the allele 2 threshold was determined automatically (true) or manually (false).

true or false

Allele2 Baseline Start

The first cycle used to calculate the baseline for allele 2.

Float

Allele2 Baseline End

The last cycle used to calculate the baseline for allele 2.

Float

Custom1… Custom6

The contents of the custom text fields found in the Results table of the experiment.

1024-character string (per field)



Melting curve

The following table describes the results data exported from melting curve experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.




Sample Name The name of the sample contained by the well. 100-character string

Target Name The name of the target assay assigned to the well. 100-character string






CT The calculated threshold cycle (CT) for the target at the specified well.

Float


Float

Ct SD The standard deviation of the average CT of the replicate wells for the specified target.

Float

Quantity • Unknown wells – The calculated quantity for the sample at the well.

• Standard wells – The quantity assigned to the standard at the well.

Float

Quantity Mean • Unknown wells – The average quantity of the replicate wells for the target/sample.

• Standard wells – The quantity assigned to the replicate wells for the target/sample.

Float

Quantity SD The standard deviation of the average quantity of the replicate wells for the target/sample.

Float

Automatic Ct Threshold

Whether the threshold was determined automatically (true) or manually (false).

true or false

Ct Threshold The threshold cycle (CT) for the sample at the well. Float

Automatic Ct Baseline

Whether the baseline was determined automatically (true) or manually (false).

true or false

Baseline Start The first cycle used to calculate the baseline. Integer

Baseline End The last cycle used to calculate the baseline. Integer

Tm1… Tm3 The first, second, and third melting temperatures (Tm) calculated in degrees Celsius.

Float


Custom1… Custom6





High resolution melting curve (HRM)


The following table describes the results data exported from high resolution melting curve experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.












Variant Calls The variant call assigned to the sample at the specified well.

Hetero, Homo 1, or Homo 2

Confidence Value

The calculated confidence of the automatic variant call.

Float (1 to 100)


Float


Float


Float

Number of Flags

The number of quality flags generated by the sample during the analysis.

Integer

Tm Melting point. Float

Tm1… Tm3 The first, second, and third melting temperatures (Tm) calculated in degrees Celsius.

Float


Custom1… Custom6



If analysis flags are present, results data is present in additional columns named for the associated flags.

true or false



HRM aligned


The following table describes the aligned data exported from high resolution melting curve experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.

HRM difference


The following table describes the difference data exported from high resolution melting curve experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.






Aligned Fluorescence

Fluorescence value Float






Difference Difference in fluorescence between the reference curve and the other melt (dissociation) curves

Float



Presence/absence

The following table describes the results data exported from presence/absence experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.












Rn The raw fluorescence for the associated well normalized to the fluorescence of the passive reference dye.

Float

Rn Mean The averaged normalized fluorescence (Rn) for the associated replicate wells that contain the same target/sample combination.

Float

Rn SD The standard deviation of the normalized fluorescence (Rn) for the associated replicate wells that contain the same target/sample combination.

Float

Threshold Value

The calculated value of the threshold for a positive call.

Float

Call The presence/absence call assigned to the sample at the specified well.

Negative Control, Blocked IPC Control, IPC

Failed, Positive, or Negative

Comments Additional text that describes the well 1024-character string


Indicates whether the threshold was determined automatically (true) or manually (false).

true or false

Ct Threshold The threshold cycle (CT) for the sample at the well.

Float


Indicates whether the baseline was determined automatically (true) or manually (false).

true or false

Baseline Start The first cycle used to calculate the baseline. Float

Baseline End The last cycle used to calculate the baseline. Float

Custom1… Custom6





Standard curve and comparative CT

The following table describes the results data exported from standard curve and comparative CT experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.





Target Name The name of the target assay added to the well. 100-character string

Task The task assigned to the target in the well. UNKNOWN, NTC, or STANDARD






Float


Float


Float



Float



Float

Quantity SD The standard deviation of the average quantity of the replicate wells for the target/sample combination

Float


Whether the threshold was determined automatically (true) or manually (false).

true or false

Ct Threshold The threshold cycle (CT) for the sample at the well Float



true or false



Custom1… Custom6



If analysis flags are present, results data is present in additional columns named for the associated flags.

true or false



Study data

The following table describes the results data exported from a study of relative quantification experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.


Experiment Name The name of the of the experiment. 100-character string


Omitted Whether the well was omitted from the analysis (true) or included (false). true or false

Sample The name of the sample contained by the well. 100-character string

Target The name of the target assay assigned to the well. 100-character string


Reporter The reporter dye that labels the probe for the target assay. 100-character string

Quencher The quencher dye that labels the probe for the target assay. 100-character string


Float


Float


Float

Ct The calculated threshold cycle (CT) for the target at the specified well. Float


Float

Delta Ct The ΔCT value of the replicate wells for the specified target/sample combination.

Float


Float


Float


Float



true or false

Ct Threshold The CT for the sample at the well. Float



true or false

Baseline Start The first cycle used to calculate the baseline. Float

Baseline End The last cycle used to calculate the baseline. Float

Efficiency The calculated efficiency of the target assay for the specified target/sample combination.

Float (1 to 100)




Technical analysis result (study)

The following table describes the technical replicate data exported from a study of relative quantification experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.





Omitted Indicates whether the well was omitted from the analysis (true) or included (false).

true or false


Float


Float


Float


Float


Float


Float


Float



Technical replicate results

The following table describes the results data exported from high resolution melting curve experiments. Because columns can be omitted from the results, the exported file may contain a subset of the data columns below.






Float


Float


Float


Float


Float


Float


Float


Chapter 4 Export File Formats and Specifications7900 export format4

7900 export format

The QuantStudio™ 6 and 7 Flex System Software can export setup and results data from experiment files (.eds) to tab-delimited text files (.txt) in a legacy export format of the Applied Biosystems® 7900HT Real-Time PCR System. The 7900 export format features a standardized data structure and markup to maximize accessibility by downstream applications. Data exported in the format can be opened by common spreadsheet applications, such as Microsoft® Excel®, or imported by laboratory information system (LIS) applications that have been configured to parse the file format.

Note: Due to the very different nature of the QuantStudio™ 6 and 7 Flex System some export types are not available.

Note: Column customization (sorting and omission) is not available. Only multiple tab-delimited text files are supported.

Exportable files The following table shows the data files that the QuantStudio™ 6 and 7 Flex System Software can export in the 7900 export format, also designated as the SDS23 export format. Each row represents a single exportable data file.

File Description See…

Setup file Describes the configuration of samples on the experiment consumable, including sample location, target or SNP assay properties, and task assignments.

page 79

Multicomponent file

Contains the spectral data used by the QuantStudio™ 6 and 7 Flex System Software to generate the multicomponent plot that displays the contribution of each dye over the duration of the PCR run.

page 80

Results file Contains the normalized, processed, and analyzed data generated by the QuantStudio™ 6 and 7 Flex System Software.

page 81


Chapter 4 Export File Formats and Specifications7900 export format 4

Setup file When setup file is selected as an export option, the QuantStudio™ 6 and 7 Flex System Software exports sample setup data to a stand-alone file. The sample setup file describes the sample configuration on the experiment consumable, including sample and assay data, positions, and task assignments.

File header

The file begins with several lines, shown in the following table, that describe the experiment file and the QuantStudio™ 6 and 7 Flex System for which it is designed.

*** Setup File Version <version number>*** Output Plate Size <number of wells>*** Output Plate ID <plate id>

Assay (detector) data

The assay data describes the qualities of the target assays present on the consumable. (In the context of the 7900HT System, target assays are referred to as “detectors”.) The section consists of multiple lines that define the total target assays followed by a column header and tab-separated data. The first line defines the total number of target assays on the consumable formatted as follows:

*** Number of Detectors <number of assays>

The column header defines the columns of exported data followed by one or more lines, where each row defines the properties of a single assay separated by tab characters.

Category Component Output

File Version Defines the version of Setup File format used to generate the document.

Integer

Plate Size Defines the number of wells in the plate modeled by the file (for example, 96 or 384).

Integer

Plate ID Defines the ID of the Assay Plate. Normally this is a barcode printed on the plate.



Detector The name of one target in the well, if applicable. If a well contains multiple targets one row is used per target.






Description The standard. 1024-character string

Comments The additional text that describes the well. 1024-character string



Well data

After the assay data, the QuantStudio™ 6 and 7 Flex System Software exports the well data that describes the configuration of samples and assays on the experiment consumable. The table below describes the well data that can be exported from absolute quantification, relative quantification, or presence/absence experiments. If a well contains more than one assay, the QuantStudio™ 6 and 7 Flex System Software lists the setup data for each additional assay in additional columns to the right of the existing data.

Multicomponent file

The QuantStudio™ 6 and 7 Flex System Software can export the data used to generate the multicomponent plot of a real-time PCR experiment. The multicomponent data tracks the raw fluorescence of all reporter dyes present on the reaction consumable throughout the duration of the experiment run.

The file begins with a line that names the export format (SDS 2.3) and the type of data contained by the file (multicomponent). A column header occurs next followed by the multicomponent data, where each row contains the data for a single well separated by tab characters. The multicomponent data contains a dye column for each dye present on the reaction consumable, including reporter dyes, quencher dyes (except non-fluorescent dyes), and the passive reference.





Detector Name

The name of one target assay applied to the well, if applicable.


Task Task the target is used for in this well. UNKNOWN, STANDARD, or NTC

Quantity The standard quantity (if applicable). This column only appears for Standard Curve and Relative Standard Curve experiments

Float or Integer




Time The time in milliseconds after the start of the run when the reading was taken.

Integer

Temp The temperature (°C) of the sample when the QuantStudio™ 6 and 7 Flex System recorded the fluorescence data.

Integer

Cycle The cycle of the run during which the QuantStudio™ 6 and 7 Flex System recorded the fluorescence data.

Integer

<Dye name> The raw fluorescence for the designated dye measured by the QuantStudio™ 6 and 7 Flex System at the specified well and cycle.

Float



Results file When selected as an export option, the QuantStudio™ 6 and 7 Flex System Software exports sample setup data to a stand-alone file. The sample setup file describes the sample configuration on the experiment consumable, including sample and assay data, positions, and task assignments.

File header

The file begins with a line that names the export format (SDS 2.3) and the type of data contained by the file (Std Results). The following lines, listed in the table below, describe the qualities of the QuantStudio™ 6 and 7 Flex System and several other general experiment properties.

The QuantStudio™ 6 and 7 Flex System Software can export the results data from an analyzed experiment file. The format and content of the results data depends on the experiment type and the analysis settings.

The section begins with a column header followed by the results data, where each row contains the data for a single well separated by tab characters. If a well contains more than one assay (target), the QuantStudio™ 6 and 7 Flex System Software lists the data for each additional assay on separate rows, repeating the well number and sample information.

This section describes the following results data formats:

■ Standard curve and comparative CT experiments. . . . . . . . . . . . . . . . . . . . . . . . . . 82

■ Genotyping experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83


Filename The path to the experiment file on the local computer hard drive.

<filename>

PlateID The plate identifier entered into the barcode filed of the experiment.


Assay Type The type of chemistry application for which the experiment is designed.

Genotyping, Standard Curve,

Relative StandardCurve, or DDCt

Quantification

Run Datetime The date and time that the QuantStudio™ 6 and 7 Flex System finished running the experiment.

<date and time>

Operator The user logged into the QuantStudio™ 6 and 7 Flex System Software at the time the experiment was run.


ThermalCycleParams

The thermal cycling profile for the experiment. 96/384-well or array card

(QuantStudio™ 7 Flex System only)



Standard curve and comparative CT experiments

The following table describes the results data exported from standard curve, relative standard curve and comparative CT experiments.





Detector Name

The name of the target assay added to the well.




Task The task assigned to the target in the well. UNKNOWN, NTC, or STANDARD


Float



Float



Float

Quantity SD The standard deviation of the average quantity of the replicate wells for the target/sample combination.

Float

Ct Median The median CT of the replicate wells for the specified target/sample combination.

Float


Float


Float


Indicates whether the baseline was determined automatically (true) or manually (false).

TRUE or FALSE





TRUE or FALSE

Ct Threshold The CT for the sample at the well Float




The following table describes the results data exported from genotyping experiments.





SNP Assay Name

The name of the SNP assay added to the well. 100-character string


Float


Float

Call The allele call assigned to the sample at the specified well.

Homozygous<allele x/allele x>, Heterozygous

<allele x/allele y>, or Negative Control

(NC)

Quality(%) The confidence of the automatic allele call. Float (1 to 100)

Method The method used to call alleles. Auto or Manual


Pass. Ref The raw fluorescence of passive reference at the well.

Float


Chapter 4 Export File Formats and SpecificationsRDML export format4

RDML export format

The QuantStudio™ 6 and 7 Flex System Software can export data from real-time quantitative PCR experiments as well-formed Real-time PCR Data Markup Language (RDML), a structured extensible markup language (XML) standard for quantitative PCR (qPCR) data. In combination with the Minimal Information (MIQPCR) guidelines, the RDML element structure describes all aspects of a qPCR experiment, including setup, analysis, and data interpretation. The exported RDML data is saved as a flat text file that can be used to transfer qPCR data between the QuantStudio™ 6 and 7 Flex System Software and third-party applications.

IMPORTANT! The RDML export format is available only for standard curve, gene expression, and relative standard curve experiments.

For more information

The RDML standard is maintained by the RDML consortium, an organization that consists of key developer groups and a member community. For more information on the RDML format, visit the RDM organization website (www.rdml.org). The website features free data management tools, including an on-line RDML file generator and RDML software libraries.

http://www.rdml.org/


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At the website, you can:

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Index

Numerics7900 export format 78

assay data 79comparative CT data 82file header (results) 81file header (setup) 79file structure 79, 80, 81genotyping experiment data 83multicomponent file 80standard curve data 82well data 80

Aanalysis completed notification 24analysis results exported notification 24ANALYSIS_COMPLETED event type 37application programming interface 10

automation notification 36automation notifications 24automation server 15methods 17web services 15

arguments, command-linebatch file creation 43results exportation 45

assay data7900 export format setup file 79plate setup file 51QuantStudio export format setup file 62ViiA 7 export format setup file 62

assay information file 41AUTHENTICATION_FAILURE return code 17automation notification API 14, 36

messages 37automation server 14, 15automation service 10

Bbarcode file

about 41format 55

barcode reader driver 10barcode verification/mapping 13barcode-to-experiment-file-mapping 10biogroup results (study) data 67biological replicate results data 68broker URI, automation notification API 36

CCALIBRATION_MAINTENANCE_REMINDER

event type 37closeTray method 18command-line application 14

command syntax and arguments 43, 45running 43

comparative CT results data7900 export format file 82QuantStudio export format 74ViiA 7 export format 74

custom application 10barcode verification/mapping 13designing 10interaction 13interfaces 14workflow 12

Ddesigning, custom application 10disable, automation notification API 36

Eenable, automation notification API 36endSession method 18


Index

event typeANALYSIS_COMPLETED 37CALIBRATION_MAINTENANCE_REMINDER

37EXPORT_COMPLETED 37REALTIME_NOTIFICATION 37RUN_COMPLETED 37RUN_STARTED 37RUN_STATUS_CHANGED 37

EXPERIMENT_NOT_FOUND return code 17EXPERIMENT_READ_ERROR return code 17EXPERIMENT_VALIDATION_ERROR return

code 17EXPERIMENT_WRITE_ERROR return code 17export formats 58

7900 file 78QuantStudio file 59RDML file 84ViiA 7 file 59

EXPORT_COMPLETED event type 37

Ffile

assay information 41barcode 41, 55export formats 58import formats 48plate setup 49sample 41, 54setup 41

file structure7900 export format, multicomponent file 807900 export format, results file 817900 export format, setup file 79barcode file format 55plate setup file 49QuantStudio export format 59sample file format 54ViiA 7 export format 59

format7900 export file 78barcode file 55plate setup file 49QuantStudio export file 59RDML export file 84sample file 54ViiA 7 export file 59

Ggenotyping results data

7900 export format 83QuantStudio export format 69ViiA 7 export format 69

getBlockType method 18getInstrumentState method 19

Hheader

7900 export format results file 817900 export format setup file 79plate setup file 49QuantStudio export format 60sample file format 54ViiA 7 export format 60

HRM results data 71aligned data 72difference data 72

Iimport, file formats 48INSTRUMENT_FAIL_TO_START return code 17INSTRUMENT_IN_ERROR return code 17INSTRUMENT_NOT_CONNECTED return code 17INSTRUMENT_PAUSED return code 17INSTRUMENT_READY return code 17INSTRUMENT_RUNNING return code 17INSTRUMENT_TRAY_CLOSED return code 17INSTRUMENT_TRAY_OPENED return code 17INSTRUMENT_UNKNOWN return code 17isTrayIn method 19

Mmelting curve results data 70messages, automation notification API 37methods 17

closeTray 18endSession 18getBlockType 18getInstrumentState 19isTrayIn 19openTray 20return codes 17runExperiment 20runExperimentAsync 21


Index

runExperimentFromTemplate 21runExperimentFromTemplateAsync 22startSession 22stopCurrentExperiment 23

multicomponent file, 7900 export format 80

Nname space URI 15notification server 10notifications 24

analysis completed 24analysis results exported 24run completed 24run started 25

OopenTray method 20

PPASSWORD_EXPIRED return code 17plate setup file

file format 49file structure 49

port name, web services 15presence/absence results data 73

QQuantStudio export format 59

biogroup results (study) data 67biological replicate results data 68comparative CT results data 74file header 60file structure 59genotyping results data 69HRM aligned results data 72HRM difference results data 72HRM results data 71melting curve results data 70presence/absence results data 73sample setup data 62standard curve results data 74study results data 75technical analysis (study) results data 76technical replicate results data 77

QuantStudio™ 6 and 7 Flex System Software 10

RRDML export file format 84REALTIME_NOTIFICATION event type 37recommended deployment 10remote notification listener 10remote notification sender 10return code 17run completed notification 24run started notification 25RUN_COMPLETED event type 37RUN_STARTED event type 37RUN_STATUS_CHANGED event type 37runExperiment method 20runExperimentAsync method 21runExperimentFromTemplate method 21runExperimentFromTemplateAsync method 22

Ssample file 41

file format 54sample setup data

genotyping experiments 63plate setup file 50presence/absence experiments 62quantification experiments 62QuantStudio export format 62sample file format 54ViiA 7 export format 62

schema file, web services 32service name 15SESSION_EXISTING return code 17SESSION_INVALID return code 17setup file 41software interaction 13standard curve results data

7900 export format 82QuantStudio export format 74ViiA 7 export format 74

startSession method 22stopCurrentExperiment method 23study results data 75support, obtaining 85

Ttechnical analysis (study) results data 76technical replicate results data 77


Index

training, information on 85

UUNINITIALIZED return code 17USER_ACCOUNT_DISABLED return code 17

VViiA 7 export format 59

biogroup results (study) data 67biological replicate results data 68comparative CT results data 74file header 60file structure 59genotyping results data 69HRM aligned results data 72HRM difference results data 72HRM results data 71melting curve results data 70presence/absence results data 73sample setup data 62standard curve results data 74study results data 75technical analysis (study) results data 76technical replicate results data 77

Wweb services 10, 14, 15

schema file 32WSDL file 26

web services, workflow 16well data

amplification data 65comparative CT 74, 82genotyping 69, 83HRM 71HRM aligned 72HRM difference 72HRM raw 64melting curve 70multicomponent 65, 80plate setup file 50presence/absence 73raw data 64sample file format 54sample setup data 62setup data 80standard curve 74, 82

study 75workflow, web services 16WSDL

document URL 15file 26

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QuantStudio 6 and 7 Flex System Softwaretools.thermofisher.com/content/sfs/manuals/4489825.pdf · 2013-11-18 · QuantStudio™ 6 and 7 Flex System Software Programming Supplement