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HRM Software Module for QuantStudio™ 6 & 7 Systems (Applied Biosystems™)

This software module expands the functionality of the QuantStudio™ 6 Flex and QuantStudio™ 7 Flex real-time PCR system software, allowing high resolution melting (HRM) analysis to be performed on PCR amplicons.

High Resolution Melt (HRM) analysis is a new, post-PCR analysis method used for identifying genetic variation in nucleic acid sequences. Simple and fast, this method is based on PCR melt (dissociation) curve techniques and is enabled by the recent availability of improved double-stranded DNA (dsDNA)-binding dyes along with next-generation real-time PCR instrumentation and analysis software. HRM analysis can discriminate DNA sequences based on their composition, length, GC content, or strand complementarity.

High Resolution Melt Software v3.1 (Applied Biosystems™)

High Resolution Melt Software v3.1 is an all-new and improved tool for High Resolution Melting (HRM) analysis. HRM analysis is a post-PCR analysis method used to identify variation in nucleic acid sequences. The method is based on detecting small differences in PCR melting (dissociation) curves. It is enabled by high-brightness, dsDNA-binding dyes used in conjunction with real-time PCR instrumentation that has precise temperature ramp control, advanced data capture capabilities, and access to software designed specifically for HRM analysis. High Resolution Melt Software v3.1 brings HRM to the QuantStudioTM 3 and 5, StepOne™ and StepOnePlus™ Real-Time PCR Systems, and the 7500 Fast Real-Time PCR System, and contains features that make fast and accurate HRM results more accessible than ever.

Key product features:

• Minimal user input to achieve results—software automatically applies default/saved analysis settings upon opening an experiment file
• Easy recall—new Analysis Settings Library saves settings for future experiments
• Greater accuracy—clustering algorithm accurately distinguishes control and variant genotypes
• Increased sensitivity—software allows input of expected number of clusters for difficult-to-detect SNPs (class 4)
• Ability to achieve more in one run—separate analysis of multiple assays run on a single plate
• Shortcuts in experiment setup—direct copy and paste functions with Excel; well information and plate layout clearly displayed in Plate View

Minimize user input to achieve results and easily recall analysis settings
High Resolution Melt Software v3.1 automatically applies default or saved analysis settings upon opening an experiment file, which allows the user to achieve results with minimal input. It also includes a new Analysis Settings Library, allowing the user to save optimized settings and easily recall them for use in future experiments.

Realize greater accuracy and increase your sensitivity
The v3.1 software utilizes an improved clustering algorithm that helps to accurately distinguish control and variant genotypes, and allows the user to input the expected number of clusters for increased sensitivity for difficult SNP genotyping.

Achieve more in one run
With the v3.1 software, you now have the ability to conduct separate analyses of multiple assays run on a single plate.

Get your experiments up and running fast with shortcuts in setup
Users of High Resolution Melt Software v3.1 can copy and paste directly from Excel spreadsheets to set up experiments quickly. Plate View also clearly displays well information and the plate layout to ease plate setup.

Download High Resolution Melt Software v3.1 (license key required) >

See our Release Notes detailing the enhancements offered in v3.1.

For HRM on the 7900HT Fast Real-Time PCR System, see High Resolution Melt Software v2.0.

GenEx Enterprise Software (Applied Biosystems™)

GenEx by Multid Analyses is software for the processing and analysis of real-time qPCR data. Its capabilities range from batch read of data files, basic data pre-processing and management to advanced cutting-edge expression profiling analyses. GenEx software provides methods to select and validate reference genes, classify samples, group genes, monitor time-dependent processes, and much more.

Basic data editing and management
GenEx software v6.1 enables the pre-processing of raw data with consistence, in the correct order, and with confidence. The pre-processing features include interplate calibration, PCR efficiency correction, optimal normalization, genomic DNA background subtraction, outlier detection, and more.

Advanced data analysis
GenEx software offers advanced statistical solutions for post-normalization data analysis. Powerful interactive presentation tools facilitate the generation of professional illustrations of even the most complex experimental designs. Current features include standard curve analyses with estimation of limit of detection (sensitivity), limit of quantification, dynamic range, repeatability and reproducibility, t-test, ANOVA and non-parametric tests with appropriate corrections and estimates of precision, and multivariate statistical tests including Hierarchical Clustering Analysis (HCA), Heatmaps, Principal Component Analysis (PCA), and Artificial Neural Networks (ANN).

GenEx Professional vs. Enterprise
GenEx Professional software provides an extensive set of pre-processing modules together with data visualization and a set of analyses including a larger number statistical analysis modules, suitable for standard curve-based analysis as well as gene expression profiling. GenEx Professional software also contains wizards for direct data import from different instruments.

GenEx Enterprise software contains all modules of GenEx Professional plus the most advanced data analyses, including Dynamic PCA, ROC curve, ANN, and Support Vector Machine (SVM). GenEx Enterprise software also provides modules for data analysis conforming to the Clinical and Laboratory Standards Institute (CLSI) standard documents.

For customers who would like to use GenEx software on multiple PCs, one at a time, GenEx licenses can be pre-installed on a USB key. Install the software on several computers and connect the USB key to the one you want to use at the time. A valid license for GenEx Professional or GenEx Enterprise software is required for purchase of a USB key (Cat. No. A33924).

Learn more about the features of version 6.1 at www.multid.se.
Download the user guide from www.multid.se.

21 CFR Part 11 Software Module for QuantStudio™ 6 & 7 Systems (Applied Biosystems™)

This software module for the QuantStudio™ 6 Flex and QuantStudio™ 7 Flex real-time PCR systems supports compliance with 21 CFR Part 11 FDA guidelines on electronic records security and prevents unauthorized access to the instrument. When loaded on the system, this software will:

• Authenticate each user's log-in information
• Lock out access and require re-authentication if the user is inactive for a set period of time
• Log any unauthorized attempts to access the system software in the Event Log
• Verify each user's permission to perform predefined Controlled Activities
• Permit E-signature function for data verification

High Resolution Melt Software v3.0.1 (Applied Biosystems™)

High Resolution Melt Software v3.0.1 is an all-new and improved tool for High Resolution Melting (HRM) analysis. HRM analysis is a post-PCR analysis method used to identify variation in nucleic acid sequences. The method is based on detecting small differences in PCR melting (dissociation) curves. It is enabled by high-brightness, dsDNA-binding dyes used in conjunction with real-time PCR instrumentation that has precise temperature ramp control, advanced data capture capabilities, and access to software designed specifically for HRM analysis. High Resolution Melt Software v3.0.1 Real-Time PCR Systems, and the 7500 Fast Real-Time PCR System, and contains features that make fast and accurate HRM results more accessible than ever.

Key product features:

• Minimal user input to achieve results—software automatically applies default/saved analysis settings upon opening an experiment file
• Easy recall—new Analysis Settings Library saves settings for future experiments
• Greater accuracy—clustering algorithm accurately distinguishes control and variant genotypes
• Increased sensitivity—software allows input of expected number of clusters for difficult-to-detect SNPs (class 4)
• Ability to achieve more in one run—separate analysis of multiple assays run on a single plate
• Shortcuts in experiment setup—direct copy and paste functions with Excel; well information and plate layout clearly displayed in Plate View

Minimize User Input to Achieve Results and Easily Recall Analysis Settings
High Resolution Melt Software v3.0.1 automatically applies default or saved analysis settings upon opening an experiment file, which allows the user to achieve results with minimal input. It also includes a new Analysis Settings Library, allowing the user to save optimized settings and easily recall them for use in future experiments.

Realize Greater Accuracy and Increase Your Sensitivity
The v3.0.1 software utilizes an improved clustering algorithm that helps to accurately distinguish control and variant genotypes, and allows the user to input the expected number of clusters for increased sensitivity for difficult SNP genotyping.

Achieve More in One Run
With the v3.0.1 software, you now have the ability to conduct separate analyses of multiple assays run on a single plate.

Get Your Experiments Up and Running Fast with Shortcuts in Setup
Users of High Resolution Melt Software v3.0.1 can copy and paste directly from Excel spreadsheets to set up experiments quickly. Plate View also clearly displays well information and the plate layout to ease plate setup.

Download a FREE 30-day trial of High Resolution Melt Software v3.0.1.

See our Release Notes detailing the enhancements offered in v3.0.1.

For users of the 7500 Fast Real-Time PCR System who have already purchased High Resolution Melt Software v3.0, download the HRM v3.0.1 patch.

For HRM on the 7900HT Fast Real-Time PCR System, see High Resolution Melt Software v2.0.

GenEx Professional Software (Applied Biosystems™)

GenEx by Multid Analyses is software for the processing and analysis of real-time qPCR data. Its capabilities range from batch read of data files, basic data pre-processing and management to advanced cutting-edge expression profiling analyses. GenEx software provides methods to select and validate reference genes, classify samples, group genes, monitor time-dependent processes, and much more.

Basic data editing and management
GenEx software v6.1 enables the pre-processing of raw data with consistence, in the correct order, and with confidence. The pre-processing features include interplate calibration, PCR efficiency correction, optimal normalization, genomic DNA background subtraction, outlier detection, and more.

Advanced data analysis
GenEx software offers advanced statistical solutions for post-normalization data analysis. Powerful interactive presentation tools facilitate the generation of professional illustrations of even the most complex experimental designs. Current features include standard curve analyses with estimation of limit of detection (sensitivity), limit of quantification, dynamic range, repeatability and reproducibility, t-test, ANOVA and non-parametric tests with appropriate corrections and estimates of precision, and multivariate statistical tests including Hierarchical Clustering Analysis (HCA), Heatmaps, Principal Component Analysis (PCA), and Artificial Neural Networks (ANN).

GenEx Professional vs. Enterprise
GenEx Professional software provides an extensive set of pre-processing modules together with data visualization and a set of analyses including a larger number statistical analysis modules, suitable for standard curve-based analysis as well as gene expression profiling. GenEx Professional software also contains wizards for direct data import from different instruments.

GenEx Enterprise software contains all modules of GenEx Professional plus the most advanced data analyses, including Dynamic PCA, ROC curve, ANN, and Support Vector Machine (SVM). GenEx Enterprise software also provides modules for data analysis conforming to the Clinical and Laboratory Standards Institute (CLSI) standard documents.

For customers who would like to use GenEx software on multiple PCs, one at a time, GenEx licenses can be pre-installed on a USB key. Install the software on several computers and connect the USB key to the one you want to use at the time. A valid license for GenEx Professional or GenEx Enterprise software is required for purchase of a USB key (Cat. No. A33924).

Learn more about the features of version 6.1 at www.multid.se.
Download the user guide from www.multid.se.

HRM Software Module for ViiA™ 7 System (Applied Biosystems™)

Expands the functionality of the ViiA7 system, allowing High Resolution Melting (HRM) analysis to be performed on PCR amplicons. HRM analysis can discriminate genetic variation by amplicon length, GC content, sequence variability or strand complementarity.

AccuSEQ™ 2.0 Real-Time PCR Software (Applied Biosystems™)

The AccuSEQ™ Real-Time PCR Detection Software is part of a system that performs analytical testing for impurities and contaminants during the biopharmaceutical manufacturing process. Designed to work with the 7500 Fast Real-Time PCR instrument, the software supports the SEQ family of analytical detection and quantitation assays. Security, audit, and signature capabilities help enable 21 CFR compliance. For rapid and accurate Mycoplasma detection, the AccuSEQ™ Software offers a plug-in analysis module for automated presence⁄ absence calls when using the MycoSEQ™ Mycoplasma Detection System. For host cell residual DNA quantitation, a custom module built into the main application can be used with the resDNASEQ™ CHO Residual DNA Quantitation System.

• Automated presence⁄absence calls for Mycoplasma detection
• Accurate quantitation of host cell line residual DNA
• Single software platform for all current and future SEQ Real-Time PCR assays
• Helps enable 21 CFR Part 11 compliance

Automated presence⁄absence calls for Mycoplasma detection
Advanced algorithms built into the AccuSEQ™ Software help enable automated presence⁄ absence calls for Mycoplasma contamination. Developed using the data interpretation guidelines for the MycoSEQ™ Mycoplasma Detection Assay, calls are made based on the Tm and derivative value of the test sample and the Ct value of the test sample and inhibition control. For in-depth review of the data, the AccuSEQ™ Software offers easy-to-use manual review tools, including a complete table of all Tm and Ct values, as well as amplification, multicomponent, and raw data plots. The AccuSEQ™ Mycoplasma SEQ experiment workflow provides a suggested plate layout, generates a reaction setup worksheet and plate layout diagram, includes pre-loaded thermal-cycling settings, and generates a summary of results and detailed reports that can be printed and saved as *.pdf, *.html, *.ppt, and *.xls files (Figure 1).

Automated residual DNA quantitation
Using the custom experiment mode, the AccuSEQ™ Software runs automated residual DNA quantitation experiments. The custom mode guides the user through the experiment and plate setup and provides easy-to-use tools for defining and setting up standards, controls, and unknowns. The user enters the number of concentrations for the standard curve, replicates, starting quantity, and serial dilution factor, and the software automatically sets up the standard curve. A customized template is available for the resDNASEQ™ CHO Residual DNA Quantitation Assay. After the run is complete, the quantities for the unknown samples, mean quantity of replicates, and standard deviation for the replicates are provided in a table format that can be exported as .pdf, .xls, or .txt formats (Figure 2).

Single software platform for all PCR assays
The AccuSEQ™ Software has been designed for use with all current and future SEQ assays through the use of plug-in modules. In combination with the 7500 Fast Real-Time PCR instrument, one platform can be used to run multiple analytical tests that are required to detect impurities and contaminants during the biopharmaceutical manufacturing process.

Helps enable 21 CFR Part 11 compliance
The AccuSEQ™ Software Security, Audit, and Electronic Signature (SAE) Manager (Figure 3) makes it easy to set up and manage the SAE requirements needed for compliance with the 21 CFR Part 11 guidance. These include:
• Security – User name and password restrictions and security policies, such as password expiration and user account suspension.
• Audit – Selection of an audit mode (Prompt⁄Silent), management of audit reasons, and sorting and printing of audit records at the experiment and system level
• Electronic Signature – Selection of an electronic signature mode (Enable⁄Disable), on-demand electronic signature, electronic signature settings, number of electronic signatures required, and electronic signature actions (Review⁄Approve⁄Sign Off) (Figure 3 and Figure 4).

For Research Use Only. Not for use in diagnostics procedures.

Windows™ 7 OS Upgrade Kit for StepOnePlus™ Real-Time PCR System

The Windows® 7 OS Upgrade Kit for StepOnePlus™ Real-Time PCR System allows you to reimage computers running Applied Biosystems® real-time PCR data collection and analysis software to enable them to run using the Microsoft® Windows® 7 operating system (OS).

The kit includes the following:
• Recovery Image of Windows® 7 64 Bit with SP1, 3 Partition, for Dell™ desktop OptiPlex™ XE only
• Recovery Image of Windows® 7 64 Bit with SP1, 3 Partition, for Dell™ Latitude™ E6520 only

Learn more about the procedures for upgrading to the Windows® 7 Operating System [PDF] >

Download Windows® 7 OS compatible StepOne™/StepOnePlus™ Software v2.3 >

7300 System SDS v1.4 Software Upgrade Kit (Applied Biosystems™)

This software upgrades earlier versions of the 7300 SDS Software to provide maximum capability and reliability. Powerful and user-friendly, the 7300 Sequence Detection Software includes:
• Simple plate setup wizard is streamlined for each application – option to setup before or after the completing the run
• Correct plate-setup mistakes after the run without losing collected data.
• One-click graphical export to PowerPoint or JPG for top notch presentations
• Flexible system can be used as a plate reader or a regular thermal cycler if needed
• Real-time amplification monitoring and flexibility to add additional PCR cycles during a run
• Lamp-lifetime monitoring ensures highest possible instrument performance

For Research Use Only. Not for use in diagnostics procedures.

21 CFR Part 11 Software Module for QuantStudio™ 12K Flex System (Applied Biosystems™)

This software module for the QuantStudio™ 12K Flex Real-Time PCR System supports compliance with 21 CFR Part 11 FDA guidelines on electronic records security and prevents unauthorized access to the instrument. When loaded on the system, this software will:

• Authenticate each user’s log-in information
• Lock out access and require re-authentication if user is inactive for a set period of time
• Log any unauthorized attempts to access the system software in the Event Log
• Verify each user’s permission to perform predefined Controlled Activities
• Permits E-signature function for data verification

Primer Express™ Software v3.0.1 License (Applied Biosystems™)

Primer Express Software v3.0.1 allows you to design your own primers and probes using TaqMan and SYBR Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed specifically for use with our StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, and QuantStudio real-time PCR systems, Primer Express Software provides customized application-specific documents for absolute⁄relative quantitation and allelic discrimination.

Download Primer Express Software v3.0.1 (license key required) >
View Release Notes detailing enhancements in v3.0.1 >

• Enables individual oligonucleotide design for real-time PCR applications.
• Supports assays based on TaqMan and SYBR Green I dye chemistries.
• Provides design flexibility, ease-of-use, and requires minimal optimization.
• Provides robust assay performance when used in accordance with Assay Development Guidelines.

Easy-to-Learn Software
Primer Express Software v3.0.1 is flexible, easy to learn and to use, and requires minimal optimization. It includes an algorithm optimized specifically for use with TaqMan-based reagents, recommended primer⁄probe concentrations, and default thermal cycling conditions. Primer Express Software also supports assays based on the SYBR Green I dye. This minimizes the need for assay optimization and streamlines the design process.

The software also allows customized designs if the probe and⁄or one or more primers are known. Default and adjustable parameters (Figure 1) provide the flexibility required for all users.

Simple to Use
Simplicity and flexibility are the hallmarks of Primer Express Software v3.0.1, which is fully compatible with all StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, and QuantStudio real-time PCR systems. Whether your research includes gene quantitation or allelic discrimination studies, Primer Express Software belongs in your lab.

Automated and Manual Primer⁄Probe Design
The Primer Express Software v3.0.1 will design your primers and probes automatically, or you can design them manually. For automated design, simply choose either TaqMan or TaqMan MGB assays. If you know the sequence, you need only to import (or copy and paste) the sequence and quickly view your results. Alternatively, if you prefer to design the primers and probes manually, the procedure is equally simple and straight-forward as well.

Compatibility with Assay Development Guidelines
Primer Express Software v3.0.1 was designed to be compatible with standard guidelines for use of our real-time PCR instruments and reagents. These guidelines are such that traditional variables, including magnesium chloride concentration and the thermal cycling protocol, should be standardized by using a master mix of reagents (enzyme, salts, buffer) and tailored primer and probe design. This approach substantially reduces assay development time and improves laboratory efficiency by allowing multiple assays per plate to run simultaneously as all require the same conditions.

Protein Thermal Shift™ Software v1.3 (Applied Biosystems™)

The Protein Thermal Shift™ Software v1.3 was developed to analyze protein melt fluorescent readings directly from Applied Biosystems® real-time PCR instrument files. Different proteins will have different Protein Thermal Shift™ profiles, each with a unique protein melt curve shape, slope, signal-to-noise ratio, and temperature melt range (see figure below for an example). The Protein Thermal Shift™ Software generates one or multiple melting temperature values (Tm) from these curves by two methods: the Boltzmann-derived Tm and the Derivative Curve-determined Tm, to serve as points of comparison between the curves and represent the relative thermal stability of the protein under different testing conditions.

>> Download a trial version (Registration required)
>> Download the software (License required)

Two Methods for Generating Tm Values
The Boltzmann method fits the data within an automatic (or manually) identified melt region to the two-state Boltzmann model to generate the Tm. Typically, for proteins with a single melt domain, the Boltzmann method is used. However, for proteins with multiple melt domains, the Derivative Curve method can be used. The Derivative Curve method uses a numerically-computed second derivative of the raw data to estimate the temperatures where up to six peaks (local maxima) may occur in the derivative profile. An empirically-derived threshold on the signal-to-noise ratio is used to determine which local maxima will be detected.

Compatible with our Real-Time PCR Systems
The Protein Thermal Shift™ analysis software is compatible with run files generated from these real-time PCR systems: QuantStudio™ 3, 5, 6, 7, and 12K Flex, StepOne™, StepOnePlus™, 7500, 7500 Fast, and ViiA™7.

Prepare Your Samples Using our Protein Thermal Shift™ Kits
Prepare your samples for analysis using our Protein Thermal Shift™ Starter Kit or Protein Thermal Shift™ Dye Kit (available separately). These kits allow users to employ a dye that binds to exposed hydrophobic residues to monitor the thermal stability of proteins using a real-time PCR instrument to identify buffer conditions that stabilize the protein of interest or screen libraries of ligands for compounds that bind the protein of interest.

DigitalSuite™ Software (Applied Biosystems™)

DigitalSuite™ Software is a state-of-the-art analysis package specifically designed to streamline the analysis and interpretation of digital data generated using a QuantStudio™ Digital PCR Kit on the QuantStudio™ 12K Flex instrument. The software is tightly integrated with the instrument platform, providing a seamless workflow from experiment start to finish, enabling the user to easily and rapidly import digital data into experimental studies. This software also enables the user to define the experimental plate setup; generate absolute results output in copies per sample, including 95% confidence intervals around this estimate; directly access real-time data for data QC purposes; and export the data for further downstream analysis.

If you have purchased a license, you may download the software here:

>> Download DigitalSuite™ Software v1.0.4

>> Download DigitalSuite™ Software v1.0.5 for Win 7 64 Bit

DigitalSuite™ Software Release Notes

If you have not purchased a license, you may download a trial version here:

>> Download a trial version of the software

Key Benefits:

• Seamless integration into QuantStudio™ Data Collection and Analysis Software
• One-click launch from within QuantStudio™ software
• Study-based format consistent with other QuantStudio™ software reduces need to learn new functionality
• Streamlined workflow
• Minimized steps to answer simplifies analysis
• Direct calculation of target copies/ µL provides absolute target quantification
• Access to real-time data from within DigitalSuite™ software enables direct user review of critical data during QC process
• Extensive data visualization
• View plate heatmaps, bar graphs, and cluster plots
• Use visual interfaces to interactively explore data
• User configurable
• Preset defaults can be adjusted to user needs, supporting a wide variety of experiment designs and analysis requirements

High Resolution Melt (HRM) App (Applied Biosystems™)

The High Resolution Melt (HRM) App hosted on Thermo Fisher Cloud is a tool for HRM analysis, which is a post-PCR analysis method used to identify variation in nucleic acid sequences. The method is based on detecting small differences in PCR melting (dissociation) curves. It is enabled by high-brightness, dsDNA-binding dyes used in conjunction with real-time PCR instrumentation that has precise temperature ramp control, advanced data capture capabilities, and access to software designed specifically for HRM analysis.

Key product features:
Minimal user input—app automatically applies default/saved analysis settings upon opening an experiment file
High accuracy—clustering algorithm accurately distinguishes control and variant genotypes
High sensitivity—app allows input of expected number of clusters for difficult-to-detect SNPs (class 4)
Efficiency—analyze multiple runs simultaneously and visualize the data

Minimize user input and easily recall analysis settings
The HRM App automatically applies default or saved analysis settings upon opening an experiment file, which allows you to achieve results with minimal input.

Realize high accuracy and sensitivity
The HRM App uses the same clustering algorithm as the desktop version, which helps to accurately distinguish control and variant genotypes, and allows the user to input the expected number of clusters for increased sensitivity for difficult SNP genotyping. It also offers data compatibility with the desktop version.

Achieve more with less work
With the HRM App, you can analyze multiple plates simultaneously. Unlike the desktop version, you can access an additional set of data review tools, such as those for amplification plots and multicomponent data.

App subscription
The following subscription plans are available at rates for 1 user or 10 users. (Please contact us if our available plans do not meet your needs.) A free trial is available for first-time users. The Terms and Conditions for Software Application Subscription Plans on the Thermo Fisher Cloud apply to each subscription plan described below:

Auto-renewal Monthly:This plan is charged month-to-month. Each month is paid up front and the subscription auto-renews every month. This plans provides the most flexibility with the lowest up-front costs.
Auto-renewal Annual: This plan is charged once a year. Each year is paid up front and auto-renews every year. This plan is more cost-effective than the month-to-month plan.
Termed Contract for One Year or Five Years: With this plan the entire term of the contract is paid up front and does not renew. This plan is most suitable when a capital expenditure is more desirable than smaller recurring payments.