Abstract: A computer-implemented method for generating a data visualization for operating a digital polymerase chain reaction (dPCR) system comprises, the method comprising receiving fluorescent emission data comprising a plurality of data points corresponding to fluorescence emission from a plurality of reaction sites of a substrate, the fluorescent emission data indicative of presence or absence of amplification product of a dPCR. The method further comprises displaying a data visualization of the plurality of data points in a spatial representation of the substrate such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites of the substrate, a first set of data points being displayed with a first indication based on meeting a first quality value threshold and second set of data points being displayed with a second indication, differing from the first indication, based on a second quality value threshold.

Abstract: A method comprises displaying, on a graphical user interface (GUI), a first data visualization comprising a positional representation of a plurality of reaction sites from at least a portion of a substrate, wherein the positional representation of the first data visualization simultaneously indicates relative data quality of the plurality of reaction sites; and altering the first data visualization displayed on the GUI to a second data visualization, the second data visualization comprising the positional representation of the plurality of reaction sites from the at least the portion of the substrate, wherein the positional representation of the second data visualization simultaneously indicates relative data quality of the plurality of reaction sites from at least the portion of the substrate based on a comparison of the data quality values of the plurality of reaction sites an adjusted quality value threshold.

Abstract: In one exemplary embodiment, a method computer-implemented method of generating an outlier wheel data visualization for a graphical user interface (GUI) is provided. The method includes receiving emission data from a plurality of amplification reactions. The method further includes generating an outlier wheel data visualization using the emission data including a plurality of lines, where each line included in the outlier wheel data visualization represents emission data from an amplification reaction of the plurality of amplification reactions, and each line having a length and a visual indicator. The length of each line represents growth of intensity of fluorescence of the emission data and the visual indicator indicates the associated cycle number of the emission data. Further, each line is associated with an angular position so that the plurality of lines is configured in a circular shape. The method includes displaying the outlier wheel data visualization on a GUI.

Abstract: A method for generating a data visualization is provided. The method includes receiving a plurality of data points related to fluorescent emissions values from a plurality of reaction sites. The fluorescent emission values include information for a first type of dye and a second type of dye. The method further includes displaying a first portion of the plurality of data points related to the first type of dye in a representation of location of the plurality of reaction sites, and displaying a second portion of the plurality of data points related to the second type of dye in the representation. The method further includes displaying the first portion of the plurality of data points in a scatter plot display. The scatter plot shows fluorescent values related to the first dye on the y-axis and fluorescent values related to the second dye on the x-axis. The method includes displaying the second portion of the plurality of data points in the scatter plot display.

Abstract: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

Abstract: In one exemplary embodiment, a method computer-implemented method of generating an outlier wheel data visualization for a graphical user interface, GUI, is provided. The method includes receiving emission data from a plurality of amplification reactions. The method further includes generating an outlier wheel data visualization using the emission data including a plurality of lines, where each line included in the outlier wheel data visualization represents emission data from an amplification reaction of the plurality of amplification reactions, and each line having a length and a visual indicator. The length of each line represents growth of intensity of fluorescence of the emission data and the visual indicator indicates the associated cycle number of the emission data. Further, each line is associated with an angular position so that the plurality of lines is configured in a circular shape. The method includes displaying the outlier wheel data visualization on a GUI.

Abstract: Systems and methods are described for quantifying a target nucleic acid. A sample comprising a target nucleic acid is segregated into a first plurality of the reaction volumes containing at least one target nucleic acid molecule and a second plurality of the reaction volumes containing no target nucleic acid molecules. The reaction volumes are subjected to an amplification assay, wherein the amplification assay is configured to amplify the target nucleic acid. An indicator of amplification is detected or measured in at least some of the plurality of reaction volumes. The target nucleic acid is quantified based on the detection or measurement. After discontinuing the amplification assay, the plurality of reaction volumes may be heated and changes in the indicators of amplification of two or more of the at least some of the reaction volumes may be detected or measured.

Abstract: System and methods for the determination of a copy number of a target genomic sequence; either a target gene or genomic sequence of interest, in a biological sample are described. Various methods utilize a model drawn from a probability density function (PDF) for the assignment of a copy number of a target genomic sequence in a biological sample. Additionally, the methods provide for the determination of a confidence value for a copy number assigned to a sample based on attributes of the sample data. Additionally, various embodiments of an interactive graphical user interface (GUI) may provide an end-user with ready analysis of large sets of data representing a plurality of samples. In various embodiments of an interactive GUI, an end-user may be provided with a synchronized display of tabular and graphical sample data determined by an initial analysis according to a statistical model of a PDF.

Abstract: A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.

Abstract: Systems and methods are described for quantifying a target nucleic acid. A sample comprising a target nucleic acid is segregated into a first plurality of the reaction volumes containing at least one target nucleic acid molecule and a second plurality of the reaction volumes containing no target nucleic acid molecules. The reaction volumes are subjected to an amplification assay, wherein the amplification assay is configured to amplify the target nucleic acid. An indicator of amplification is detected or measured in at least some of the plurality of reaction volumes. The target nucleic acid is quantified based on the detection or measurement. After discontinuing the amplification assay, the plurality of reaction volumes may be heated and changes in the indicators of amplification of two or more of the at least some of the reaction volumes may be detected or measured.

Abstract: A method for determining false positives calls in a biological data plot is provided. The method includes identifying a first data cluster as non-amplification data points within the biological data plot and identifying a second data cluster as wild-type positives within the biological data plot. The method further includes estimating a position in the biological data plot of a center of the first and second data clusters. The method further includes determining, for each data point within the first data cluster, a probability of belonging to the first data cluster and determining, for each data point within the second data cluster, a probability of belonging to the second data cluster. The method includes applying a probability threshold for each data point within the first and second data cluster to identify false positives.

Abstract: A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.

Abstract: A system for analyzing biological data, comprising: a storage configured to store a plurality of data files containing biological data obtained from a plurality of devices; a server configured to: host a plurality of applications, each configured to be implemented on the server and to provide analysis, manipulation, comparison, visualization, or a combination thereof, of the biological data included in the data files, wherein the plurality of applications allow a user to analyze different data files related to the same sample and compare the results of the analysis.

Abstract: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

Abstract: In some embodiments, a method or system for visualizing data generated from one or more reaction devices, chips, or reaction sites may be provided. On a scatter plot, data points may be displayed indicative of results from nucleic amplification, wherein the nucleic acid amplification comprises a first target and a second target and the data points are designated as being indicative of amplification of the first target, the second target, both targets, or neither target. In response to user input, an adjustable threshold may be varied used to designate the data points. And, in response to the varying, designations and a display of the designations may be altered for one or more of the data points whose designation is changed based on the varied threshold.

Abstract: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

Abstract: In one exemplary embodiment, a method computer-implemented method of generating an outlier wheel data visualization for a graphical user interface, GUI, is provided. The method includes receiving emission data from a plurality of amplification reactions. The method further includes generating an outlier wheel data visualization using the emission data including a plurality of lines, where each line included in the outlier wheel data visualization represents emission data from an amplification reaction of the plurality of amplification reactions, and each line having a length and a visual indicator. The length of each line represents growth of intensity of fluorescence of the emission data and the visual indicator indicates the associated cycle number of the emission data. Further, each line is associated with an angular position so that the plurality of lines is configured in a circular shape. The method includes displaying the outlier wheel data visualization on a GUI.

Abstract: A method for performing digital polymerase chain reaction (dPCR) is provided. The method includes partitioning a biological sample volume including a plurality of target nucleic acids into a plurality of partitions, where at least one partition includes at least one target nucleic acid. The method further includes determining a model for volume variation of the plurality of partitions and determining a number of partitions including at least one target nucleic acid. The method includes generating a concentration of target nucleic acids in the biological sample based on the model for volume variation and the fraction of partitions including at least one target nucleic acid.

Abstract: The present teachings relate to embodiments of systems and methods for the analysis of melt curve data for a plurality of samples. According to various embodiments, a melting temperature (Tm) may be determined across a range of different types of protein melt curve data, having variability over a plurality of analytical attributes in order to accommodate the complexity of protein melt curve data. The combination of a plurality of samples, coupled with the complexity of the data gives rise for a need to process the data in a manner that readily facilitates end-user to analysis of the data. Various embodiments of an interactive graphical user interface (GUI) according to the present teachings provide for rapid and sequential changes that may be made by an end user to displayed protein melt curve data to allow such analysis.