Abstract: Some embodiments provide methods, systems and computer-readable media that for identifying corresponding distributions of functional subpopulations of cells from high dimensional data across multiple samples and verifying the accuracy of the identified subpopulations.

Abstract: Some embodiments provide methods, systems and computer-readable media that employ adaptive binning and dissimilarity scores based on a quadratic form distance for multidimensional data for matching clusters in data corresponding to different sample. Some embodiments provide methods, systems and computer-readable media for rendering a first interactive display including a two-dimensional plot of at least a portion of a multidimensional data set and a corresponding second interactive display including a plurality of single parameter charts or histograms, each displaying information corresponding to one-dimensional measurements of a different parameter in the multidimensional data set.

Abstract: The described invention provides a method and/or system for analyzing data using population clustering through density based merging, and a method for guiding clustering strategy through entropy-based ranking score.

Abstract: A method for defining distributions of functional subpopulations of cells in a cell population.

Abstract: A method and apparatus for quantitatively measuring differences between portions of a multivariate, multi-dimensional sample distribution, may comprise summarizing the data by dividing the data into clusters each having a signature representative of a position of the cluster and a fraction of the entire distribution within the cluster; matching a plurality of first supplier signatures to a respective one of a plurality of second receiver signatures using a cost factor indicative of the separation between first signature elements and second signature elements; and determining a measurement of the work required to transform the first signature to the second signature. The step of determining a measurement of the work may comprise applying the earth mover distance (“EMD”) algorithm between the first signature or elements of the first signature and the respective second signatures or elements of the respective second signature.

Abstract: Some embodiments provide methods, systems and computer-readable media that employ adaptive binning and dissimilarity scores based on a quadratic form distance for multidimensional data for matching clusters in data corresponding to different sample. Some embodiments provide methods, systems and computer-readable media for rendering a first interactive display including a two-dimensional plot of at least a portion of a multidimensional data set and a corresponding second interactive display including a plurality of single parameter charts or histograms, each displaying information corresponding to one-dimensional measurements of a different parameter in the multidimensional data set.

Abstract: The described invention provides a method and/or system for analyzing data using population clustering through density based merging, and a method for guiding clustering strategy through entropy-based ranking score.

Abstract: The invention provides a system and method for selecting an optimal multimarker reagent combination for the identification and/or quantification of molecules in or on cells with or without reference to fluorescence or other properties of at least one fluorescent dye or other instrument-measurable atom or molecule associated directly or indirectly with the reagent combination. The method includes specifying, using a computer, a plurality of markers to be detected by a plurality of reagents, generating, using a computer, a plurality of reagent combinations comprising the plurality of reagents to detect the plurality of markers, wherein the reagent combinations are ranked according to at least one user-defined or system-defined criterion, and selecting the optimal reagent combination or providing a rank-ordered list of combinations.

Abstract: A method and apparatus for quantitatively measuring differences between portions of a multivariate, multi-dimensional sample distribution, may comprise summarizing the data by dividing the data into clusters each having a signature representative of a position of the cluster and a fraction of the entire distribution within the cluster; matching a plurality of first supplier signatures to a respective one of a plurality of second receiver signatures using a cost factor indicative of the separation between first signature elements and second signature elements; and determining a measurement of the work required to transform the first signature to the second signature. The step of determining a measurement of the work may comprise applying the earth mover distance (“EMD”) algorithm between the first signature or elements of the first signature and the respective second signatures or elements of the respective second signature.

Abstract: The invention provides a system and method for selecting an optimal multimarker reagent combination for the identification and/or quantification of molecules in or on cells with or without reference to fluorescence or other properties of at least one fluorescent dye or other instrument-measurable atom or molecule associated directly or indirectly with the reagent combination. The method includes specifying, using a computer, a plurality of markers to be detected by a plurality of reagents, generating, using a computer, a plurality of reagent combinations comprising the plurality of reagents to detect the plurality of markers, wherein the reagent combinations are ranked according to at least one user-defined or system-defined criterion, and selecting the optimal reagent combination or providing a rank-ordered list of combinations.

Abstract: The present invention is related to databases and the exchange of scientific information. Specifically the invention disclosed a unified scientific database that allows researchers to easily share their data with other researches. The present invention also allows for the ease of data collection, annotation, storage, management, retrieval and analysis of scientific data through and into the database. In addition, it allows for archival storage and retrieval of data collected directly from laboratory instruments to ensure data consistency for patent and other purposes. It also allows for ease of sharing data between laboratories in remote locations. The present invention also supports the automated creation of experimental protocols.

Abstract: A system and method to initialize registers with an EEPROM stored boot sequence is described. The method includes reading configuration records from an EEPROM coupled to an ASIC upon system reset. The configuration records specify target configuration registers and data to be written to the registers. The configuration records are translated to register write requests and data is written to the target registers via a bus of the ASIC to initialize the registers. Other masters, such as a processor, may be blocked from accessing the registers during the initialization.

Abstract: The present invention provides methods of analyzing and/or displaying data. In one aspect, the invention provides methods for visualizing or displaying high dynamic range data obtained from flow cytometry analyses. Related systems and computer programs products are also provided.

Abstract: The present invention is related to databases and the exchange of scientific information. Specifically the invention disclosed a unified scientific database that allows researchers to easily share their data with other researches. The present invention also allows for the ease of data collection, annotation, storage, management, retrieval and analysis of scientific data through and into the database. In addition, it allows for archival storage and retrieval of data collected directly from laboratory instruments to ensure data consistency for patent and other purposes. It also allows for ease of sharing data between laboratories in remote locations. The present invention also supports the automated creation of experimental protocols.

Abstract: A system and method to initialize registers with an EEPROM stored boot sequence is described. The method includes reading configuration records from an EEPROM coupled to an ASIC upon system reset. The configuration records specify target configuration registers and data to be written to the registers. The configuration records are translated to register write requests and data is written to the target registers via a bus of the ASIC to initialize the registers. Other masters, such as a processor, may be blocked from accessing the registers during the initialization.

Abstract: The present invention provides methods of analyzing and/or displaying data. In one aspect, the invention provides methods for visualizing or displaying high dynamic range data obtained from flow cytometry analyses. Related systems and computer programs products are also provided.

Abstract: The present invention is related to databases and the exchange of scientific information. Specifically the invention disclosed a unified scientific database that allows researchers to easily share their data with other researches. The present invention also allows for the ease of data collection, annotation, storage, management, retrieval and analysis of scientific data through and into the database. In addition, it allows for archival storage and retrieval of data collected directly from laboratory instruments to ensure data consistency for patent and other purposes. It also allows for ease of sharing data between laboratories in remote locations. The present invention also supports the automated creation of experimental protocols.

Abstract: This invention relates a series of methods for the visual representation and subsequent application of analyses on complex data sets. In particular, this invention is useful for the analysis of multiple sample sets that share common features, for which similar types of analyses are desired. Three concepts are embodied to aid in this analysis: “Functional equivalence by Algorithmic Polymorphism” (FEAP), in which an analysis algorithm is abstracted through the use of an associated name; a genealogical metaphor for the representation of successive or parallel analysis steps, in which “families” of analyses can be easily copied between different sample data sets; and batch analysis through the creation of multi-sample analysis surrogates (MSAS), which are groups of samples wherein analyses applied to an MSAS is then applied to every sample within the MSAS group.

Abstract: A system for characterizing objects to be sorted in real time and making sorting decisions using lasers to excite fluorescing dyes used to tag objects such as cells which flow through the laser beam in a stream of conductive fluid. The scattered light and fluorescent light at various frequencies define a multidimensional space. These light characteristics are sensed and digitized. The data so gathered is buffered and then compared to a binary classification tree. The individual parameters cause a certain path through the binary decision tree to be taken while the cell is passing from the point in the stream where the light characteristics are gathered to a point where electrostatically charged electrodes deflect individual statically charged drops containing cells to be sorted into various sorting bins. When the decision tree has been traversed, the sorting decision for the drop containing the cell which had those parameters is done.

Abstract: Waste drilling mud is stabilized for earthern burial. The waste drilling mud may be treated by flocculating, aggregating, agglomerating and dewatering the waste drilling mud and separating out free water. The free water may be reused or disposed of in a disposal well. The thickened, dewatered drilling mud solids may be further treated with a water absorbing binder to produce a residue which has sufficient bearing strength to support an earthen overburden and may be disposed of by burial. Suitable flocculating, agglomerating and dewatering polyelectrolytes may be used, including polyacrylamides, quarternary amine polymers and mixtures thereof. The water absorbing binders may include inorganic and organic materials, such as natural and synthetic water absorbing gums, polymers and inorganic colloidal absorbers.