Abstract: Provided herein is a method for identifying a sequence variant in an enriched sample. In certain embodiments, this method may comprise: (a) obtaining: (i) a plurality of sequence reads from a sample that has been enriched for a genomic region and (ii) a reference sequence for the genomic region; (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies that correspond to potential variants; (c) determining which of the potential variants are true and which are artifacts by examining the sequence reads that make up each of the discrete sequence assemblies; (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and (e) outputting a report indicating whether the sample comprises a sequence variant.

Abstract: Aspects of the present innovations relate to systems and/or methods involving multimedia modules, objects or animations. According to an illustrative implementation, one method may include accepting at least one input keyword relating to a subject for the animation and performing processing associated with templates. Further, templates may generates different types of output, and each template may include components for display time, screen location, and animation parameters. Other aspects of the innovations may involve providing search results, retrieving data from a plurality of web sites or data collections, assembling information into multimedia modules or animations, and/or providing module or animation for playback.

Abstract: Aspects of the present innovations relate to systems and/or methods involving multimedia modules, objects or animations. According to an illustrative implementation, one method may include accepting at least one input keyword relating to a subject for the animation and performing processing associated with templates. Further, templates may generates different types of output, and each template may include components for display time, screen location, and animation parameters. Other aspects of the innovations may involve providing search results, retrieving data from a plurality of web sites or data collections, assembling information into multimedia modules or animations, and/or providing module or animation for playback.

Abstract: Aspects of the present innovations relate to systems and/or methods involving multimedia modules, objects or animations. According to an illustrative implementation, one method may include accepting at least one input keyword relating to a subject for the animation and performing processing associated with templates. Further, templates may generates different types of output, and each template may include components for display time, screen location, and animation parameters. Other aspects of the innovations may involve providing search results, retrieving data from a plurality of web sites or data collections, assembling information into multimedia modules or animations, and/or providing module or animation for playback.

Abstract: Aspects of the present innovations relate to systems and/or methods involving multimedia modules, objects or animations. According to an illustrative implementation, one method may include accepting at least one input keyword relating to a subject for the animation and performing processing associated with templates. Further, templates may generates different types of output, and each template may include components for display time, screen location, and animation parameters. Other aspects of the innovations may involve providing search results, retrieving data from a plurality of web sites or data collections, assembling information into multimedia modules or animations, and/or providing module or animation for playback.

Abstract: Provided herein, among other things, is a computer-implemented method for assigning a sequence read to a genomic location, the method including: a) accessing a file containing a sequence read, wherein the sequence read is obtained from a nucleic acid sample that has been enriched by hybridization to a plurality of capture sequences; and b) assigning the sequence read to a genomic location by: i) identifying a capture sequence as being a match with the sequence read if the sequence read contains one or more subsequences of the capture sequence; ii) calculating, using a computer, a score indicating the degree of sequence similarity between each of the matched capture sequences and the sequence read; and iii) assigning the sequence read to the genomic location if the calculated score for a matched capture sequence is above a threshold.

Abstract: Provided herein is a method for identifying a sequence variant in an enriched sample. In certain embodiments, this method may comprise: (a) obtaining: (i) a plurality of sequence reads from a sample that has been enriched for a genomic region and (ii) a reference sequence for the genomic region; (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies that correspond to potential variants; (c) determining which of the potential variants are true and which are artifacts by examining the sequence reads that make up each of the discrete sequence assemblies; (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and (e) outputting a report indicating whether the sample comprises a sequence variant.

Abstract: Methods, systems and computer readable media for quantifying and removing offset bias signals in a chemical array data set having one or more channels. In one embodiment, for each channel of data in the data set, a first set of features is selected from the data set. Surface intensities are calculated for features in the first selected set of features and surface intensifies of features not in the first selected set are calculated from the calculated surface intensities. A second set of features is selected, the intensity values of which are within a range of correspondingly located surface intensity values defined by upper and lower threshold intensities. Secondary surface intensifies are calculated for features in the second selected set of features and secondary surface intensities for all other locations on the array that were not locations corresponding to the features having secondary surface intensities calculated therefore, are calculated.

Abstract: A method to allow an analyst or other user of molecular-array data to directly tailor pixel-intensity integration of scanned pixel-based representations of features of a molecular array to produce feature signals. The method is embodied in a graphical user interface that allows an analyst or other molecular-array user to input pixel-intensity-weighting functions into a computational system that applies the weighting functions prior to producing integrated feature signals. The GUI provides a user with the ability to select the origin of a feature-centric rectilinear coordinate system, to input a function that specifies the function that is applied to the raw pixel intensities within the region of interest prior to integration of the pixel intensities within the region of interest to produce a feature signal.

Abstract: Methods, systems and computer readable media for quantifying and removing offset bias signals in a chemical array data set having one or more channels. In one embodiment, for each channel of data in the data set, a first set of features is selected from the data set. Surface intensities are calculated for features in the first selected set of features and surface intensifies of features not in the first selected set are calculated from the calculated surface intensities. A second set of features is selected, the intensity values of which are within a range of correspondingly located surface intensity values defined by upper and lower threshold intensities. Secondary surface intensifies are calculated for features in the second selected set of features and secondary surface intensities for all other locations on the array that were not locations corresponding to the features having secondary surface intensities calculated therefore, are calculated.

Abstract: Methods systems and computer readable media for manipulating and displaying sparse data contained within very large datasets. Particular applications includes those to proteomics and metabolomics. Navigation of the large data sets from a global perspective may be practically implemented, so that a user is not confined to a narrow slice of data at a time, thus providing context of the whole dataset while viewing data within the dataset.

Abstract: Systems, methods and computer readable media for extracting data from features on a chemical array, using a feature extraction module including feature extraction algorithms configured to calculate characteristics of array features. A reference table is provided that associates probe names of probes contained on the array with at least one additional identifier. The reference table is accessible by the feature extraction module to convert any one of the at least one additional identifiers to the probe names, and the probe names to at least one of the at least one additional identifiers.

Abstract: Methods, systems and computer readable media for automatically feature extracting array images in batch mode. At least two images to be feature extracted are loaded into a batch project, and the system automatically and sequentially feature extracts the images in the batch project. At least one of the images may be feature extracted based upon a different grid template or protocol than at least one other of the images. Methods, systems and computer readable media are provided to automatically feature extract a single array image having an identifier indicating that it is a multipack, multiple array image. A system provided for feature extracting array images in batch mode includes a user interface with a feature enabling a user to select images to be loaded into a batch project; and based upon the loaded images in the batch project, the system may automatically assign a grid template to each image loaded into the batch project.

Abstract: Methods systems and computer readable media for manipulating and displaying sparse data contained within very large datasets. Particular applications includes those to proteomics and metabolomics. Navigation of the large data sets from a global perspective may be practically implemented, so that a user is not confined to a narrow slice of data at a time, thus providing context of the whole dataset while viewing data within the dataset.

Abstract: Methods, systems and computer readable media for aligning an array for determining a layout of features of the array, which are provided in a two-dimensional array. A first block of features of the array is selected, the first block having a predefined width in the direction of one of the X and Y axes, and a length sufficient to extend over all of the features in the direction of the other of the X and Y axes. A second block of features is selected, the second block having a predefined width in the same direction as the width of the first block, and a length sufficient to extend over all of the features in the direction of the other of the X and Y axes, wherein the second block contains features not contained by the first block. The features contained in the first block are projected in the direction of the width of the first block and the features contained in the second block are projected in the direction of the width of the second block.

Abstract: Systems, methods and recordable media for fast, automatic grid finding of microarrays, based on reducing the dimensionality of the image data.

Abstract: A method to allow an analyst or other user of molecular-array data to directly tailor pixel-intensity integration of scanned pixel-based representations of features of a molecular array to produce feature signals. The method is embodied in a graphical user interface that allows an analyst or other molecular-array user to input pixel-intensity-weighting functions into a computational system that applies the weighting functions prior to producing integrated feature signals. The GUI provides a user with the ability to select the origin of a feature-centric rectilinear coordinate system, to input a function that specifies the function that is applied to the raw pixel intensities within the region of interest prior to integration of the pixel intensities within the region of interest to produce a feature signal.

Abstract: Mass spectometer system and method of use are disclosed. Briefly described, one embodiment of the mass spectrometry system, among others, includes a radio frequency multipole assembly, an inner structure, and a laser diode array system. The inner structure has an outside, an inside, and an opening. The inner structure substantially surrounds the radio frequency multipole assembly. The laser diode array system is disposed on the outside of the inner structure adjacent the side opening such that laser radiation emitted from the laser diode array system travels through the side opening.

Abstract: A technique for analyzing ions by determining the time of flight of the ions in a time of flight mass spectrometer using internal calibration. In the technique, a calibration step includes the steps of launching a packet of ions from a source to a detector, detecting the time needed for the ions to arrive at the detector to obtain a time-of-flight mass spectrum, and selecting data from the mass spectrum corresponding to a plurality of ions of consecutive masses and use the selected data to determine the relationship between time of flight data and the masses of the ions of consecutive masses for calibration of the relation between times of flight and masses in the mass spectrometer.

Abstract: A technique for analyzing ions by determining the time of flight of the ions from a source before detection at a detector. In the technique a series of pulses is generated according to an encoded sequence. Pulses from the series of pulses are selected to launch a plurality of packets of ions from the source, each of the selected pulses launching a packet of ions such that ions launched in the adjacent packets overlap prior to reaching the detector. At the end of the series another cycle of the series is generated again and some of the pulses in the series are selected in the another cycle to launch a plurality of packets of ions from the source. The cycles of pulse generation and selection to launch ions are repeated. The time of arrival of the ions of each packet in the detector is determined to obtain signals corresponding to overlapping spectra of the time of arrival of the packets of ions.