Abstract: A system and method generates configurations used for accessing electronic mailboxes. A database stores the configuration conventions that are sets of e-mail expressions formed by symbols. A transformer module expands configuration conventions stored in the database to generate configurations based on user supplied context data.

Abstract: A system is described for providing a wavelength of light that comprises: a scanner that provides a first wavelength; and an optical assembly that emits a second wavelength based, at least in part upon the first wavelength, wherein the second wavelength is not the result of a fluorescent emission.

Abstract: A method for displaying genotype information associated with probe array experiments is described that includes the acts of receiving sets of emission intensity data, wherein each set of emission intensity data includes emission intensity values each associated with a probe disposed upon a probe array; generating genotype calls, wherein each of the genotype calls is based, at least in part, upon the emission intensity values; assembling the genotype calls into one or more genotype data sets; and displaying each of the genotype data sets in one or more panes of a graphical user interface.

Abstract: A genomic web portal provides an ontological map having nodes and edges. The computer-implemented portal system makes use of information correlating one or more probe-set identifiers with a plurality of ontological categories or terms, thereby generating probe-set identifier association data. The probe-set identifiers are associated with one or more probe sets of one or more probe arrays that may be involved in microarray experiments. The system correlates the probe-set identifier association data with graph traversal data and displays an ontological map based on this correlation.

Abstract: A system for analyzing alternative splice variant sequences is described, comprising an input manager for receiving alternative splice variant sequences that are identified by one or more probe sets, a correlator that correlates functional domains with each of the alternative splice variant sequences and an associater that associates putative functions with the alternative splice variant sequences based upon a combination of the functional domains. A method for analyzing alternative splice variant sequences is also described, comprising the acts of receiving alternative splice variant sequences that are identified by one or more probe sets, correlating functional domains with the alternative splice variant sequences and associating putative functions with the alternative splice variant sequences based upon a combination of the functional domains.

Abstract: A method is described that includes the acts of receiving related biological sequences; and representing each of the related biological sequences as objects of a data model, where at least one of the objects is enabled to map at least one of the related biological sequences with at least one other of the related biological sequences.

Abstract: A system for providing an interactive interface for biological sequence information is described that includes a GUI manager to manage and display graphical elements, each associated with a user selection of one or more biological sequences, in the panes of a graphical user interface, where the one or more biological sequences includes a chromosome sequence; and one or more biological sequence tools that provide one or more tools to process information based upon a user selection of at least one of the graphical elements.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Abstract: A system is described that associates grids with a probe array image based upon a positional placement of one or more control features, aligns the grids with one or more pixels based upon a metric value determined by one or more characteristics of the one or more pixels, and generates cell intensity values. The system may also associate grids with a probe array image based upon a positional placement of one or more control features, determine a ratio of pixel intensity values associated with areas of the grid and adjust the positional association of the grid based upon the determined ratio. The system may also associate grids with a probe array image based upon a positional placement of one or more control features and generate cell intensity values based upon weighted pixel intensity values associated with areas of the grid.

Abstract: A computer program analyzes an image including features that correspond to emissions detected from a biological probe array. The program aligns one or more grids, each having one or more grid cells, with all or portions of the image; selects one or more grid cells to be associated with features based on distributions of pixel intensity values within the grid cells; locates a shape, such as a circle, in each selected grid cell based on distributions of pixel intensity values within the grid cells; and associates one or more intensity values with a feature based on intensities of feature pixels, or feature pixels and portions of feature pixels, within the shape located in the selected grid cell associated with the feature. The features may correspond to spots of biological material such as nucleic acid, peptide, protein fragment, protein, antibody, ligand, receptor, or small molecule.

Abstract: A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data, The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

Abstract: The present invention provides a novel growth factor polynucleotide, growth factor polypeptide, gene delivery vehicles comprising and/or expressing the growth factor polynucleotide, antibodies and fragments capable of specifically binding to the growth factor polypeptide, receptors of the growth factor polypeptide, modulators of the growth factor activity, and modulators of growth factor expression. Also provided by the invention are host cells and transgenic organisms comprising the gene delivery vehicle of the present invention. Also provided by the invention are computer readable media containing the polynucleotide or polypeptide sequences of the present invention. Further provided are methods of using these compositions for diagnosis and treatment of growth factor associated diseases.