Abstract: A system and method for performing domain-specific knowledge based metasearches. A metasearch engine is provided for accessing a searching text-based documents using generic search engines while simultaneously being able to access publication based databases and sequence databases as well as in-house proprietary databases and any database capable of being interfaced with a web interface so as to produce search results in text format. A data mining module is also provided for organizing raw data obtained by unsupervised clustering, simple relevance ranking, and categorization, all of which are done independently of one another. The system is capable of storing previous search data for use in query refinement or subsequent searches based upon the stored data. A search results collection browser may be provided for analyzing current browsing patterns of the user for developing weighting factors to be used in ordering the results of future searches.

Abstract: Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Abstract: Methods, reagents and kits are disclosed for selecting target-specific oligonucleotide probes, which may be used in analyzing a target nucleic acid sequence. In one aspect the present invention is directed to selecting a set of target-specific oligonucleotide probes. A cross-hybridization oligonucleotide probe is identified based on a candidate target-specific oligonucleotide probe for the target nucleic acid sequence. The cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event having a predetermined probability. Cross-hybridization results are determined employing the cross-hybridization oligonucleotide probe and the target-specific oligonucleotide probe. The target-specific oligonucleotide probe is selected or rejected for the set based on the cross-hybridization results.

Abstract: Methods, systems and computer readable media for statistically analyzing apparent anomalies in CGH data, wherein the CGH data is ordered corresponding to locations of matter on chromosomes from which the CGH data was derived. A set of CGH ratio values is considered and Z-score values are computed for each CGH ratio value. The Z-score values are classified based upon a predetermined cutoff value. The number of Z-scores that are greater than the predetermined cutoff value are counted, the number of Z-scores that are less than a negative of the predetermined cutoff value are counted, and the total number of Z-scores are counted. A subset of the set of CGH ratios are considered, being defined by a window of predetermined size. A secondary Z-score is computed to measure the significance of at least one of overabundance and underabundance of at least one of significant positive deviations and significant negative deviations in the subset.

Abstract: Systems, methods and recordable media for interactively importing, creating, and manipulating biological diagrams. Such diagrams may be used for linking and navigating to other sources of biological information.

Abstract: Methods, systems and computer readable media for visualizing multiple data values adjacent graphical representations of entities in a diagram representing biological relationships between the entities. A diagram of interconnected entities representing biological relationships between the entities is displayed. A data set having rows of data values, each row containing values representing a single entity is provided, wherein at least some of the entities are represented on the diagram. At least one row of data values from the dataset is overlaid on the displayed diagram such that the row of data values appears adjacent the entity on the diagram that matches the entity in the data set that the row of data characterizes. The display of the row of data values is scaled so that components of the display are dimensionally proportional to numerical values of the data values taken from the data set.

Abstract: Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.

Abstract: A method and system for generating virtual-microarray feature data from a virtualizing catalog array comprising a catalog microarray associated with data that can be together processed to produce any of numerous sets of virtual-microarray feature data. The catalog array portion of the virtualizing microarray may include many thousands, tens of thousands, or hundreds of thousands of different features from which a very large number of feature subsets may be generated. The data associated with the virtualizing microarray allows for rapid and transparent partitioning of the catalog-microarray features. Logic included within a microarray scanner, a computer system used to process data scanned from microarrays, a microarray-data visualization system, or other microarray-related processing entities can be used to generate feature data for any number of user-specified virtual arrays based on partitioning of the features included in the catalog-microarray component of the virtualizing microarray.

Abstract: Systems and methods for displaying gene- and/or protein-related data with respect to chromosome maps at locations identifying relevant positioning of the genes with which the gene- and/or protein related data are associated. Multiple experiments may be plotted onto the display adjacent one or more chromosome maps. Automatic extraction of genomic location, based on accession numbers or other unique identifiers and cross connection with expression data is provided. Statistical assessments of correlations between expression and genome localization may be performed. Zooming capabilities, thumbnail/fullview toggling, browsability and linked data may be included as features of the visualization systems described.

Abstract: A system and methods for selecting single-features from a microarray scan image of genomic data and rearranging the selected single-features of the microarray into a virtual array having a format or arrangement that is more relevant or informative to the analyst or user than that of the original microarray scan image.

Abstract: Visualization techniques tools and systems for displaying network diagrams to convey both focus and context to a user of the display. Network diagrams may be displayed to emulate a three dimensional presentation. Network diagrams may be presented with items of interest in sharp definition and the remainder of a diagram or diagrams being blurred or having relative degrees of sharpness/blurriness.

Abstract: A belt hanger, such as a belt clip or belt loop, includes a body having opposing inner and outer walls extending downwardly from a bridge portion and defining a throat opening for receiving a user's belt or waistband. A keeper is movably mounted to the body below the bridge portion to form an adjustable lower boundary of the throat opening. The body preferably includes a set of vertically spaced engagement features, such as notches or detents, that are sized for engagement with corresponding lock features of the keeper to facilitate adjustment and positioning of the keeper at a selected one of several possible vertical positions, without the use of tools.

Abstract: Software systems, methods and recordable media for organizing and manipulating diverse data sets to facilitate identification, trends, correlations and other useful relationships among the data. Extremely large data sets such as microarray data and other biological data are graphically displayed and sorted in an effort to develop visual similarities, correlations or trends that can be seen by a user of the present invention. Various schemes for graphical representations of the data, as well as sorting schemes are provided, including sorting schemes performed relative to pseudo-data vectors.

Abstract: Software systems and methods for organizing and manipulating diverse data sets to facilitate identification, trends, correlations and other useful relationships among the data. Extremely large data set such as microarray data and other biological data are graphically displayed and sorted in an effort to develop visual similarities, correlations or trends that can be seen by a user of the present invention. Various schemes for graphical representations of the data, as well as sorting schemes are provided. Additionally, non-experimental or other data can be displayed and tracked along with the data upon which the sorting schemes are processed.

Abstract: System, tools and methods for inspecting very large data sets of microarray, protein array or other large-scale biological experiments along with other relevant supporting data. Widely diverse but related and potentially correlated data (such as gene expression and clinical observations) can be combined to search for meaningful correlations and trends using innate human pattern recognition.