Abstract: Disclosed herein is a PRocess Orchestration and Repository Origination Code (‘PROC’) for simultaneously configuring a data repository, preferably in the form of a structured data container, and encoding a workflow for populating the data container with items of information from designated decentralized sources of disparate type and format. PROC provides a general-purpose method for compiling, transforming and presenting items of information in a data container according to a preset standard governing structure and content. PROC encodes both the structure of the data container as well as the process for procuring and distributing the intended content. Accordingly, PROC provides a method for the real-time integration of primary data from disparate decentralized sources, including sources dynamically created during Script execution, and items of information derived from primary data, into a persistent or temporary structured container.

Abstract: Disclosed herein is a PRocess Orchestration and Repository Origination Code (‘PROC’) for simultaneously configuring a data repository, preferably in the form of a structured data container, and encoding a workflow for populating the data container with items of information from designated decentralized sources of disparate type and format. PROC provides a general-purpose method for compiling, transforming and presenting items of information in a data container according to a preset standard governing structure and content. PROC encodes both the structure of the data container as well as the process for procuring and distributing the intended content. Accordingly, PROC provides a method for the real-time integration of primary data from disparate decentralized sources, including sources dynamically created during Script execution, and items of information derived from primary data, into a persistent or temporary structured container.

Abstract: The invention relates to a semantic data acquisition, storage and presentation system comprising SentenceClasses wherein SentenceClasses comprise SentenceClassLabels and SentenceClassData, each such label in the form of a RelationalPhrase or an alias thereof, and data, for each class, organized in conformance with the class-defining relation, as expressed in the form of the RelationalPhrase. Instantiation of SentenceClasses, by replacing substitution variables in RelationalPhrases with associated items of SentenceClassData, produces Sentences that provides context to the instantiated items. The system of the invention also comprises methods and processes including for: acquiring, transforming and recording data; operating on SentenceClasses including forming new SentenceClasses; and instantiating, rendering and presenting Sentences in human or machine-readable format.

Abstract: The invention relates to a semantic data acquisition, storage and presentation system comprising SentenceClasses wherein SentenceClasses comprise SentenceClassLabels and SentenceClassData, each such label in the form of a RelationalPhrase or an alias thereof, and data, for each class, organized in conformance with the class-defining relation, as expressed in the form of the RelationalPhrase. Instantiation of SentenceClasses, by replacing substitution variables in RelationalPhrases with associated items of SentenceClassData, produces Sentences that provides context to the instantiated items. The system of the invention also comprises methods and processes including for: acquiring, transforming and recording data; operating on SentenceClasses including forming new SentenceClasses; and instantiating, rendering and presenting Sentences in human or machine-readable format.

Abstract: The invention relates to jCode programs which perform programmatic creation of strings comprising hyperlinked data and references thereto, and to the programmatic creation of documents, including XML documents and other format documents, referencing internal and external data sources. JSON can be used to express jCode programs, as can other custom designed languages, or XML or YAML.

Abstract: The present invention discloses a universal data container, in the form of a generic tabular representation, and methods of navigating and transforming said generic tabular representation by invoking standard SQL-Expressions, implementing the equivalent of XPath expressions, obviating the need for SQL extensions or format-specific query languages, the container accommodating disparate sources regardless of type or format, placing structured and unstructured sources on an equal footing.

Abstract: Disclosed is a method for querying by pattern matching a relational data store, including a collection of records having a preset number of attributes, wherein the representation of the content of a structured or unstructured data source also encodes the structure of the data source, and including these steps: providing at least one query comprising at least a find- and a where-clause, wherein the where-clause comprises one or more query patterns, and the find-clause specifies a subset of attributes optionally including aliases thereof; executing the query by: applying predicates in the one or more query patterns to identify a subset of matching or non-matching records; forming the intersection of the two or more subsets of records for two or more patterns; in accordance with the find-clause, selecting specified attributes and applying any aliases; and thereby identifying the subset of records satisfying constraints expressed in the query patterns.

Abstract: The present invention discloses a universal data container, in the form of a generic tabular representation, and methods of navigating and transforming said generic tabular representation by invoking standard SQL-Expressions, implementing the equivalent of XPath expressions, obviating the need for SQL extensions or format-specific query languages, the container accommodating disparate sources regardless of type or format, placing structured and unstructured sources on an equal footing.

Abstract: The invention relates to jCode programs which perform programmatic creation of strings comprising hyperlinked data and references thereto, and to the programmatic creation of documents, including XML documents and other format documents, referencing internal and external data sources. JSON can be used to express jCode programs, as can other custom designed languages, or XML or YAML.

Abstract: The invention relates to a semantic data acquisition, storage and presentation system comprising SentenceClasses wherein SentenceClasses comprise SentenceClassLabels and SentenceClassData, each such label in the form of a RelationalPhrase or an alias thereof, and data, for each class, organized in conformance with the class-defining relation, as expressed in the form of the RelationalPhrase. Instantiation of SentenceClasses, by replacing substitution variables in RelationalPhrases with associated items of SentenceClassData, produces Sentences that provides context to the instantiated items. The system of the invention also comprises methods and processes including for: acquiring, transforming and recording data; operating on SentenceClasses including forming new SentenceClasses; and instantiating, rendering and presenting Sentences in human or machine-readable format.

Abstract: The invention relates to jCode programs which perform programmatic creation of strings comprising hyperlinked data and references thereto, and to the programmatic creation of documents, including XML documents and other format documents, referencing internal and external data sources. JSON can be used to express jCode programs, as can other custom designed languages, or XML or YAML.

Abstract: The invention provides methods and processes for the identification of polymorphisms at one ore more designated sites, without interference from non-designated sites located within proximity of such designated sites. Probes are provided capable of interrogation of such designated sites in order to determine the composition of each such designated site. By the methods of this invention, one ore more mutations within the CFTR gene and the HLA gene complex can be identified.

Abstract: Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including a method of preventing a significant reduction in duplexes detectable in a hybridization assay involving (i) selecting probe lengths for sets of oligonucleotide probes, wherein probes include different subsequences such that at least one subsequence is complementary to a subsequence in a cognate target; wherein probes for longer cognate targets are longer in length than probes for shorter cognate targets, (ii) selecting, for each set of probes, a density of oligonucleotides probes attached per unit area on a solid phase carrier which is below a limit at which the significant reduction in detectable duplexes is predicated to take place, (iii) producing the probes and affixing them to different solid phase carriers at the selected density, and (iv) annealing targets to the probes, wherein signal intensities of probes and targets of different lengths are about the same.

Abstract: Disclosed is a novel method of allele profiling, or nucleic acid sieving, with pooled Sanger sequencing as a first (aka “screening”) stage; where the first step is: amplifying a single sequence, delineated by forward and reverse primers which may represent a single exon, or a segment thereof, or a contiguous stretch of multiple exons and introns. The amplicons produced from a pool of samples include the amplified sequence, and these are next converted into fragments in the standard Sanger labeling reaction. Ambiguities will appear as superposed peaks at any heterozygous position of interest, as the origin of the variant signal cannot be uniquely attributable to a specific sample, or samples, in the pool. These ambiguities may be resolved by the allele profiling process; or, resolution can be done with source-tagged primers generating source-tagged amplicons, which generate position shifts in labels, which can be decoded to resolve the ambiguities.

Abstract: The invention relates to forming locus-specific (or gene-specific) pools of cells from various potential donors, where the cells that express or display HLA molecules, or other polymorphic cell surface markers, and identifying the pattern of responses across these pools, notably aggregation of cells, or their acquisition of fluorescence when exposed to a labeled secondary antibody, when exposed to sera from a potential recipient. Pools of cells from different potential donors are designed and constructed in accordance with allele partitions that are identified by amino acid sequence tags, preferably defined in terms of single or combinations of variable amino acid positions encoded by the constituent alleles in the partition.

Abstract: A process of identifying a plurality of biological samples having particular desired attributes by testing pooled samples and selecting, for intended uses such as transfusion, or for subsequent analysis that is thereby enriched for such samples, pooled samples which have, or may have, said desired attributes. The preferred number of samples per pool “d” is determined by selecting an integer value as d which produces the maximum or a value near the maximum of the product of: d times the expected number of unambiguous sample pools, where a sample pool is unambiguous if all of the samples have the desired attributes, and is otherwise ambiguous if at least one sample has the desired attributes. The value selected as d can be greater than the maximum product above, so as to enlarge the total number of samples assayed in determining the desired attributes.

Abstract: This invention provides high unit density arrays of microparticles and methods of assembling such arrays. The microparticles in the arrays may be functionalized with chemical or biological entities specific to a given target analyte. The high unit density arrays of this invention are formed on chips which may be combined to form multichip arrays according to the methods described herein. The chips and/or multichip arrays of this invention are useful for chemical and biological assays.

Abstract: This invention provides high unit density arrays of microparticles and methods of assembling such arrays. The microparticles in the arrays may be functionalized with chemical or biological entities specific to a given target analyte. The high unit density arrays of this invention are formed on chips which may be combined to form multichip arrays according to the methods described herein. The chips and/or multichip arrays of this invention are useful for chemical and biological assays.

Abstract: Systems and methods are provided the autocentering, autofocusing, acquiring, decoding, aligning, analyzing and exchanging among various parties, images, where the images are of arrays of signals associated with ligand-receptor interactions, and more particularly, ligand-receptor interactions where a multitude of receptors are associated with microparticles or microbeads. The beads are encoded to indicate the identity of the receptor attached, and therefore, an assay image and decoding image are aligned to effect the decoding. The images or data extracted from such images can be exchanged between de-centralized assay locations and a centralized location where the data are analyzed to indicate assay results. Access to data can be restricted to authorized parties in possession of certain encoding information, so as to preserve confidentiality.

Abstract: Systems and methods are provided the autocentering, autofocusing, acquiring, decoding, aligning, analyzing and exchanging among various parties, images, where the images are of arrays of signals associated with ligand-receptor interactions, and more particularly, ligand-receptor interactions where a multitude of receptors are associated with microparticles or microbeads. The beads are encoded to indicate the identity of the receptor attached, and therefore, an assay image and decoding image are aligned to effect the decoding. The images or data extracted from such images can be exchanged between de-centralized assay locations and a centralized location where the data are analyzed to indicate assay results. Access to data can be restricted to authorized parties in possession of certain encoding information, so as to preserve confidentiality.