Abstract: Provided herein are methods for simultaneously identifying genomic copy number variations (CNVs) and sequence variations in an enriched genomic sample and compositions, systems, and kits for performing such methods. In some aspects, the methods include: (a) obtaining a plurality of sequence reads from an enriched genomic sample that includes a plurality of genomic backbone regions and a plurality of genomic mutation regions of interest in a genomic locus of a subject; (b) obtaining a plurality of sequence reads from corresponding genomic backbone regions and genomic mutation regions of at least one reference genomic sample; (c) assembling the plurality sequence reads from the enriched genomic sample and the at least one reference genomic sample; and (d) determining, based on computational analysis of the assembly, whether the genomic locus has a copy number variation (CNV) and/or a sequence variation.

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: Provided herein are methods for simultaneously identifying genomic copy number variations (CNVs) and sequence variations in an enriched genomic sample and compositions, systems, and kits for performing such methods. In some aspects, the methods include: (a) obtaining a plurality of sequence reads from an enriched genomic sample that includes a plurality of genomic backbone regions and a plurality of genomic mutation regions of interest in a genomic locus of a subject; (b) obtaining a plurality of sequence reads from corresponding genomic backbone regions and genomic mutation regions of at least one reference genomic sample; (c) assembling the plurality sequence reads from the enriched genomic sample and the at least one reference genomic sample; and (d) determining, based on computational analysis of the assembly, whether the genomic locus has a copy number variation (CNV) and/or a sequence variation.

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: The preferred embodiment of the present invention is directed to a method, system and apparatus to automate the sale and purchase of entertainment tickets along with concessions and/or merchandize, individually or as a package, in the electronic media comprising web, mobile apps and social media channels.

Abstract: An apparatus and method for optical lithography verification includes filtering a lithography simulation of proposed sub-lightwave pattern formations during at feast one design phase or manufacturing phase of an article of manufacture having sub-lightwave structures and then detecting design phase or manufacturing phase defects in response to the filtering of the lithography simulation.

Abstract: The preferred embodiment of the present invention is directed to a method, and system to automate real time price negotiation and bargaining followed by actual purchase of merchandize or service at a retail location. The merchandize can range from real goods and/or service(s) available at any store or retail outlet to entertainment such as movies, concerts, sporting events and others.

Abstract: A photomask dataset corresponding to a target-pattern is verified by simulating a resist-pattern that will be formed in a resist layer by a lithography process, simulating an etched-pattern that will be etched in a layer by a plasma process wherein said simulation comprises calculating a flux of particles impacting a feature, and determining whether the etched-pattern substantially conforms to the target-pattern.

Abstract: An apparatus and method for optical lithography verification includes filtering a lithography simulation of proposed sub-lightwave pattern formations during at least one design phase or manufacturing phase of an article of manufacture having sub-lightwave structures and then detecting design phase or manufacturing phase defects in response to the filtering of the lithography simulation.

Abstract: A hierarchical representation encapsulates the detailed internal composition of a sub-circuit using the notion of a cell definition (a CellDef). The CellDef serves as a natural unit for operational reuse. If the computation required for the analysis or manipulation (e.g. parasitic extraction, RET, design rule confirmation (DRC), or OPC) based on a CellDef or one cell instance can be applied, with no or minimal additional effort, to all or a significant subset of other instances of the cell, very substantial reduction in computational effort may be realized. Furthermore, a hierarchical representation also allows for the partitioning of the overall analysis/manipulation task into a collection of subtasks, e.g. one per CellDef. Multiple jobs may then be distributed across a large number of computational nodes on a network for concurrent execution. While this may not reduce the aggregate computational time, a major reduction in the overall turnaround time (TAT) is in itself extremely beneficial.

Abstract: A method and system for reducing the computation time required to apply position-dependent corrections to lithography, usually mask, data is disclosed. Optical proximity or process corrections are determined for a few instances of a repeating cluster or object, usually at widely separated locations and then interpolating the corrections to the other instances of the repeating cluster based on their positions in the exposure field. Or, optical proximity corrections can be applied to the repeating cluster of objects for different values of flare intensity, or another parameter of patterning imperfection, such as by calculating the value of the flare at the location of each instance of the repeating cluster, and interpolating the optical proximity corrections to those values of flare.

Abstract: An apparatus and method for optical lithography verification includes filtering a lithography simulation of proposed sub-lightwave pattern formations during at least one design phase or manufacturing phase of an article of manufacture having sub-lightwave structures and then detecting design phase or manufacturing phase defects in response to the filtering of the lithography simulation.

Abstract: A hierarchical representation encapsulates the detailed internal composition of a sub-circuit using the notion of a cell definition (a CellDef). The CellDef serves as a natural unit for operational reuse. If the computation required for the analysis or manipulation (e.g. parasitic extraction, RET, design rule confirmation (DRC), or OPC) based on a CellDef or one cell instance can be applied, with no or minimal additional effort, to all or a significant subset of other instances of the cell, very substantial reduction in computational effort may be realized. Furthermore, a hierarchical representation also allows for the partitioning of the overall analysis/manipulation task into a collection of subtasks, e.g. one per CellDef. Multiple jobs may then be distributed across a large number of computational nodes on a network for concurrent execution. While this may not reduce the aggregate computational time, a major reduction in the overall turnaround time (TAT) is in itself extremely beneficial.

Abstract: A method and system for reducing the computation time required to apply position-dependent corrections to lithography, usually mask, data is disclosed. Optical proximity or process corrections are determined for a few instances of a repeating cluster or object, usually at widely separated locations and then interpolating the corrections to the other instances of the repeating cluster based on their positions in the exposure field. Or, optical proximity corrections can be applied to the repeating cluster of objects for different values of flare intensity, or another parameter of patterning imperfection, such as by calculating the value of the flare at the location of each instance of the repeating cluster, and interpolating the optical proximity corrections to those values of flare.