Bioarray Solutions Ltd.

Other

Local Corporation

Local.com Corporation

Doug Norman, Interchange Corp.

Xiongwu Xia

Michael Seul

Chiu Wo Chau

Scott Determan

Tatiana Vener

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.

Analysis, secure access to, and transmission of array images

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 a 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 coding information, so as to preserve confidentiality.

Methods and algorithms for automated allele assignments within an integrated software environment are provided. These methods and algorithms offer a multiplicity of functionalities including: data management; system configuration including user authorization, training set analysis and probe masking; pattern analysis including string matching and probe flipping; and interactive redaction of data. The methods and algorithms further include methods of setting thresholds, refining thresholds, and probe masking of signals produced by probes which do not contribute significantly to discriminating among alleles.

Automated analysis of multiplexed probe-target interaction patterns: pattern matching and allele identification

A local search engine geographically indexes information for searching by identifying a geocoded web page of a web site and identifying at least one geocodable web page of the web site. The system identifies a geocode contained within content of the geocoded web page of the web site. The geocode indicates a physical location of an entity associated with the web site. The system indexes content of the geocoded web page and content of the geocodable web page. The indexing including associating the geocode contained within content of the geocoded web page to the indexed content of the geocoded web page and the geocodable web page to allow geographical searching of the content of the web pages.

Search engine and indexing technique

Search engine and indexing techniques

Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe ('primer'), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a 'degree of matching' score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.

Concurrent optimization in selection of primer and capture probe sets for nucleic acid analysis

Disclosed are methods and algorithms (and their implementation) supporting the automated analysis and interactive review and refinement ('redaction') of the analysis within an integrated software environment, for automated allele assignments. The implementation, preferably with a software system and a program referred to as the Automated Allele Assignment ('AAA') program, provides a multiplicity of functionalities including: data management by way of an integrated interface to a portable database to permit visualizing, importing, exporting and creating customizable summary reports; system configuration (&#x201c;Set-up&#x201d;) including user authorization, training set analysis and probe masking; Pattern Analysis including string matching and probe flipping; and Interactive Redaction combining real-time database computations and &#x201c;cut-and-paste&#x201d; editing, generating &#x201c;warning&#x201d; statements and supporting annotation. It also includes a thresholding function, a method of setting thresholds, a method of refining thresholds by matching an experimental binary string (&#x201c;reaction pattern&#x201d;) setting for that probe, probe masking of signals produced by probes which do not contribute significantly to discriminating among alleles.

Growing community of inventors

Dayton, NJ, United States of America

Xiongwu Xia