Comparative gene transcript analysis

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

DATA BASES OF REGULATORI SEQUENCES, METHODS TO YOUR PRODUCTION AND USE

ARCHIVES AND ANALYSIS SYSTEM

RHAMNOSE INDUZIERBARES EXPRESS ION SYSTEM

PROCEDURE FOR THE CLASSIFICATION OF SEQUENCES IN FAMILIES

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

PROCEDURE FOR THE SCREENEN OF GENOMI DNS, INSBESONDERER WITH MORE TRANSGENER AND PURPOSEFUL MUTAGENESE

Systems and methods for RNA analysis in functional confirmation of cancer mutations

Contemplated systems and methods integrate genomic/exomic data with transcriptomic data by correlating a cancer associated mutation in the genome/exome with the transcription level of the affected gene carrying the mutation, particularly where the mutation is a 3-terminal nonsense mutation.

METHODS OF IDENTIFYING PATIENTS AT RISK OF DEVELOPING ENCEPHALITIS FOLLOWING IMMUNOTHERAPY FOR ALZHEIMER'S DISEASE

SYSTEM AND METHOD FOR STORING MASS SPECTROMETRY DATA

The present invention relates to a system and methods for facilitating the analysis of proteomic expression data. In this system, complex sequence- correlated peptide expression information and mass spectrum data are processed and stored in a relational database. Using a parallel computational method, the expression data and results are parsed and associated to rapidly yield peptide sequence information. The system automates necessary tasks associated with peptide data analysis and organizes large amounts of information needed to perform the data analysis in a logical and accessible manner.

A SYSTEM AND METHOD FOR MANAGING GENE EXPRESSION DATA

The present invention pertain to a system and method of analyzing gene expression, gene annotation, and sample information in a relational format supporting efficient exploration and analysis, comprising: providing data warehouse which comprises a gene expression database for storing quantitative gene expression measurements for tissues and cell lines screened using various assays; a clinical database for storing information on bio-samples and donors; and a fragment index for biological properties for DNA fragments; receiving a query regarding gene expression of one or more DNA fragments; determining the level of gene expression of the one or more DNA fragments; correlating the level of gene expression with the clinical database and the fragment index; and displaying the results of said correlation.

DEVICE FOR QUANTITATIVE ANALYSIS OF A METABOLITE PROFILE

STATUS DETERMINATION

... ²²²The present invention provides a method of determining the status of a ²subject. In particular, this is achieved by obtaining subject data including ²respective values for each of a number of parameters, the parameter values ²being indicative of the current biological status of the subject. The subject ²data is compared to predetermined data which includes values for at least some ²of the parameters and an indication of the condition. The status of the ²subject, and in particular, the presence and/or absence of the one or more ²conditions, can then be determined in accordance with the results of the ²comparison.² ...

A SYSTEM, METHOD, AND COMPUTER PROGRAM PRODUCT USING A DATABASE IN A COMPUTING SYSTEM TO COMPILE AND COMPARE METABOLOMIC DATA OBTAINED FROM A PLURALITY OF SAMPLES

The present invention generates a visual display of metabolomic data compiled by a database and associated processor. More particularly, the present invention provides a database for automatically receiving a three-dimensional spectrometry data set for a group of samples. The present invention also provides a processor device for manipulating the data sets to produce plots that are directly comparable to a plurality of characteristic plots corresponding to a plurality of selected metabolites. Furthermore, the processor device may generate a visual display indicating the presence of the selected metabolites across the group of samples. Thus, the present invention enables a user to analyze a series of complex data sets in a visual display that may indicate the presence of the selected metabolites across the group of samples. Furthermore, the visual display generated by embodiments of the present invention also expedites the subjective analysis of the spectrometry data sets.

SYSTEM AND METHOD FOR MODELING GENETIC, BIOCHEMICAL, BIOPHYSICAL AND ANATOMICAL INFORMATION

Genetic, biochemical, biophysical and anatomical information is integrated at the cellular and subcellular level. At least one database containing biological information is used to generate at least one data structure having at least one attribute associated therewith. An interface interactively views and links together attributes of a plurality of data structures to create at least one hierarchical description of subcellular and cellular function. A computational engine generates at least one mathematical equation from the hierarchical description. Genetic information is accessed, tabulated and combined with functional information on the biochemical and physiological role of gene products. Computational models of genetic, biochemical and biophysical processes within cells are automatically formulated, solved and analyzed based on combination of genetic and functional information adduced. A dynamic tool is thereby provided for achieving objectives, such as increased understanding of biological ...

STATUS DETERMINATION

The present invention provides a method of determining the status of a subject. In particular, this is achieved by obtaining subject data including respective values for each of a number of parameters, the parameter values being indicative of the current biological status of the subject. The subject data is compared to predetermined data which includes values for at least some of the parameters and an indication of the condition. The status of the subject, and in particular, the presence and/or absence of the one or more conditions, can then be determined in accordance with the results of the comparison.

METHODS AND SYSTEMS FOR SEARCHING GENOMIC DATABASES

The instant invention provides methods and systems for searching genomic databases using polypeptide sequence information, such as those obtained from peptide sequencing projects, especially those using mass spectrometers. According to the instant invention, polypeptide sequences can be reverse translated into multiple sequence tags wich are then used to search for identical or similar sequences in genomic databases, such as unanotated genomic databases of human or other organisms. Alternatively, the polypeptide sequences can be directly compared to sequences translated from at least 3, preferably all 6 reading frames of genomic sequences. The instant invention also provides systems for performing the methods of the instant invention, including computer systems, and systems including said computer systems and mass spectrometers linked to said computer systems. The instant invention further provides methods of conducting proteomic businesses using the methods of the instant invention.

SELF-IMPROVING CLASSIFICATION SYSTEM

SYSTEMS AND METHODS FOR MONITORING BEHAVIOR INFORMATICS

A system and method used to assess animal behavior includes a module (1510) having sensors (1505) that collects a variety of physical and biological data from a test subject. Interpretation of the data is provided to assess the test subject's behavior, neurology, biochemistry and physiology. The module is useful in observing the effects of a drug on the test animal and providing information on the drug's signature. Another advantage is module's portability that allows it to be used in standard laboratory cages. (NOT SURE ABOUT THIS PORTABILITY) This portability allows the animal to be tested in its own habitat, that can reduce any erroneous data due to stressing the animal when removed to a test cage. Additionally, the module's design allows for parallel data collection and interpretation from several laboratory animals undergoing different experiments. Multi-dimensional modeling of the test subject based the system's interpretation of the data allows pattern recognition of the drug signature ...

METHOD AND APPARATUS FOR ANALYSIS OF MOLECULAR CONFIGURATIONS AND COMBINATIONS

A method for the prediction of adverse cross-reactions between lead candidate biomolecules and potential reactant molecules, often biopolymers, is described. In a computational system, reactions are modeled within a suitable environment, in order to determine a reaction profile between a lead candidate molecule and a potential reactant molecule. A risk assessment is then generated for each lead based on a plurality of reaction profiles for the lead with respect to a plurality of potential reactant molecules. The method includes provision for the redesign and optimization of the lead candidate, possibly iterative in nature, in order to avoid predicted adverse cross- reactions.

ARTIFICIAL INTELLIGENCE SYSTEM FOR GENETIC ANALYSIS

The present invention provides a complete artificial intelligence system for the acquisition and analysis of nucleic acid array hybridization information. The system is divided into at least one central data processing facility and one or more user facilities, linked by encrypted network connections or similar links. Each user facility may include an optical scanning system to collect hybridization signals from a nucleic acid array, an image processing system to convert the optical data into a set of hybridization parameters, a connection to a data network, and a user interface to display, manipulate, search, and analyze hybridization information. This system reads data from a gene chip or DNA microarray, or a proteomics chip, analyzes test results based on maintained parameters, evaluates patient risk for various ailments, recommends methods of treatment, presents information to medical and/or private individuals, and notifies test participants when new treatment becomes available.

SYSTEMS AND METHODS FOR TESTING A BIOLOGICAL SAMPLE

Systems and methods for testing samples, particularly biological samples are provided. The system includes an instrument for detecting molecules in samples, and a processor that communicates with the instrument to provide results-based control of the instrument to effect assay-basd judging. For example, a system, including software, is provided that directs and performs assays such as diagnostic assays that employ a mass spectrometer. The output of the system, rather than a mass spectrum or other raw data form, is the diagnostic outcome, such as a genotype.

BIOLOGICAL DATA PROCESSING

A multi-database query system which queries a plurality of databases and servers, including an input which receives queries in a structured form and a translation server which translates at least a part of a received query into commands recognized by a data manipulation server.

EVENT BASED SYSTEM AND METHOD FOR MANAGING CLINICAL TRIAL DATA

A system and method for integrating clinical trial data housed in disparate systems. The integration system listens for a clinical trial event broadcasted by any one of the disparate systems. The clinical trial events are the same or similarly defined among the disparate systems. The integration system receives notice of a clinical trial event from one of the disparate systems and then sends a query to the disparate systems requesting metadata corresponding with the clinical trial event. The metadata is comprised of attributes of the clinical trial event and the values of such metadata may differ among the disparate systems. The responsive metadata is stored in an unstructured format and can be displayed in substantially real-time via a graphical user interface.

CLINICAL SUPPORT SYSTEM AND METHOD

There is provided a computer-implemented method and device for providing clinical support. A user may input to the device a medical condition as well as a number of patient characteristics. The device may use a logic tree to determine, based on the medical condition, an initial list of therapeutic treatment options, such as specific drug(s) and associated dosage regimes, for treating the medical condition. The initial list may be refined by using a logic tree to determine, based on the patient characteristic(s), which of the therapeutic treatment options may not be appropriate for the patient, and such therapeutic treatment options may be removed and/or replaced with alternative therapeutic treatment options.

Computer-implemented procedure for the search of in at least one data base stored molecular-biological information.

Die vorliegende Erfindung besteht in einem Verfahren zum Auffinden und Anzeigen molekularbiologischer Informationen, die in zumindest einer Datenbank gespeichert sind, wobei eine bevorzugte Verwirklichung des Verfahrens unter Verwendung eines Computerprogramms besteht und wobei das Programm auch über ein Computernetzwerk, beispielsweise das Internet, zugänglich ist.

Organic molecular to the retrieval engine.

Vorgeschlagen wird ein bio-molekularer Retrieval-Engine zum Suchen, Selektieren und interaktiven Analysieren komplexer Strukturen in grossen, heterogenen Datensätzen mittels entsprechender Drill-down- und Roll-up-Operationen, sowie ein entsprechendes Verfahren. Die heterogenen Datensätze werden mittels des biomolekularen Retrieval-Engine nach bio-molekularen 3D-Strukturen und Verbindungen mit bestimmten Eigenschaften gefiltert. Beim Ladeprozess von Daten einer selektierten Datenbank und/oder Datenquelle in den bio-molekularen Retrieval-Engine werden die einzelnen Zeilen der Datenquellen mittels einer eineindeutigen Nomenklatur indexiert. Dieselbe Indexierung wird auf jede weitere selektierte und zu ladende Datenquelle angewendet, wobei die selektierten Datenquellen heterogene, verschiedenartige Datenbanken umfassen und die Indexierung als Primärschlüsssel verwendet wird. Mittels einer Resync-Operation werden die selektierten, heterogenen Datenquellen und der Retrieval-Engine asynchron gekoppelt ...

Biomedical and bio-molecular to the retrieval engine.

Die Erfindung betrifft einen biomedizinischen oder bio-molekularen Retrieval-Engine zum Suchen, Selektieren und interaktiven Analysieren komplexer Strukturen in grossen, heterogenen Datensätzen mittels entsprechenden Drilldowns und Roll-up-Operationen. Die heterogenen Datensätze werden mittels des bio-molekularen Retrieval-Engines nach bio-molekularn, 3D-Strukturen und Verbindungen mit bestimmten Eigenschaften gefiltert. Beim Ladeprozess von Daten einer selektierten Datenbank und/oder Datenquelle werden die einzelnen Zeilen der Datenquellen mittels einer eineindeutigen Nomenklatur indexiert. Dieselbe Indexierung wird auf jede weitere selektierte und zu ladende Datenquelle angewendet, wobei die selektierten Datenquellen heterogene, verschiedenartige Datenbanken umfassen und die Indexierung als Primärschlüssel verwendet wird. Mittels einer Resync-Operation werden die selektierten, heterogenen Datenquellen und die Retrieval-Engine asynchron gekoppelt. Der Inhalt der Daten der heterogenen Datenquellen ...

СПОСОБ ГЕНЕРИРОВАНИЯ МОЛЕКУЛЯРНО-ФУНКЦИОНАЛЬНОЙ СЕТИ

Способ генерирования молекулярно-функциональной сети, включающей в себя биологические события, путем осуществления связанного поиска с использованием базы данных о связях между биологическими молекулами, включая информацию о биологических событиях, и способ прогнозирования пути между произвольной биологической молекулой и произвольным биологическим событием в указанной сети, или способ прогнозирования биологических событий, с которыми связана произвольная биологическая молекула в указанной сети.

SYSTEMS AND METHODS FOR SUPPORT OF CLINICAL SOLUTIONS

制造系统,其控制装置、控制方法、控制系统及控制程序

... 本发明提供用于对试剂检查装置进行的检查进行控制的控制装置、及其控制方法、控制系统以及控制程序。IJ方式试剂检查装置(3)基于有关输入的检查项目的检查信息对吐出装置发出吐出试剂的指示，从可以拆装的DNA芯片组件(2)进行检查结果的读取，将该检查结果的检查数据与被输入的被检查者识别信息与该当的检查项目一起通过通信线路输出。控制装置(5)通过通信线路从IJ方式试剂检查装置(3)与检查项目及其检查数据一起接收被检查者识别信息，与该检查者识别信息建立关联并存储该检查项目和该检查数据，进行基于该检查数据的诊断的委托。 ...

特异结合分析方法及用于其的特异结合分析装置

... 为提供减少前界现象、本底及杂质的影响，能对试料中的分析对象物简便、迅速且正确地定量或定性的特异结合分析方法及用于其的特异结合分析装置，预先按包含设想的分析对象物的各试料，生成与来自特异结合反应的信号强度有关的数据库，基于上述数据库决定试料的信号强度的测定模式，从而决定上述试料中的分析对象物的浓度。 ...

A method for conceptualizing protein interaction networks using Gene Ontology

Server-client network system for genotyping analysis and computer readable medium used therein

System and method for managing genetic information

방향성 비순환 구조에서 쌍형성된-말단 데이터를 사용하기 위한 시스템 및 방법

... 유기체로부터의 트랜스크립톰으로부터 적어도 한 쌍의 쌍형성된-말단 판독물을 수득하는 단계, 방향성 비순환 데이터 구조 (데이터 구조는 RNA 서열, 예컨대 엑손 또는 전사체를 나타내는 노드 및 노드 쌍을 연결하는 에지를 가짐)에서 상기 쌍의 제1 판독물과 노드 사이에 최적 점수를 갖는 정렬을 찾아내는 단계, 쌍형성된-말단 판독물 쌍의 삽입 길이와 실질적으로 유사한 길이를 갖는 경로에 의해 하류 노드에 연결된 노드를 포함하는 후보 경로를 확인하는 단계, 및 쌍형성된-말단 판독물을 후보 경로에 대해 정렬하여 최적-점수화 정렬을 결정하는 단계를 포함하는, 트랜스크립톰을 분석하는 방법이 개시된다.

ONLINE MARKETPLACE FOR ANIMAL GENETICS

An Internet-based marketplace is provided for animals, gametes and embryos wherein a database retains specific genetic identifiers correlated to the animals, embryos and gametes. A method, an apparatus, a server and a client are provided that allow a remote user to submit a query on one or more genetic identifiers to a centralized database located on the server for the purpose of allowing a user to identify matching stock, to certify stock such as to reduce fraud, to report lost or found stock, to trade stock by either fixed priced selling or auction, and to facilitate shipment of stock. An animal can be identified and a cloned embryo prepared and shipped to the requester such as in a specialized shipping container that stabilizes the cloned embryo. © KIPO & WIPO 2008 ...

CERTAIN SPECIES-SPECIFIC PRIMER AMONG ENTEROCOCCUS SPECIES, METHOD FOR ISOLATING AND IDENTIFYING CORRESPONDING STRAIN BY USING SAME, AND COMPOSITION THEREOF

The present invention relates to a multiplex-PCR method for selecting an enterococcus strain and, more specifically, to a multiplex-PCR method using a template as a colony by targeting four species of enterococcus (E. faecalis, E. faecium, E. hirae, E. durans). The present invention can identify bacteria of four species of enterococcus (E. faecalis, E. faecium, E. hirae, E. durans) in a simple and economical method by, with a newly designed computer programming analysis method, searching a gene specifically in each of enterococcus species, producing a primer, and performing a PCR, and thus checking the identification of existing bacteria, which could be known only through sequencing, through a PCR method. Moreover, the present invention can save time and is economical when developing feed additives and probiotics spending most time in isolating and identifying bacteria since analysis and appliance on other genus such as lactobacillus, bacillus as well as enterococcus are possible based ...

비정상적인 핵형을 검출하기 위한 방법 및 시스템

... 비정상적인 핵형을 검출하기 위한 방법 및 시스템이 개시된다. 예시적인 방법은, 판독 커버리지 데이터, 이형접합 SNP의 대립유전자 균형 분포, 및 이형접합성이 관찰되지 않은 염색체 분절을 결정하는 단계를 포함할 수 있다. 이어서, 상기 방법 및 시스템은 비정상적인 핵형의 표시일 수 있는 하나 이상의 메트릭을 결정할 수 있다.

GENETIC INFORMATION SUPPLYING METHOD FOR DISPLAYING ATTRIBUTE INFORMATION OF GENETIC INFORMATION, A GENETIC INFORMATION SERVER FOR THE SAME, AND A COMPUTER READABLE MEDIUM RECORDED WITH A BROWSER PROGRAM

PURPOSE: A genetic information supplying method, a genetic information server for the same, and a computer readable medium recorded with a browser program are provided to compare a genetic sequence, related information, and transition information by displaying attribute information. CONSTITUTION: A communication unit(110) transmits attribute information related to genetic information which is displayed to a default track to a terminal device. If the terminal device requests merge of the attribute information, a merging unit(120) merges the attribute information. A controlling unit(140) transmits the merged attribute information to the terminal device. A storing unit(130) stores the attribute information related to the genetic information. COPYRIGHT KIPO 2012 ...

APPARATUS AND METHOD FOR PREDICTING IMPORTANT SITE OF PROTEIN BY USING PROBABILITY GRAPH MODEL

Disclosed is an apparatus for predicting an important site of protein by using a probability graph model. The apparatus for predicting an important site of protein by using a probability graph model comprises: an input unit which receives an unknown sequence for a sequence of amino acid or nucleic acid; a database in which information of the sequence of amino acid or nucleic acid has been stored, and a 3D structure of protein has been stored; and a control unit which predicts an important site of the unknown sequence by using the database, wherein the control unit measures evolutionary correlation between different locations and evolutionary dependence of individual acid residues by calculating a Markov Random Field (MRF) model parameter based on at least one of a multi-sequence arrangement generated based on sequences evolutionarily related to the received sequence of amino acid or nucleic acid, an MRF model generated by using a protein structure of the received sequence of amino acid ...

개인의 유전체 데이터를 이용하는 실-시간 개인화를 위한 시스템 및 방법

... 본 발명의 원리들은 실시간 또는 거의 실시간 애플리케이션을 위해 개인 생물학적 데이터를 프로세싱하기 위한 방법들 및 시스템을 제공한다. 대표적인 시스템은 수신된 기준 유전체 및 수신된 개인 유전체를 포함한다. 유전체는 하나 이상의 서버에 의해 네트워크를 거쳐 액세스된다. 개인과 연관된 또는 개인과 떨어진 하나 이상의 센서로부터의 입력이 센서 데이터 및 유전체 데이터를 고려하여 실-시간 또는 거의 실-시간 제시들, 추천들, 경고들 등을 제공하기 위해 개인의 유전체 데이터 또는 개인의 유전체 데이터 및 기준 유전체(들)의 비교의 결과들과 함께 사용된다. 대표적인 방법은 개인 유전체를 수신하는 단계 및 임의로 적합한 기준 유전체를 선택하는 단계를 포함한다. 시스템은 기준 유전체 및 개인 유전체 간 차이들을 결정하기 위해 관심 있는 상태에 대응하는 하나 이상의 선택된 유전자형(들) 및/또는 표현형(들)에 대해, 이의 부분들의, 기준 유전체와 개인 유전체를 비교한다. 관심 있는 선택된 상태에 직접적으로 또는 간접적으로 대응하는 센서가 선택되고 센서에 대한 최적의 값들이 계산된다. 센서는 개인과 근접하게 배치되고 출력이 모니터링된다. 경보 및 보고가 센서 출력에 응답하여 제공된다. 본 발명은 생물학적 데이터의 분석 및 그러한 데이터의 일상 생활로의 통합을 위한 시스템들 및 방법들에 관한 것이다.

METHODS AND SYSTEMS FOR IN SILICO EXPERIMENTAL DESIGN AND FOR PROVIDING A BIOTECHNOLOGY PRODUCT TO A CUSTOMER

Provided herein is a method and computer program product for designing and/or simulating a biotechnology experiment in silico; and for providing and generating revenue from a customized list of one or more biotechnology products and/or services related to the in silico designed or simulated biotechnology experiment or the product of that experiment In illustrative examples, the products and or services are indirectly related to a biomolecule designed by the in silico designed biotechnology experiment. In addition, provided herein is a method and computer system for generating revenue, that includes providing a customer with a first computer program product for designing or performing a biotechnology experiment in silico; and providing the customer with access to a purchase function for purchasing a second computer program product for designing or performing a biotechnology experiment in silico. Typically, functionality of the first computer product is less they and/or different than the ...

SYSTEMS, DEVICES, AND METHODS FOR ANALYZING MACROMOLECULES, BIOMOLECULES, AND THE LIKE

Systems, devices, and methods for analyzing hybridization of target molecules to probes on substrate-bound oligonucleotide, peptide, or protein arrays. In one aspect, the system includes a computer-readable memory medium and a controller. The system may further include a computer-readable memory medium including thermodynamic data configured as a data structure for use in analyzing biological samples. In some embodiments, the data structure comprises a thermodynamic data section having: thermodynamic data representative of dangling ends of two or more bases; thermodynamic data representative of unpaired single strands of two or more bases adjacent to a Watson-Crick base pairing; thermodynamic data representative of unpaired single strands of one or more bases adjacent to a non-Watson-Crick base pairing; thermodynamic data representative of tandem base pair mismatches of two or more bases; thermodynamic data representative of length-dependent terminal mismatches of nucleic acid bases; thermodynamic ...

STATISTICAL GENETICS ANALYSIS SYSTEM, STATISTICAL GENETICS ANALYSIS METHOD, AND STATISTICAL GENETICS ANALYSIS PROGRAM

An LD index computation device generates genotype data of possible multiple loci including two specific loci with a collection of multi-loci genotype data of individuals. The LD index computation device computes for each possible multiple loci including the two specific loci maximum likelihood estimates of haplotype frequencies and converts the computed maximum likelihood estimates into haplotype frequencies between two loci. The LD index computation device computes variances and confidence intervals through a plurality of different methods and converts the computed variances and the computed confidence intervals into information of two loci. The LD index computation device compares variances relating to two loci computed through the different methods and determines whether the maximum likelihood estimates fall within the confidence intervals and stores confidence intervals and corresponding two-loci haplotype frequencies in a confidence interval estimation result storage unit. The LD index ...

DATA MANAGEMENT SYSTEM AND METHOD FOR PHARMACEUTICAL DEVELOPMENT

A data management system for pharmaceutical development includes a processor and a memory operably connected to the processor. The memory is configured to store a discovery module for processing data regarding an investigation of the therapeutic value of a target molecule. The memory also is configured to store a development component for processing data regarding the creation and testing of a drug related to the target molecule. The memory also is configured to store a documentation module for capturing data regarding testing and trial results related to the drug. The memory also is configured to store a delivery module for processing data regarding the production of the drug. The memory also is configured to store a commercialization module for processing data regarding the commercialization of the drug.

GAMETE DONOR SELECTION BASED ON GENETIC CALCULATIONS

Gamete donor selection includes receiving a specification including a phenotype of interest, receiving a genotype of a recipient and a plurality of genotypes of a respective plurality of donors, determining statistical information pertaining to the phenotype of interest based at least in part on different pairings of the genotype of the recipient and a genotype of a donor in the plurality of donors, and identifying a preferred donor among the plurality of donors, based at least in part on the statistical information determined.

A SYSTEM, METHOD, AND COMPUTER PROGRAM PRODUCT USING A DATABASE IN A COMPUTING SYSTEM TO COMPILE AND COMPARE METABOLOMIC DATA OBTAINED FROM A PLURALITY OF SAMPLES

The present invention generates a visual display of metabolomic data compiled by a database and associated processor. More particularly, the present invention provides a database for automatically receiving a three-dimensional spectrometry data set for a group of samples. The present invention also provides a processor device for manipulating the data sets to produce plots that are directly comparable to a plurality of characteristic plots corresponding to a plurality of selected metabolites. Furthermore, the processor device may generate a visual display indicating the presence of the selected metabolites across the group of samples. Thus, the present invention enables a user to analyze a series of complex data sets in a visual display that may indicate the presence of the selected metabolites across the group of samples. Furthermore, the visual display generated by embodiments of the present invention also expedites the subjective analysis of the spectrometry data sets.

COMPOSITIONS AND METHODS FOR MODELING HUMAN METABOLISM

The present invention provides Homo sapiens Recon 1, a manually assembled, functionally validated, bottom-up reconstruction of human metabolism. Recon l's 1496 genes, 2004 proteins, 2766 metabolites, and 3311 biochemical and transport reactions were extracted from more than 50 years of legacy biochemical knowledge and Build 35 of the human genome sequence.

METHOD FOR ROBUST COMPARISON OF DATA

The present invention provides relatively robust comparison of bioinformatic data, such as gene expression data, by providing a computer-implemented method,a computer program product and a computer readable medium, that analyzes data according to the appended patent claims. The invention provides stability with respect to re-sampling of data.

SYSTEM AND METHOD FOR STORING MASS SPECTROMETRY DATA

The present invention relates to a system and methods for facilitating the analysis of proteomic expression data. In this system, complex sequence-correlated peptide expression information and mass spectrum data are processed and stored in a relational database. Using a parallel computational method, the expression data and results are parsed and associated to rapidly yield peptide sequence information. The system automates necessary tasks associated with peptide data analysis and organizes large amounts of information needed to perform the data analysis in a logical and accessible manner.

COMPOSITIONS AND METHODS OF USE OF STANDARDIZED MIXTURES

The present invention is directed to methods and compositions for evaluating nucleic acids, methods of preparing such compositions, and applications and business methods employing such compositions and methods. In particular, the present invention provides business methods for operating a gene expression measurement service.

METHOD OF VISUALIZING NON-TARGETED METABOLOMIC DATA GENERATED FROM FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETERS

The invention can be summarized as follows. The present invention provides a method of displaying spectroscopic data comprising the steps of, i)obtaining spectroscopic data from a plurality of samples, each sample comprising one or more components wherein each component is characterized by an ordered pair (X,Y) of data comprising data element value X and data element value Y, wherein X is a data element value, equivalent or directly proportional to the mass of the component, and Y is a data element value equivalent or directly proportional to the amount of the component; ii) identifying all unique components comprising a common data element value X in said samples; computing the average of all X therefrom; and determining the average and optionally, the standard deviation for all Y values from all ordered data pairs comprising a common X; iii) generating a data structure comprising an array of codable cells, each cell assigned a color or other identifiable characteristic based on the relationship ...

COMPOSITIONS AND METHODS FOR DIAGNOSING AND TREATING HYPERTHYROIDISM IN COMPANION ANIMALS

An isolated DNA molecule comprising a fragment of the gene encoding the feline NIS is disclosed as well as methods of use thereof. Also provided are methods for rational diet design of food composition suitable for administration to feline companion animals afflicted with hyperthyroidism, comprising (a) accessing at least one database that comprises a first data set relating functional gene profile of a biofluid or tissue sample from an animal to physiological condition of the animal, where the functional gene profile is that of the feline NIS gene; (b) accessing at least one database that comprises a second data set relating effects of bioactive dietary components on the functional gene profile; (c) using an algorithm drawing on these data sets, processing input data defining physiological condition to derive a nutritional formula promoting wellness of a feline companion animal afflicted with hyperthyroidism; and (d) preparing a food composition based on the nutritional formula.

METHODS OF IDENTIFYING AN ORGANISM

This disclosure features methods of identifying an organism. The methods include: (a) obtaining a nucleic acid sample from an organism; (b) imaging said nucleic acid; (c) obtaining a restriction map of said nucleic acid; and (d) correlating the restriction map of said nucleic acid with a restriction map database, thereby identifying the organism.

ANONYMOUS TESTING SYSTEM AND KIT

Disclosed are methods and kits for conducting anonymous genetic testing. The methods and kits include provide a patient with an Alias ID and Password. The Alias ID is used to track a genetic sample from the patient. Both the Alias ID and Password are then used by the patient to obtain the results of the genetic test. The methods and kits allow a patient to have a genetic test performed while remaining anonymous.

METHOD FOR PATIENT GENOTYPING

The present invention is a system and method for utilizing human genetic and genomic information to guide prescription dispensing and improved drug safety in a pharmacy setting. The system and method of the present invention utilizes a dedicated information management system and software to utilize patient-specific genetic information to screen for increased risk of adverse drug reactions and therapeutic responses at the time of drug dispensing.

SYSTEM AND METHOD FOR MANAGEMENT AND EVALUATION OF GENOTYPING DATA

Provided are systems and methods for improving efficiency in high throughput genotyping operations by implementing a unique workflow management architecture that permits faster and more accurate determination and evaluation of genotyping and haplotyping, and software to accomplish the same. The system provides a user with a highly-accurate summary and multiple-field breakdown of panels of genotyping data samples for batch approval and batch selection of ambiguous or potentially unique sample sets which can be selected for further analysis. Also provided are tools for evaluating and improving the operation of a genotyping laboratory to maximize the testing and typing of the significant quantities of raw data used in genotyping that are produced in high-throughput laboratory environments.

GENE EXPRESSION AND EVALUATION SYSTEM

An efficient and easy to use query system for a gene expression database. Using such a system, one can easily identify genes or expressed sequence tags whose expression correlates to particular tissue types. Various tissue types may correspond to different diseases, states of disease progression, different organs, different species, etc. Researchers may now use large scale gene expression databases to full advantage.

INTERACTION SITE PREDICTING APPARATUS, METHOD OF INTERACTION SITE PREDICTION, PROGRAM AND RECORDING MEDIUM

It is intended to provide, for study of protein-protein interaction, an interaction site predicting apparatus, method of interaction site prediction, program and recording medium. Accordingly, a data base containing three-dimensional information and statistical information is created from information on known steric configurations of protein-protein complexes so as to enable analysis of protein-protein interaction. Further, with the use of this data base, there are accomplished with high precision prediction of the interaction site of protein in unknown steric configuration of protein-protein complex, prediction of the interaction site of protein whose steric configuration is unknown and prediction of relative positioning in the steric configuration of protein-protein complex. Still further, there are accomplished optimization of results of homology modeling of the steric configuration of multiple-chain protein and evaluation of alignment of the steric configuration of protein-protein complex ...

METHOD AND SYSTEM FOR PROVIDING A CUSTOMER BIOPOLYMER TO A CUSTOMER

The present invention relates to a method and a system for providing a customer biopolymer to a customer. The sequence of a customer biopolymer is transferred to a production control system of a biopolymer service provider, synthesized on a production machine of the service provider and delivered to the customer, wherein no human action is necessary to initiate or control the synthesis process.

DETECTION OF GENETIC SEQUENCES USING A BIPARTITE PROBE

The present invention concerns a method to improve detection or quantification of a genetic sequence in a genetic sample using a bipartite probe. A bipartite probe is made of a nucleic acid binding sequence capable of hybridizing a target genetic sequence and a binding probe sequence capable of hybridizing to a detectable amplification molecule through a nucleic acid sequence capable of hybridizing to the binding probe sequence of the bipartite probe. The amplification molecule (6) can be a dendriver that includes a label in its core and/or on any of its arms. Moreover, a secondary signal generation molecule (11) may also be added to the mixture to further increase signal. Similarly, tertiary (20) and quaternary (30), etc. amplification molecules may successively be added to yield increase signal.

SYSTEM AND METHOD FOR GENERATING AN AMALGAMATED DATABASE

A method for creating an amalgamated bioinformatics database from at least a ferst database and a second database is presented. Concepts are identified in a ferst field from the records of the first database. A second field from the records of the second database which has data related to the first field is also identified. A ferst set of concepts is identified by traversing a mediating database using terms associated with the first field and a second set of concepts is also identified by traversing the mediating database using terms associated with the second field. Either the ferst set of concepts or the second set of concepts, or both, is identified using non-trivial terminological mapping. The set of related concepts in the ferst set of concepts and the second set of concepts is identified and a record is generated in the amalgamated bioinformatics database including data from records of the first database, data from records of the second database and the related concepts from the mediating ...

METHOD AND SYSTEM FOR MICROBIOME-DERIVED DIAGNOSTICS AND THERAPEUTICS FOR AUTOIMMUNE SYSTEM CONDITIONS

A method for at least one of characterizing, diagnosing, and treating an autoimmune disorder in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the autoimmune condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the autoimmune condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.

Methods for establishing and analyzing the conformation of amino acid sequences

The present invention relates to methods for establishing and analyzing the conformation of amino acid sequences. In particular, the invention relates to methods for the validation of the conformation of given amino acid-based molecules, methods for conformation determination starting from a linear amino acid sequence as well as methods for the alignment of two or more amino acid sequences.

System and method for review in studies including toxicity and risk assessment studies

Systems and methods for reviewing and managing toxicology and risk assessment studies, including the reviewing of specimen images.

Computer system for providing information about the risk of an atypical clinical event based upon genetic information

A method in a computer system for preventing atypical clinical events related to information identified by DNA testing a person is provided. The method includes receiving clinical agent information. The method also includes determining if a gene is associated with the clinical agent information, and if so, obtaining a genetic test result value for the associated gene of the person. The method further includes comparing the genetic test result value to a list of polymorphism values associated with an atypical clinical event, and determining whether the genetic test result value correlates to a polymorphism value on the list, and if so, outputting information about the atypical clinical event associated with the polymorphism value.

METHOD AND SYSTEM FOR MICROBIOME-DERIVED DIAGNOSTICS AND THERAPEUTICS FOR AUTOIMMUNE SYSTEM CONDITIONS

A method for at least one of characterizing, diagnosing, and treating an autoimmune disorder in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the autoimmune condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the autoimmune condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.

Glycan markers for diagnosing and monitoring disease

The present invention provides ultra-sensitive methods for detecting changes in glycosylation that are correlated with pre-cancerous or early cancerous states. Because the chance of complete recovery is increased with earlier detection of cancer, the present invention provides therapeutically useful methods of early detection, diagnosis, staging and prognostication.

BROAD-BASED DISEASE ASSOCIATION FROM A GENE TRANSCRIPT TEST

SYSTEMS AND METHODS FOR TRANSMISSION AND PRE-PROCESSING OF SEQUENCING DATA

SYSTEMS AND METHODS FOR PROTECTING AND GOVERNING GENOMIC AND OTHER INFORMATION

Information management system for biochemical information

An information management system for managing biological information (200). The information management system comprises by structured descriptions of biological pathways (700) that are formed of at least pathways (212), biochemical entities (218), connections (216) and interactions (222), such that each pathway (212) relates to one or more connections (216); each connection (216) joins one biochemical entity (218) and one interaction (222); and each pathway (212) relates to a specific location (214).

METHODS AND SYSTEMS FOR IDENTIFICATION OF CAUSAL GENOMIC VARIANTS

Systems and methods for monitoring behaviour informatics

A system and method used to assess animal behavior includes a module having sensors that collects a variety of physical and biological data from a test subject. Interpretation of the data is provided to assess the test subject's behavior, neurology, biochemistry and physiology. The module is useful in observing the effects of a drug on the test animal and providing information on the drug's signature. Another advantage is module's portability that allows it to be used in standard laboratory cages. This portability allows the animal to be tested in its own habitat, that can reduce any erroneous data due to stressing the animal when removed to a test cage. Additionally, the module's design allows for parallel data collection and interpretation from several laboratory animals undergoing different experiments. Multidimensional modeling of the test subject based the system's interpretation of the data allows pattern recognition of the drug signature and predictive drug analysis.

System, method and apparatus for transgenic and targeted mutagenesis screening

The present invention provides a method and apparatus for to conduct transgenic and targeted mutagenesis screening of genomic DNA. This invention also provides a system for screening DNA for a designated genetic sequence. The system includes a computer having a processor, memory and web browser, wherein the computer receives instructions concerning the designated genetic sequence and other screening parameter selection from a remote user via a form of electronic communication, and an automatic screening device that analyzes samples of genomic DNA for the designated sequence.

Methods and systems for annotating biomolecular sequences

Polypeptide sequences and polynucleotide sequences are provided. Also provided are annotative information concerning such sequences and uses for these sequences.

A METHOD AND RELATIONAL DATABASE MANAGEMENT SYSTEM FOR STORING, COMPARING, AND DISPLAYING RESULTS PRODUCED BY ANALYSES OF GENE ARRAY DATA

A method and system for analyzing data over a network are described. A Web server communicates with a storage system that stores genomic information in a database. Client systems connect to the Web server over a network, such as the Internet, using standard Web protocols (e.g., HTTP). The Web server sends Web pages to the client through which pages the user of the client can load genomic information into the database. The client user obtains the genomic information for uploading from genomic samples of organisms hybridized to chips or arrays. With the database populated with genomic information, the client user interactively selects and performs an analysis on selected samples over the network. The result produced by the analysis is a list of genes or a list of gene lists that becomes part of the database. These gene lists or lists of gene lists can then be compared with other previously stored lists or with user-generated and/or user-selected gene lists. Accordingly, subsequent users of ...

A comprehensive searchable medical record system supporting healthcare delivery and experiment

Among the many potential embodiments is a searchable electronic medical record system comprising: an interface for receiving data representing a search item; at least one repository associating a subject identifier with medical information specific to a particular subject comprising: genomic information, clinical data, and laboratory test results; and a search processor for searching said at least one repository to find medical information comprising said search item.

方向性クローニング用ベクター

ARTIFICIAL INTELLIGENCE SYSTEM FOR GENE ANALYSIS

PROBLEM TO BE SOLVED: To provide a system that conducts medical, experimental and industrial analysis on a biological sample, and that links and correlates with patient's profiles, medical status, various anxieties and medical treatment, and the like. SOLUTION: A central data-processing equipment includes a Web server which communicates with remote user equipment, supports data analysis, and provides the function on security and commerce, an application server which executes various kinds of processing, a database server that stores patient information, statistical data, etc., and an operation server which performs order control, order management, order tracking, etc. A user diagnostic part of the remote user equipment includes a DNA microarray or a gene chip, an array or a chip scanner, a PC system, a user interface for system behavior, a gene pattern processing function, a pattern-matching request of chip ID for the central-process equipment, a report generation function, and the like ...

PROCEDURE FOR THE IDENTIFICATION OF SPECTRA

METHOD FOR THE DETERMINATION OF THE RESISTANCE AGAINST MEDICINES

COMPUTER-BASED PROCEDURE AND SYSTEM FOR THE SCREENEN OF GENOMI DNS

PROCEDURE FOR KONFORMATIONSANALYSE OF AMINO ACID SEQUENCES

MARKING REAGENT AND OPERATING TECHNIQUE

PROCEDURE FOR THE IDENTIFICATION OF POLYMORPHEN GENETIC MARKERS

DATA ANALYSIS OF DNS MARKIERUNGSPROFILEN

Compressing, storing and searching sequence data

The redundancy in genomic sequence data is exploited by compressing sequence data in such a way as to allow direct computation on the compressed data using methods that are referred to herein as “compressive” algorithms. This approach reduces the task of computing on many similar genomes to only slightly more than that of operating on just one. In this approach, the redundancy among genomes is translated into computational acceleration by storing genomes in a compressed format that respects the structure of similarities and differences important to analysis. Specifically, these differences are the nucleotide substitutions, insertions, deletions, and rearrangements introduced by evolution. Once such a compressed library has been created, analysis is performed on it in time proportional to its compressed size, rather than having to reconstruct the full data set every time one wishes to query it.

Data analysis of dna sequences

Systems and methods for data analysis are provided. In one embodiment, a method for analysis is provided, including electronically receiving sequence data; electronically receiving one or more reference data sequences related to at least an expression vector; associating the sequence data with at least one of the reference data sequences to identify a transgene flanking sequence; searching a genome for one or more insertion sites of the transgene flanking sequence; and annotating the genome and the one or more insertion sites within the genome when one or more insertion sites are found in said searching step.

SYSTEM AND METHOD FOR PROCESSING REFERENCE SEQUENCE FOR ANALYZING GENOME SEQUENCE

Provided are systems and methods for processing a reference sequence. Exemplary systems for processing a reference sequence may include a seed extractor configured to extract a seed from a reference sequence; a determiner configured to determine whether an unidentified base is present or absent in a seed extracted by the seed extractor; and an index generator configured to add a seed to an index when unidentified bases are absent from an extracted seed. 1. A system for processing a reference sequence , comprising:a seed extractor configured to extract a seed from a reference sequence;a determiner configured to determine whether an unidentified base is present or absent in a seed extracted by the seed extractor; andan index generator configured to add a seed to an index when unidentified bases are absent from a seed.2. The system of claim 1 , wherein the determiner is configured to determine that an unidentified base is present in a seed when a base denoted by a letter other than A claim 1 , C claim 1 , G or T is present in a seed.3. The system of claim 1 , wherein the determiner is configured to determine that an unidentified base is present in a seed when a base denoted by the letter N is present in a seed.4. A system for analyzing a genome claim 1 , wherein said system comprises the system of any one of to .5. An apparatus claim 1 , comprising:at least one processor;a memory; andat least one program,wherein the at least one program is stored in the memory and executed by the at least one processor, said program comprising commands for:extracting a seed from a reference sequence;determining whether an unidentified base is present or absent in the extracted seed; andadding the seed to an index when unidentified bases are absent from said extracted seed.6. A method for processing a reference sequence claim 1 , comprising the steps of:(1) extracting a seed from a reference sequence;(2) determining whether an unidentified base is present or absent in the extracted seed ...

Classification of Protein Sequences and Uses of Classified Proteins

A searchable protein database is disclosed. The protein database comprises a plurality of entries, each entry having a sufficiently short predicting sequence and a protein classifier corresponding to the predicting sequence. An unclassified protein sequence can be classifiable by the database via searching therein for a motif of amino acids matching a predicting sequence of the database, thereby attributing to the unclassified protein a protein classifier. 110-. (canceled)11. A method of classifying a protein sequence , comprising searching the protein sequence for a motif of amino acids matching a predicting sequence present in a protein database , and using the protein classifier corresponding to said predicting sequence for classifying the protein sequence;said protein database having a plurality of entries, each having a predicting sequence which comprises less than L amino acids and a protein classifier corresponding to said predicting sequence.12. The method of claim 11 , further comprising repeating said step of searching at least once claim 11 , thereby providing a plurality of motifs of amino acids matching predicting sequences present in said protein database.13. The method of claim 11 , further comprising issuing a report containing classification of the protein sequence.14. The method of claim 11 , wherein said classifying the protein sequence comprises determining presence or absence of at least one active pocket or active site on the protein sequence.15. The method of claim 14 , further comprising determining the location of said at least one active pocket or active site.16. Apparatus for classifying a protein sequence claim 14 , comprising:a searcher, capable of accessing a protein database, said searcher being operable to search the protein sequence for a motif of amino acids matching a predicting sequence present in said protein database, said protein database having a plurality of entries, each having a predicting sequence which comprises less than ...

Finding relatives in a database

Determining a relative relationship of people who share a common ancestor within a number of generations includes: obtaining recombinable deoxyribonucleic acid (DNA) sequence information of a first user and recombinable DNA sequence information of a plurality of users; processing, using a plurality of computer processors, the recombinable DNA sequence information of the plurality of users in parallel; and determining, based at least in part on a result of processing the recombinable DNA sequence information of the plurality of users in parallel, a predicted degree of relative relationship between the first user and a user among the plurality of users. The predicted degree of relative relationship corresponds to a number of generations within which the first user and the user among the plurality of users share a common ancestor.

ORGANIZATION, VISUALIZATION AND UTILIZATION OF GENOMIC DATA ON ELECTRONIC DEVICES

Described herein are methods, devices and systems for simple organization, visualization and use of genome data (e.g. human genome data) on electronic devices (e.g. portable devices). In some embodiments, the data are organized and/or visualized according to phenotype traits, genes, and/or markers in a similar manner to the organization and/or visualization of digital music contents. This concept allows a new procedure for genomic data organization and facilitates the development of genomic data visualization tools. The methods described herein can be implemented with consumer-oriented software on electronic devices, computers, and portable devices, for the use of genomic related data in the field of personalized medicine for predictive, preventive and participative wireless healthcare. 2. The GUI of claim 1 , wherein the metadata further comprises one or more of: a disease name claim 1 , a phenotype claim 1 , a gene name claim 1 , a protein name claim 1 , a chromosome claim 1 , a nucleotide accession claim 1 , a protein accession claim 1 , a protein UID claim 1 , a EC/RN number claim 1 , a filter claim 1 , a locus link ID claim 1 , a MIM claim 1 , a modification date claim 1 , a property claim 1 , a PubMed UID claim 1 , a taxonomy ID claim 1 , a text word claim 1 , and a UniGene cluster number.3. The GUI of claim 1 , wherein the phenotypic traits claim 1 , diseases claim 1 , or a combination thereof are represented by images.4. The GUI of claim 3 , wherein the images further comprise genes and/or genetic markers correlated with the phenotypic trait or disease.5. The GUI of claim 3 , wherein the images are scrollable by touching the display of the mobile device with a vertical claim 3 , horizontal claim 3 , or circular motion.6. The GUI of claim 3 , wherein the images further comprise an indication when the phenotypic trait or diseases is clinically relevant in an individual.7. The GUI of claim 6 , wherein the indication is a color code.8. The GUI of claim 1 , ...

PARALLELIZATION OF SYNTHETIC EVENTS WITH GENETIC SURPRISAL DATA REPRESENTING A GENETIC SEQUENCE OF AN ORGANISM

A method, system, and computer program product for parallelization of updating synthetic events with genetic surprisal data comprising dividing the synthetic event into cohort parts and assigning the cohort parts to one of a plurality of computer processing elements. Within each processing element: searching data records of patients for genetic surprisal data; generating a cluster comprising a centroid by populating the cluster based on all of the matches of the data records; calculating a new centroid for each cluster; calculating a Euclidean distance in multiple dimensions for each match of data records to the new centroid for each cluster; reassigning each match of data to the new centroid of each cluster based on the shortest calculated Euclidean distance to the new centroid for each cluster; and determining at least one cohort part from the clusters and recombining the cohort parts into updated synthetic events based on the metadata. 110.-. (canceled)11. A computer program product for parallelization of updating synthetic events with genetic surprisal data representing a genetic sequence of an organism comprising:one or more computer-readable, tangible storage devices;program instructions, stored on at least one of the one or more storage devices, to receive a synthetic event and associated metadata from a user, wherein the metadata comprises at least one genetic surprisal data attribute;program instructions, stored on at least one of the one or more storage devices, to divide the synthetic event into cohort parts and assign the cohort parts and associated synthetic event metadata to one of the plurality of computer processing elements; and search data records of patients for genetic surprisal data and store matches of the data records in a repository;', 'generate a cluster comprising a centroid by populating the cluster based on all of the matches of the data records;', 'calculate a new centroid for each cluster;', 'calculate a Euclidean distance in multiple ...

METHOD FOR ROBUST COMPARISON OF DATA

The present invention provides relatively robust comparison of bioinformatic data, such as gene expression data, by providing a computer-implemented method, a computer program product and a computer readable medium, that analyzes data according to the appended patent claims. The invention provides stability with respect to re-sampling of data. 1. A computer-implemented method for identifying a set having a relationship between a plurality i of bioinformatics data samples of each of a plurality of measurement variables g , based on a ranking method for sorting the data , the relationship being indicative of a biological state , the computer-implemented method comprising:sorting the bioinformatics data into a list l according to the ranking provided by the ranking method;{'sub': l', 'l', 'ij', 'i', 'j, 'computing an exchangeability score of pairs or subsets of variables of the ordered bioinformatics data, resulting in an exchangeability matrix V, wherein each entry (V)is the normalized exchangeability score of measurement variables gand g, and carrying information about the exchangeability between each of the plurality of measurement variables g;'}{'sub': 'l', 'expanding the ordered lists l of the data, based on the exchangeability matrix V; and'}{'sub': 'l', 'comparing the expanded experimental list vector lwith another list vector comprising a plurality of measurement variables g and thereby determining the relationship between the samples, thereby reducing the plurality i into an identified set of data samples being indicative of the biological state.'}2. The computer-implemented method according to claim 1 , wherein the expanding comprises:{'sub': 'l', 'claim-text': {'br': None, 'i': A', '=u', 'r, 'sub': l', 'ii', 'i, '()()'}, 'computing a diagonal position matrix A, by defining diagonal elements as{'sub': 'i', 'img': [{'@id': 'CUSTOM-CHARACTER-00067', '@he': '2.79mm', '@wi': '2.46mm', '@file': 'US20140074864A1-20140313-P00003.TIF', '@alt': 'custom-character', '@ ...

Diagnostics Platform for Mitochondrial Dysfunctions/Diseases

The present invention concerns machine learning based methods and systems for diagnosing and treating genetic diseases characterized by mitochondrial dysfunctions. A library of reference learning models is developed based on in vitro reference samples obtained from cell-cultures exposed to specific mitochondrial inhibitors. Each model is able to predict a specific labeled mitochondrial dysfunction induced in the cell-culture by the inhibitor/stressor. The reference models are then applied to target samples drawn in vivo from target subjects who are known to have specific genetic mitochondrial diseases. A mapping is developed between mitochondrial dysfunctions predicted in the subjects and their known mitochondrial diseases. This mapping and the reference models are then applied to a clinical sample of an undiagnosed patient in whom a diagnosis of a mitochondrial dysfunction and an associated mitochondrial disease is made. If there is a known rescuer for the mitochondrial dysfunction, it may be recommended in a personalized, targeted therapy. 1. A diagnostic method comprising the steps of:(a) introducing in one or more dosages a mitochondrial inhibitor into each of one or more cell-cultures grown in vitro from one or more cell-lines, said mitochondrial inhibitor inducing a mitochondrial dysfunction into said each of one or more cell-cultures;(b) drawing from each of said one or more cell-cultures one or more reference samples at one or more times since said introducing;(c) making one or more reference biomarker measurements from corresponding each of said one or more reference samples;(d) learning by a learning module one or more reference models each able to predict said mitochondrial dysfunction in an unseen biomarker measurement, said learning module comprising a microprocessor executing program instructions stored in a non-transitory storage medium coupled to said microprocessor;(e) drawing from one or more target subjects one or more target samples in vivo and ...

METHODS AND APPARATUSES FOR GENERATING REFERENCE GENOME DATA, GENERATING DIFFERENCE GENOME DATA, AND RECOVERING DATA

According to one embodiment, a method of generating reference genome data includes: determining, based on a plurality of base sequence data of different subjects, base information relating to at least one position in a base sequence according to a frequency of appearance of each of a plurality of base information at the position. The method further includes generating reference genome data to associate the determined base information with the position. 1. A method of generating reference genome data , comprising:reading a plurality of base sequence data of different subjects from a hardware storage;determining, based on the plurality of base sequence data of different subjects, base information relating to at least one position in a base sequence according to a frequency of appearance of each of a plurality of base information at the position; andgenerating reference genome data to associate the determined base information with the position.2. The method of generating reference genome data according to claim 1 , whereinthe at least one position is at least one position of SNP.3. The method of generating reference genome data according to claim 1 , whereinthe at least one position is each of a plurality of positions of SNP,the determining comprises determining, for each position of SNP, base information with a highest frequency of appearance among the plurality of base information in the plurality of base sequence data to the base information at the position of SNP, andthe generating comprises generating the reference genome data to associate each determined base information with each corresponding position of SNP.4. The method of generating reference genome data according to claim 1 , whereinthe plurality of subjects belong to a same attribute class.5. The method of generating reference genome data according to claim 3 , whereinthe generating comprises generating the reference genome data to further associate base information, at a position other than the position ...

HYBRIDIZED STORAGE OPTIMIZATION FOR GENOMIC WORKLOADS

A method for more efficiently storing genomic includes designating multiple different data storage techniques for storing genomic data generated by a genomic pipeline. The method further identifies a file, made up of multiple blocks, generated by the genomic pipeline. The method determines which data storage technique is most optimal to store each block of the file. In doing so, the method may consider the type of the file, the stage of the genomic pipeline that generated the file, the access frequency for blocks of the file, the most accessed blocks of the file, and the like. The method stores each block using the data storage technique determined to be most optimal after completion of a designated stage of the genomic pipeline, such that blocks of the file are stored using several different data storage techniques. A corresponding system and computer program product are also disclosed. 1. A method for more efficiently storing genomic data , the method comprising:designating a plurality of different data storage techniques for storing genomic data generated by a genomic pipeline;identifying a file, made up of a plurality of blocks, generated by the genomic pipeline;determining which data storage technique is most optimal to store each block of the file; andstoring each block using the data storage technique determined to be most optimal after completion of a designated stage of the genomic pipeline, such that blocks of the file are stored using several different data storage techniques.2. The method of claim 1 , wherein determining which data storage technique is most optimal comprises taking into account a file type associated with the file.3. The method of claim 1 , wherein determining which data storage technique is most optimal comprises taking into account a stage of the genomic pipeline that generated the file.4. The method of claim 1 , wherein determining which data storage technique is most optimal comprises taking into account an access frequency ...

SYSTEMS AND METHODS FOR SOURCE SIGNAL SEPARATION

A method includes receiving an input signal comprising an original domain signal and creating a first window data set and a second window data set from the signal, wherein an initiation of the second window data set is offset from an initiation of the first window data set, converting the first window data set and the second window data set to a frequency domain and storing the resulting data as data in a second domain different from the original domain, performing complex spectral phase evolution (CSPE) on the second domain data to estimate component frequencies of the first and second window data sets, using the component frequencies estimated in the CSPE, sampling a set of second-domain high resolution windows to select a mathematical representation comprising a second-domain high resolution window that fits at least one of the amplitude, phase, amplitude modulation and frequency modulation of a component of an underlying signal wherein the component comprises at least one oscillator peak, generating an output signal from the mathematical representation of the original signal as at least one of: an audio file; one or more audio signal components; and one or more speech vectors and outputting the output signal to an external system. 1. A method comprising:receiving a biomedical signal; and computing a plurality of oscillator peaks for the biomedical signal;', 'tracking one or more of the plurality of oscillator peaks to form one or more tracklets; and', 'grouping the one or more tracklets based, at least in part, on at least one characteristic harmonic of the one or more tracklets to create a first fingerprint., 'creating a fingerprint of the biomedical signal wherein said creating comprises the steps of2. The method of claim 1 , further comprising comparing the first fingerprint to a previously computed second fingerprint.3. The method of wherein the comparing further comprises comparing the first fingerprint to the previously computed second fingerprint to ...

Systems, methods, and apparatuses for sequence alignment

Systems, methods, and apparatuses are disclosed for reducing the computational time of assigning a species to an infection isolate. A method for dividing a search index into one or more sub-indices based on a phylogenetic tree of reference sequences is disclosed. A method for dividing reads into test sets and aligning to sub-indices for assigning a species to an infection isolate is disclosed. A system for aligning sequence reads to a database of reference sequences using sub-indices is disclosed.

SYNTHETIC WGS BIOINFORMATICS VALIDATION

Systems, methods, and devices for generating synthetic genomic datasets and validating bioinformatic pipelines for genomic analysis are disclosed. In preferred embodiments, synthetic maternal and paternal datasets with known variants are used with matched normal synthetic datasets to validate various bioinformatic pipelines. Bioinformatic pipelines are evaluated using the synthetic datasets to assess design changes and improvements. Accuracy, PPV, specificity, sensitivity, reproducibility, and limit of detection of the pipelines in calling variants in synthetic datasets is reported. 1. A computer-implemented method of generating a synthetic digital genomic dataset , comprising:obtaining a reference genome and introducing a plurality of SNPs at a predetermined frequency and distribution into at least one autosome and an X-chromosome of the reference genome to so prepare a synthetic maternal genome;introducing a plurality of SNPs at a predetermined frequency and distribution into at least one autosome and an X- or Y-chromosome of the reference genome to so prepare a synthetic paternal genome; andmerging the maternal and paternal synthetic genomes into a combined synthetic digital genomic dataset.2. The method of further comprising a step of sampling the combined dataset to thereby produce a plurality of simulated reads.3. The method of wherein the step of sampling is performed to simulate a read coverage of at least 25×.4. The method of wherein the step of sampling is performed using a read error and base quality profile representative of a frozen tissue sample.5. The method of wherein the step of sampling is performed to produce simulated reads having a length of between 100 and 400 bases.6. The method of further comprising a step of including into the combined dataset a list identifying type and position of the SNPs relative to the reference genome.7. The method further comprising a step of introducing into at least one of the synthetic maternal and paternal genome ...

WHOLE POOL AMPLIFICATION AND IN-SEQUENCER RANDOM-ACCESS OF DATA ENCODED BY POLYNUCLEOTIDES

This disclosure describes an efficient method to copy all polynucleotides encoding digital data of digital files in a polynucleotide storage container while maintaining random access capabilities over a collection of files or data items in the container. The disclosure further describes a process whereby random-access and sequencing of the polynucleotides are combined in a single step. 1. A method comprising:encoding a series of bits as a plurality of polynucleotide sequences, wherein the series of bits comprises digital data of a first data file;assigning at least one identifier to the plurality of polynucleotide sequences of the first data file;encoding a series of bits as a plurality of polynucleotide sequences, wherein the series of bits comprises digital data of a second data file;assigning at least one identifier to the plurality of polynucleotide sequences of the second data file; wherein the identifier for the polynucleotides encoding the first data file is different than the identifiers for the polynucleotides encoding the second data file polynucleotides;assigning a universal sequence to the polynucleotide sequences of the first and second data file, wherein the assigned universal sequence is the same for all polynucleotides; andgenerating polynucleotide sequence data that includes polynucleotide sequences with a payload region; the identifier as an identifier region, and the universal sequence.2. The method of further comprising polynucleotides for more than two data files claim 1 , wherein the identifiers are different for each data file.4. The method of further comprising:selecting at least one primer that corresponds to the nucleotides of the universal sequence and amplifying, using the primers, the polynucleotides in the container to produce an amplification product of all polynucleotides in the container.5. The method of further comprising:aliquoting the amplification product to additional containers in the storage system; thereby providing ...

COMPUTING DEVICE WITH IMPROVED USER INTERFACE FOR INTERPRETING AND VISUALIZING DATA

The present disclosure provides, in some embodiments, a computing device comprising an improved user interface. In some embodiments, the improved user interface enables the visualization of clinically relevant information pertaining to interacting gene variants, including therapeutic recommendations. In some embodiments, the improved user interface facilitates the contemporaneous visualization of clinically relevant information pertaining to individual gene variants and the visualization of clinically relevant information pertaining to an interaction between gene variants, including therapeutic recommendations. In some embodiments, the visualization(s), through the improved user interface, facilitates the rapid interpretation of clinically relevant information by a medical professional such that decisions regarding patient care may be made accurately and efficiently. 112-. (canceled)13. A method for treating a human patient comprising:receiving a user input of a diagnosed disease or condition of a human patient, wherein the diagnosed disease or condition is a type of cancer;based on the received user input, displaying, on a computing device having a display screen, a first representation comprising (i) one or more therapeutic recommendations based on an identified clinically relevant interaction between at least two human gene variants of a plurality of human gene variants for the diagnosed disease or condition of the human patient, and (ii) an identification of the at least two human gene variants for which the clinically relevant interaction was identified, wherein the one or more therapeutic recommendations are one or more therapies sensitive for the diagnosed disease or condition;contemporaneously displaying, on the display screen, and based on the received user input, a second representation comprising clinically relevant information pertaining to at least one of the at least two human gene variants for which the interaction was identified; wherein the ...

STABLE PAIR-WISE E-VALUE

This invention is related to systems and methods for obtaining a bioinformatic pair-wise E-value that is stable and not dependent on the size of a protein or nucleic acid sequence database. Exemplary embodiments are provided for defining at least one database for each protein contained in a multi-protein database and generating E-values between a query protein and each protein in each single-protein database provides a stable pair-wise E-value for each query-to-database protein comparison. 1. A computerized system for stable pair-wise E-value generation and/or allergen classification for a query sequence , comprising ,(a) an input device and an output device/interface;(b) an analysis system interface coupled to memory of a computer;(c) an operating system comprising at least one database;(d) a stable pair-wise E-value module; and(e) a classification module.2. The computerized system of claim 1 , wherein the input device is selected from the group consisting of any amino acid sequence claim 1 , automated sequencer claim 1 , sequencing data input device claim 1 , and sequencing data storage device.3. The computerized system of claim 1 , wherein the output interface comprises a list of potential allergen hits.4. The computerized system of claim 1 , wherein the at least one database comprises a consensus allergen database.5. The computerized system of claim 1 , wherein the stable pair-wise E-value module generates one stable pair-wise E-value for the query sequence against each sequence in the database used.6. The computerized system of claim 2 , wherein the classification module classifies sequences in the database used based on a pre-determined E-value.7. The computerized system of claim 6 , wherein the pre-determined E-value is equal or less than 0.1.8. The computerized system of claim 6 , wherein the pre-determined E-value is from 0.1 to 1×10.9. The computerized system of claim 5 , wherein the stable E-value is independent of the size of database used.10. The ...

DIGITAL MEASUREMENTS FROM TARGETED SEQUENCING

Disclosed herein are methods, compositions and kits for quantitating one or more specific nucleic acids within a plurality of nucleic acids. In some embodiments, a sequencing library is constructed from enriched probe extension products specific for the specific nucleic acids and sequenced. In some embodiments, the resulting reads are used for removing duplicate reads. In some embodiments, counting of verified probes is used to quantitate or determine the number of specific nucleic acid molecules in the starting nucleic acid sample. 1. A method for quantitating a plurality of specific nucleic acid molecules in a composition comprising: a. generating a plurality of probe extension products , wherein each probe extension product comprises a probe sequence that is complementary to a probe target region within a specific nucleic acid molecule; b. sequencing the plurality of probe extension products to generate a sequence for each of the plurality of probe extension products; c. aligning the sequence of each of the plurality of probe extension products to a reference sequence database , wherein the reference sequence database comprises probe sequences; and d. determining the number of alignments for the sequence of each probe extension product with a sequence in the reference sequence database , wherein the number of alignments indicates the quantity of each of the specific nucleic acid molecule that the probe of the probe extension product is complementary to.2. A method for quantitating a plurality of specific nucleic acid molecules comprising: a. generating a plurality of probe extension products , wherein each probe extension product comprises (i) a first adapter , and (ii) a probe sequence complementary to a probe target region within a specific nucleic acid molecule; b. sequencing the plurality of probe extension products to generate sequence data comprising a sequence for each of the plurality of probe extension products; c. identifying the presence of the probe ...

CENTRALIZED CONSENT MANAGEMENT

A consent management system (CMS) manages a number of individual consent data records of data subjects. The CMS stores predefined consent templates to be instantiated when an individual consent data record is created. The CMS represents a centralized system for management of individual consent data records that are created, stored, and maintained in relation to provided consent by data subjects for purposes of operations related to stored personal data records by associated application systems. The CMS may run on an on-premise, cloud, or personal device computing platform. 1. A computer implemented method to manage consent data records , the method comprising:instantiating a consent template selected from a plurality of consent templates to create a consent data record at a consent management system (CMS), wherein the consent data record is associated with a data controller, a data subject, a data record, a validation period, and an application system related to the data record;storing the consent data record at the CMS, wherein the CMS comprises a plurality of consent data records associated with the data subject, wherein a consent data record from the plurality of consent data records is associated with an application system from a plurality of application systems;based on evaluation of validation periods of the plurality of consent data records, sending a notification for expiration of a first record from the plurality of consent data records; andproviding an interface comprised in the notification to request a renewal of the first record.2. The method of claim 1 , further comprising:defining a data model for the consent template to comprise one or more attributes; andpreconfiguring an attribute from the one or more attributes with a default attribute value for creation of the consent data record at the CMS, wherein the consent data record defines authorized purpose to process personal data from the data record associated with the data subject.3. The method of ...

DEVICE, SYSTEM AND METHOD FOR SECURING AND COMPARING GENOMIC DATA

The present disclosure presents methods, systems, and devices for encrypting and comparing genomic data. The comparison of genomic data allows the owner of the data to ensure security of the data even when the party conducting the comparison is beyond the control of the owner of the data. The encryption of the genomic data enables the transmission, storage, and use of the genomic data in a secure media. 153.-. (canceled)54. A method for comparing genomic data comprising:transforming, by a processor of an electronic device, a portion of a first genomic data into a first coded genomic data and a portion of a second genomic data into a second coded genomic data;storing the second coded genomic data on the electronic device;comparing, by the processor, the first coded genomic data and the second coded genomic data at one or more common locations;generating, by the processor, match data based upon the comparison of the first coded genomic data and the second coded genomic data; andtransmitting, from the processor, the match data.55. The method as recited in claim 54 , wherein transforming the portion of the first genomic data and the portion of the second genomic data includes applying a cryptographic hash function.56. The method as recited in claim 54 , wherein transforming the portion of the first genomic data and the portion of the second genomic data includes applying a homomorphic encryption function.57. The method as recited in claim 54 , wherein the first genomic data and the second genomic data are each one of unencrypted data or encrypted data.58. The method as recited in claim 54 , wherein the portion of the first genomic data is one or more predetermined loci of the first genomic data.59. The method as recited in claim 58 , wherein the determination of the one or more predetermined loci of the first genomic data is obtained by application of a selection function.60. The method as recited in claim 58 , wherein the predetermined loci are based upon a requested ...

HEALTHCARE ANALYSIS STREAM MANAGEMENT

Apparatus, systems and methods for pre-processing, analyzing, and storing genomic data through a scalable, distributed analysis system across a network is presented. 152-. (canceled)53. A genomic analysis system comprising:a sequencing device interface configured to acquire sequence data from a plurality of sequencing devices, where the sequence data is from a plurality of patients;an analysis network; anda plurality of analysis computer nodes interconnected via the analysis network forming a genomic analysis engine having patient-specific analysis network topologies coupled with the sequencing device interface, and configured to process the sequence data from the patients in parallel into patient-specific genome data according to processing routes of the patient-specific analysis network topologies.54. The system of claim 53 , wherein the analysis engine is configured to process sequence data from at least 10 patients in parallel.55. The system of claim 53 , wherein the analysis engine is configured to process sequence data into the genome data at a rate of at least X patients per Y unit of time claim 53 , where X is at least 3 and Y is at most one day claim 53 , and wherein X is ten and Y is one day.56. The system of claim 53 , wherein the analysis engine is configured to process sequence data into the genome data at a rate of at least X patients per Y unit of time claim 53 , where X is at least 3 and Y is at most one day claim 53 , and wherein X is ten and Y is one hour.57. The system of claim 53 , wherein the analysis network comprises an optic fiber data link.58. The system of claim 57 , wherein the analysis network comprises a continent spanning network.59. The system of claim 53 , wherein the sequencing device interface is configured to obtain the sequence data from at least 100 sequencing devices in parallel.60. The system of claim 53 , wherein the genome data comprises genomic data associated with a demographic of the patients.61. The system of claim 53 , ...

METHODS FOR SCREENING AND SELECTING TARGET AGENTS FROM MOLECULAR DATABASES

The present disclosure relates to methods for screening for a modulator of a target protein. The present disclosure further relates to a systematic disease drug repositioning (SMART) method which integrates experimental and computational biology methods systematically with public transcriptomic profile data to enable fast-track identification and confirmation of novel drug candidates. 1. A method for screening for a modulator of a target protein , comprising:contacting a cell with at least one primary candidate agent;identifying the at least one primary candidate agent that modulates the target protein;obtaining publicly available large transcriptomic profiles of cellular responses to the at least one primary candidate agent;performing a first iteration to extract gene expression signatures for the at least one primary candidate agent;ranking all secondary candidate agents from the publicly available large transcriptomic profiles of cellular responses based on a similarity score of the transcriptomic profile to the at least one primary candidate agent;selecting the modulator of a target protein from the secondary candidate agents when the similarity score is above a determined threshold.2. The method of claim 1 , wherein the target protein is tau.3. The method of claim 1 , wherein the modulator affects tau phosphorylation.4. The method of claim 1 , wherein the similarity score of the transcriptomic profile is measured by a cMAP algorithm.5. The method of claim 1 , wherein at least one additional iteration is performed claim 1 , wherein the modulator of a target protein is added back to the list of primary candidate agents claim 1 , and new modulators of the target protein are obtained by repeating the screening process.6. The method of claim 1 , wherein the gene expression signatures include whole genome transcriptomic profiles.7. The method of claim 1 , wherein the gene expression signatures include transcriptomic profiles for selected gene sets.8. A computer ...

GENETIC AND GENEALOGICAL ANALYSIS FOR IDENTIFICATION OF BIRTH LOCATION AND SURNAME INFORMATION

A system identifies ancestral birth locations or surnames estimated to be associated with an individual's ancestors using an individual's genetic sample. The system identifies users who are genetic matches to the individual and determines whether and how often a birth location or surname appears in the pedigrees of those users. Birth locations or surnames that appear frequently throughout the pedigrees of genetically matching users may represent birth locations or surnames that are affiliated with the individual's ancestors. The system determines whether the frequency of appearance of a birth location or surname is statistically significant to eliminate biases for certain birth locations or surnames that appear more frequently than others. The birth location or surname may be provided to the individual based on an also-determined enrichment score. 1. A method comprising:receiving, from an individual, at least one sequence of genetic data;identifying a subset of genetic matches for the individual from a set of users, each matching user associated with a pedigree comprising a genealogical graph for that matching user;accessing, for each matching user, a corresponding one of the pedigrees to identify a subset of matching pedigrees;determining a match frequency for a birth location amongst the subset of matching pedigrees;determining a background frequency for the birth location amongst a set of pedigrees corresponding to the set of users;calculating a summary statistic based on the match frequency and the background frequency;determining an enrichment score for the birth location based on the summary statistic, the enrichment score representing a significance of the birth location to ancestors of the individual; andproviding the birth location to a computing device associated with the individual based on the determined enrichment score for the birth location.2. The method of wherein the sequence of genetic data comprises a pair of haplotypes for the individual.3. The ...

BIOPROCESS METHOD AND SYSTEM

Methods, systems and apparatus for performing a biological process are provided, wherein the method comprises implementation of at least one unit operation, and wherein the unit operation is defined according to a standardised element structure, the element structure comprising a plurality of functional section blocks, and wherein the section blocks comprise at least one of the group consisting of: imports; parameters; data; physical inputs; requirements; setup; and execution steps. 1. A method for performing a biological process wherein the method comprises implementation of at least one unit operation , and wherein the unit operation is defined according to a standardised element structure , the element structure comprising a plurality of functional section blocks , and wherein the section blocks comprise at least one of the group consisting of: imports; parameters; data; physical inputs; requirements; setup; and execution steps.2. The method of claim 1 , wherein the element structure further comprises at least one additional section block selected from the group consisting of: physical outputs claim 1 , analysis and validation steps.3. The method of wherein the element structure comprises at least the sections blocks defining: imports; parameters; data; physical inputs; requirements; setup; and execution steps.4. The method of claim 1 , wherein the biological process comprises at least two unit operations claim 1 , wherein each unit operation defined according to a standardised element structure.5. The method of claim 4 , wherein the at least two unit operations are non-identical.6. The method of claim 1 , wherein the unit operation is selected from the group consisting of: a conversion; a reaction; a purification; a construct assembly step; an assay or analysis such as a quantification of a product claim 1 , a by-product or reagent; a nucleotide or protein/peptide synthesis; a cell culture; an incubation; a restriction; a ligation; a mutation; an inoculation; a ...

METHOD AND SYSTEM FOR COMPRESSING GENOME SEQUENCES USING GRAPHIC PROCESSING UNITS

The present invention provides a method for compressing genome sequences readers using GPU processing unit. The method comprising the steps of: identifying position of each given genome reader characters string in the sequence of a reference genome, determining alignment of each reader string within the reference genome, comparing each reader characters string to corresponding reference genome sequence based on determined alignment, filtering characters in each reader by GPU processor by eliminating similar characters and extracting only characters differences in association to their position in the genome sequence and recording filtered data of each reader in association to its alignment in genome reference at the genome compressed database. 1. A method for compressing genome sequences readers using GPU processing unit , said method comprising the steps of:identifying position of each given genome reader characters string in the sequence of a reference genome;determining alignment of each reader string within the reference genome;comparing each reader characters string to corresponding reference genome sequence based on determined alignment;filtering characters in each reader by GPU processor by eliminating similar characters and extracting only characters differences in association to their position in the genome sequence;recording filtered data of each reader in association to it's alignment in genome reference at the genome compressed database.2. The method of further comprising the step: on the fly clustering readers creating logical separation for storing data in chunks while maintaining the logical and physical storage boundaries as a metadata.3. The method pf wherein the clustering is performed by applying histograms.4. The method of further comprising the steps of:check a given SQL query parametersdetermining readers strings to be retrieved based on query parameters;retrieve determined strings; andapplying non-mutating query operators including at least one ...

Finding relatives in a database

Determining relative relationships of people who share a common ancestor within at least a threshold number of generations includes: receiving recombinable deoxyribonucleic acid (DNA) sequence information of a first user and recombinable DNA sequence information of a plurality of users; processing, using one or more computer processors, the recombinable DNA sequence information of the plurality of users in parallel; determining, based at least in part on a result of processing the recombinable DNA information of the plurality of users in parallel, a predicted degree of relationship between the first user and a user among the plurality of users, the predicted degree of relative relationship corresponding to a number of generations within which the first user and the second user share a common ancestor.

SYSTEMS AND METHODS FOR STORING, PROCESSING AND UTILIZING PROPRIETARY GENETIC INFORMATION

A method of genetic testing utilizing a system of servers, databases, computers, software applications, or any other computing module. The computing modules allow for creation of a genetic test script and the analysis of genetic information based on the genetic test script. The system can also account for the use of proprietary biomarkers. 1. A method for conducting genetic testing , comprising:scanning a genome or portion of a genome of a patient with a remote client containing an interpretations list to determine the presence of one or more genetic mutations associated with a disease; and providing a risk factor corresponding to a determination of the presence of the one or more genetic mutations;wherein the genome or portion of the genome is stored in a storage area network collocated with the remote client;wherein the interpretations list contains a risk factor for the disease based on the one or more genetic mutations;wherein the risk factor is used in diagnosis of at least one condition or disease; andwherein the step of scanning a genome or portion of a genome of a patient to determine the presence of the one or more genetic mutations:(a) retrieving a list of genetic mutations from the interpretations list;(b) scanning the genome or portion of a genome of the patient for each of the one or more genetic mutations in the interpretations list; and(c) determining a number of mutations present in the genome or portion of a genome.2. The method of claim 1 , further comprising:accessing a proprietary records database containing records of proprietary biomarkers and rights holders of the proprietary biomarkers;determining the presence of a proprietary biomarker in the genome or portion of the genome of the patient;automatically forwarding information obtained from scanning the genome or portion of the genome to determine the presence of the proprietary biomarker to one or more of a payer party user and a rights holder user associated with the proprietary biomarker ...

METHOD OF IDENTIFYING A GENE ASSOCIATED WITH A DISEASE OR PATHOLOGICAL CONDITION OF THE DISEASE

A method of identifying a gene associated with a disease or pathological condition of the disease includes: a) obtaining a first group of exome sequences from a first population suffering from the disease or pathological condition and a second group of exome sequences from a second population not having the disease or pathological condition; b) identifying one or more variants in the first group by comparing it with the second group, and optionally with a public database, to generate a first set of variant data; c) applying a variant quality score calibration tool with a truth sensitivity threshold to remove false-positive variants having a sensitivity lower than the threshold and background variants from the first set of variant data so as to obtain a second set of variant data; d) removing synonymous variants from the second set of variant data to obtain a third set of variant data; and e) identifying one or more deleterious variants from the third set of variant data using a gene burden analysis, optionally generating a fourth set of variant data. 1. A method of identifying a gene associated with a disease or pathological condition of the disease , comprising the steps of:a) obtaining a first group of exome sequences from a first population of individuals and a second group of exome sequences from a second population of individuals, wherein the first population of individuals suffer from the disease or pathological condition of the disease, and the second population of individuals do not have the disease or pathological condition of the disease;b) identifying one or more variants in the first group of exome sequences by comparing the first group of exome sequences with the second group of exome sequences, and optionally with a public database, to generate a first set of variant data;c) applying a variant quality score calibration tool with a truth sensitivity threshold to remove false-positive variants having a sensitivity lower than the threshold and background ...

High Throughput Patient Genomic Sequencing And Clinical Reporting Systems

Contemplated panomic systems and methods significantly improve accuracy of genetic testing by taking into account matched normal data and expression levels of various genes in diseased tissue. Analysis and physician guidance is further improved by combining so identified clinically relevant changes with pathway analysis to thereby allow for classification of a tumor and/or identification of potentially druggable targets within affected pathways. 1. A method of calculating a treatment recommendation using omics information , comprising: (1) omic information of a patient, wherein the omic information is generated from genomic sequence information of a genomic sequence in a diseased and a matched normal sample;', '(2) a transcription level for the genomic sequence in at least the diseased sample;, 'obtaining, by an analysis engine, from an omics data base or sequencing facilityusing, via the analysis engine, the omic information and the transcription level for the genomic sequence in at least the diseased sample in a pathway model to calculate a pathway activity of a pathway containing the genomic sequence;identifying, via the analysis engine, a druggable target based on the calculated pathway activity; andupdating or generating a patient record with a treatment recommendation using the calculated pathway activity.2. The method of wherein the omic information comprises a differential sequence object that further comprises the transcription level for the genomic sequence in at least the diseased sample.3. The method of wherein the pathway model comprises an ensemble of treatment models claim 1 , a trained treatment outcome prediction model claim 1 , a pathway expression model claim 1 , a pathway recognition algorithm using data integration on genomic models (PARADIGM) claim 1 , or a drug response model.4. The method of wherein the omic information of the patient and the transcription level are coordinately provided from a sequencing facility.5. The method of further ...

ONTOLOGICAL MEDICAL CODING METHOD, SYSTEM, AND APPARATUS

Diagnosis and procedure terminology are ontologically organized according to context-based categories and medical concepts. The medical concepts are linked to aliases and medical codes used to document patient care. A user is guided to select and document additional medical concepts based on a medical concept dependency that has been created between certain medical concepts, some of which are required. A visual concept tree presents for user consideration all categories and medical concepts necessary to determine appropriate medical codes based on the disease, condition or injury in accordance with a ranking algorithm and user documentation preferences. Potential medical codes are also optionally presented for user consideration based on collected documentation and selected medical concepts.

METHODS AND SYSTEMS FOR DE NOVO PEPTIDE SEQUENCING USING DEEP LEARNING

The present systems and methods introduce deep learning to de novo peptide sequencing from tandem mass spectrometry data. The systems and methods achieve improvements in sequencing accuracy over existing systems and methods and enables complete assembly of novel protein sequences without assisting databases. The present systems and methods are re-trainable to adapt to new sources of data and provides a complete end-to-end training and prediction solution, which is advantageous given the growing massive amount of data. The systems and methods combine deep learning and dynamic programming to solve optimization problems. 1. A computer implemented system for de novo sequencing of peptides from mass spectrometry data using neural networks , the computer implemented system comprising:a processor and at least one memory providing a plurality of layered nodes configured to form an artificial neural network for generating a probability measure for one or more candidates to a next amino acid in an amino acid sequence, the artificial neural network trained on known mass spectrometry spectrum data containing a plurality of known fragment ions peaks of known sequences differing in length and differing by one or more amino acids; 'at least one convolutional layer for filtering mass spectrometry spectrum data to detect fragment ion peaks; and', 'wherein the plurality of layered nodes receives a mass spectrometry spectrum data as input, the plurality of layered nodes comprising obtain an input prefix representing a determined amino acid sequence of the peptide,', 'identify a next amino acid based on a candidate next amino acid having a greatest probability measure based on the output of the artificial neural network and the mass spectrometry spectrum data of the peptide; and', 'update the determined amino acid sequence with the next amino acid., 'the processor configured to2. The system of claim 1 , wherein the plurality of layered nodes comprise at least one fully-connected layer ...

BIOMARKER SEARCH METHOD, BIOMARKER SEARCH DEVICE, AND PROGRAM

A device for searching a biomarker to be used for determining whether or not a first treatment has an effect on a disease, the biomarker search device includes: a first storage; a second storage storing; a third storage; a fourth storage; a signature molecular information detector; a regression analyzer; a network generator; and a biomarker determinator. 1. A method for searching a biomarker to be used for determining whether or not a first treatment has an effect on a disease , comprising:reading, from a storage, omics information of a plurality of patients before treatment and omics information of control;detecting signature molecular information peculiar to disease from the omics information comprising a plurality of molecular information items, based on the read omics information of patients and the read omics information of control; andobtaining a biomarker from the signature molecular information, whereinupon obtaining the biomarker,selecting at least one molecular information item to be processed from the signature molecular information,reading the clinical information of a plurality of patients before treatment and the information of the effect of treatment in a plurality of patients from a storage,carrying out a regression analysis using the effect of treatment as an objective variable, and using the clinical information before treatment and variable data of the molecular information to be processed as explanatory variables,generating a network structure based on partial correlation between a first node, a second node and a third node, the first node being the effect of treatment, the second node being the clinical information before treatment, and the third node being the molecular information to be processed, when the determination coefficient of the regression analysis is equal to or more than a first threshold value, anddetermining whether or not there is a causal relationship equal to or more than a second threshold value between the molecular ...

METHODS FOR PROTEOME DOCKING TO IDENTIFY PROTEIN-LIGAND INTERACTIONS

The invention involves a method for identifying a target protein. The invention involves receiving a request to identify a target protein based on a ligand; identifying, using the ligand, a first protein, where the ligand binds with the first protein to form a ligand-protein complex; generating, a first binding site profile for the first protein, where the first binding site profile describes molecular properties of the first protein; obtaining, from a controlled server, structure data describing molecular properties of surfaces for a multitude of proteins, where the multitude of proteins comprises the target protein; identifying, using the first binding site profile and the structure data, the target protein; and presenting the target protein to a user. 1. A method for identifying a target protein , comprising:receiving a request to identify a target protein based on a ligand;identifying, using the ligand, a first protein, wherein the ligand binds with the first protein to form a ligand-protein complex;generating a first binding site profile for the first protein, wherein the first binding site profile describes molecular properties of the first protein;obtaining, from a controlled server, structure data describing molecular properties of surfaces for a plurality of proteins, wherein the plurality of proteins comprises the target protein;identifying, using the first binding site profile and the structure data, the target protein; andpresenting the target protein to a user.2. The method of claim 1 ,wherein the target protein comprises a plurality of target binding sites, andwherein the structure data further describes molecular properties of the plurality of target binding sites.3. The method of claim 2 , wherein identifying the target protein further comprises:identifying, using the first binding site profile and the structure data, a target binding site of the plurality of target binding sites;presenting the target binding site to the user.4. The method of claim 1 ...

IDENTIFYING SMALL SCALE VARIATIONS ACROSS SETS OF BACTERIAL GENOMES

One or more sequences are decomposed into one or more fixed length subsequences. The one or more sequences are associated with one or more respective genome samples. One or more contiguous ranges of the one or more fixed length subsequences are identified. A given one of the one or more contiguous ranges is analyzed to identify at least one group of variants of the fixed length subsequences within the given contiguous range. Analyzing the given contiguous range to identify the at least one group of variants comprises comparing the one or more fixed length subsequences of the given contiguous range to each other. It is determined whether the at least one group of variants partitions the one or more genome samples in satisfaction of at least one partitioning criterion. 1. A method for identifying variations across a collection of genomes , the method comprising:decomposing one or more sequences into one or more fixed length subsequences, wherein the one or more sequences are associated with one or more respective genome samples;identifying one or more contiguous ranges of the one or more fixed length subsequences;analyzing a given one of the one or more contiguous ranges to identify at least one group of variants of the fixed length subsequences within the given contiguous range, wherein analyzing the given contiguous range to identify the at least one group of variants comprises comparing the one or more fixed length subsequences of the given contiguous range to each other; anddetermining whether the at least one group of variants partitions the one or more genome samples in satisfaction of at least one partitioning criterion;wherein the steps of the method are implemented by at least one processing device comprising a processor operatively coupled to a memory.2. The method of claim 1 , wherein the one or more sequences comprise at least one of a read and a contig.3. The method of claim 1 , wherein the one or more fixed length subsequences comprise k-mers.4. The ...

METHOD FOR BUILDING A DATABASE

The present invention effectively utilizes data reflecting the expression of measurement target genes and non-measurement target genes other than the measurement target genes or functions of the gene products obtained by next generation sequencing analysis or microarray analysis. 1. A method for constructing a database of gene related information including gene related measurement data reflecting expression of a gene in a biological sample or a function of a gene product , andusing the database to search for new marker candidates, the method comprising:a step of acquiring information specifying an analysis target gene;a step of acquiring the gene-related measurement data for a non-analysis target gene other than the analysis target gene;a step of outputting gene related information of the non-analysis target gene to the database, anda step of storing in the database the gene related information of the gene not to be analyzed and the biological sample related information which is information related to the biological sample from which the gene related measurement data was obtained.2. The method according to claim 1 , whereinthe gene to be analyzed is used for at least one analysis selected from a group including disease risk assessment, screening, differential diagnosis, prognosis prediction, recurrence prediction, efficacy prediction, and disease monitoring.3. The method according to claim 1 , whereinthe marker is a disease biomarker or a target molecule for the treatment of a disease.4. The method according to claim 1 , whereinthe biological sample is obtained from at least one type of foci selected from a group including a predetermined disease, a predetermined disease type and a stage of a predetermined disease.5. The method according to claim 1 , whereinthere are a plurality of biological samples, and the plurality of biological samples are collected from different diseased foci of different patients.6. The method according to claim 1 , whereinthe gene-related ...

NASAL-RELATED CHARACTERIZATION ASSOCIATED WITH THE NOSE MICROBIOME

Embodiments of a method and/or system (e.g., for nasal-related characterization) can include determining a microorganism dataset associated with a set of subjects; and/or performing a characterization process based on the microorganism dataset, where performing the characterization process can additionally or alternatively include performing a nasal-related characterization process, and/or determining one or more therapies, such as for one or more nasal-related conditions. 1. A method for nasal-related characterization associated with microorganisms , the method comprising:determining a microorganism sequence dataset associated with a set of subjects, based on microorganism nucleic acids from samples collected from nose sites of the set of subjects;determining a set of microbiome composition features based on the microorganism sequence dataset;generating a nasal-related characterization model based on the set of microbiome composition features and supplementary data associated with the set of subjects; anddetermining a nasal-related characterization associated with a user based on the nasal-related characterization model and a user sample collected at a nose site of the user.2Abiotrophia, Achromobacter, Acinetobacter, Actinobacillus, Actinomyces, Aggregatibacter, Alistipes, Alloprevotella, Anaerococcus, Anaerostipes, Anoxybacillus, Aquabacterium, Arthrobacter, Atopobium, Bacillus, Bacteroides, Bergeyella, Bifidobacterium, Blautia, Bradyrhizobium, Brevibacterium, Brevundimonas, Burkholderia, Campylobacter, Capnocytophaga, Caulobacter, Centipeda, Chryseobacterium, Collinsella, Corynebacterium, Deinococcus, Delftia, Dermabacter, Dialister, Dolosigranulum, Dorea, Enterobacter, Faecalibacterium, Finegoldia, Flavobacterium, Fusicatenibacter, Fusobacterium, Gemella, Granulicatella, Haemophilus, Herbaspirillum, Hydrogenophilus, Klebsiella, Kluyvera, Kocuria, Lactobacillus, Lactococcus, Lautropia, Leptotrichia, Malassezia, Megasphaera, Meiothermus, Methylobacterium, ...

SYNTHETIC GENOMIC VARIANT-BASED SECURE TRANSACTION DEVICES, SYSTEMS AND METHODS

Various devices, systems, structures and methods are disclosed related to securely authorizing a transaction by synchronizing digital genomic data with associated synthetic genomic variants. An embodiment of the present invention utilizes digital genomic data associated with an entity, such as a person, who may utilize a genome-based security device to complete a transaction. In one embodiment, a person may use a genome-based security device to communicate with an external device over a wireless or other communication interface, synchronize digital genomic data and an associated synthetic variant received from the external device with digital genomic data and associated synthetic variant stored on the genome-based security device. 1. A genome-based security device comprising:a memory storing digital genomic data associated with at least one entity, wherein the digital genomic data comprises at least one synthetic variant and actual genomic data unique to the at least one entity wherein the synthetic variant is different from the actual genomic data and at least a portion of the synthetic variant includes one or more base pairs that do not match a corresponding portion of the actual genomic data; synchronizes the digital genomic data comprising the at least one synthetic variant and the actual genomic data with external digital genomic data comprising at least one external synthetic variant and external actual genomic data unique to the at least one entity and received from an external device wherein at least a portion of the external synthetic variant includes one or more base pairs that do not match a corresponding portion of the external actual genomic data; and', 'authorizes a transaction upon synchronization of the at least one synthetic variant with respect to the external synthetic variant; and, 'a processing unit configurable to execute instructions which upon executiona communication interface coupled with the processing unit configured to communicatively ...

COMPOSITIONS AND METHODS FOR DIAGNOSING AND TREATING HYPERTHYROIDISM IN COMPANION ANIMALS

An isolated DNA molecule comprising a fragment of the gene encoding the feline NIS is disclosed as well as methods of use thereof. Also provided are methods for rational diet design of food composition suitable for administration to feline companion animals afflicted with hyperthyroidism, comprising (a) accessing at least one database that comprises a first data set relating functional gene profile of a biofluid or tissue sample from an animal to physiological condition of the animal, where the functional gene profile is that of the feline NIS gene; (b) accessing at least one database that comprises a second data set relating effects of bioactive dietary components on the functional gene profile; (c) using an algorithm drawing on these data sets, processing input data defining physiological condition to derive a nutritional formula promoting wellness of a feline companion animal afflicted with hyperthyroidism; and (d) preparing a food composition based on the nutritional formula. 1. An isolated DNA molecule comprising (a) the nucleotide sequence of SEQ ID NO:1 , or (b) a nucleotide sequence that is completely complementary to the nucleotide sequence of SEQ ID NO:1.2. An isolated DNA molecule comprising at least 25 contiguous nucleotides of SEQ ID NO:1 or at least 25 contiguous nucleotides completely complementary to the nucleotide sequence of SEQ ID NO:1.3. The isolated DNA molecule of claim 2 , wherein the 25 contiguous nucleotides are within a coding sequence of the feline sodium/iodide symporter protein (NIS protein).4. An isolated RNAi or antisense nucleic acid molecule that selectively binds to the nucleic acid molecule of .5. The isolated RNAi or antisense nucleic acid molecule of claim 4 , wherein the RNAi molecule selectively binds to a coding sequence of the feline sodium/iodide symporter protein (NIS protein).6. An isolated protein comprising the amino acid sequence of SEQ ID NO:2.7. An isolated antibody that selectively binds to the peptide of SEQ ID NO:2 ...

Systems and Methods for Analysis and Interpretation of Nucleic Acid Sequence Data

Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated. 1. A system , comprising:a first data store configured to store genetic sequence information comprising called variants;a second data store configured to store sequence annotation data; [ receive the called variants from the first data store, and', 'associate functional type annotations from the second data store with the called variants, and, 'a functional annotations engine configured to, receive the called variants from the first data store, and', 'associate interpretive type annotations from the second data store with the called variants;, 'an interpretive annotations engine configured to], 'an annotations component communicatively connected with the first data store and the second data store, comprisinga reporting module communicatively connected with the first data store and the second data store and configured to generate a report of the called variants, the functional annotations, and the interpretive annotations.2. A system of claim 1 , wherein the functional type annotation includes an indication of a change in an amino acid sequence claim 1 , an indication of a change in an expression level of a protein claim 1 , an indication of a change in the splicing of a transcript claim 1 , or any combination thereof.3. A system of claim 1 , wherein the functional-type annotations includes a listing of transcripts impacted by the called variant.4. A system of claim 3 , wherein the functional-type annotations includes a protein function impact score for the called variant.5. A system of claim 4 , wherein the functional-type annotations includes base information for codons with the called variant.6. A system of claim ...

METHOD AND APPARATUS FOR SEPARATING QUALITY LEVELS IN SEQUENCE DATA AND SEQUENCING LONGER READS

Sequencing reads from a measurement system may be classified based on quality scores associated with the measurement system, and corresponding error characteristics may be provided. The sequencing reads may correspond to at least one of deoxyribonucleic acid (DNA), complementary DNA (cDNA), or ribonucleic acid (RNA). 1. A method of processing sequencing reads , the method comprising:accessing a plurality of sequencing reads associated with a measurement system, each sequencing read including a sequence of base values, and one or more locations of each sequencing read being associated with a quality score that characterizes operations of the measurement system at the one or more locations;specifying one or more quality conditions based on values of the quality score;using the one or more quality conditions to specify one or more quality classifications for the sequencing reads, each quality classification being based on satisfying at least one corresponding quality condition at locations of the sequencing reads; andproviding an error characteristic corresponding to each quality classification.2. The method of claim 1 , wherein a given sequencing read having a given quality classification satisfies the corresponding one or more quality conditions uniformly across locations in the given sequencing read.3. The method of claim 1 , wherein each error characteristic includes an estimated error corresponding to the measurement system across a portion of a corresponding sequencing read.4. The method of claim 1 , wherein each quality condition corresponds to applying at least one threshold value to values of the quality score.5. The method of claim 1 , wherein the quality score corresponds to a Phred score.6. The method of claim 1 , wherein a quality score at a given location characterizes a signal intensity relative to signal intensities nearby locations.7. The method of claim 1 , wherein the measurement system is a genomic measurement system.8. The method of claim 1 , ...

COMPUTATIONAL METHOD FOR PREDICTING FUNCTIONAL SITES OF BIOLOGICAL MOLECULES

In a general aspect, a method for inferring one or more biomolecule-to-biomolecule interaction sites includes receiving data representative of a plurality of prediction models. Each prediction model is associated with a different atom type of a plurality of atom types and characterizes biomolecule-to-biomolecule interaction site specific patterns common to a plurality of three dimensional probability density maps. Each three dimensional probability density map is associated with a corresponding biomolecule of a plurality of biomolecules included in a training data set and represents a probability of a non-covalent interacting atom on a surface of the corresponding biomolecule interacting with the atom type associated with the prediction model. Data representative of a query biomolecule is received, the data including one or more unknown biomolecule-to-biomolecule interaction sites. The one or more unknown biomolecule-to-biomolecule interaction sites of the query biomolecule are inferred based on the data representative of the plurality of prediction models. 1. A non-transitory computer readable medium comprising instructions for inferring one or more biomolecule-to-biomolecule interaction sites , the instructions , when executed by at least one processor , comprising functionality to:receive data representative of a plurality of prediction models, each prediction model associated with a different atom type of a plurality of atom types and characterizing biomolecule-to-biomolecule interaction site specific patterns common to a plurality of three dimensional probability density maps, each three dimensional probability density map associated with a corresponding biomolecule of a plurality of biomolecules included in a training data set and representative of a probability of a non-covalent interacting atom on a surface of the corresponding biomolecule interacting with the atom type associated with the prediction model;receive data representative of a query biomolecule ...

Stepwise and Blockwise Biochemical Network Laboratory Breadboard Systems and Techniques for Signaling, Disease Research, Drug Discovery, Cell Biology, and Other Applications

A “breadboard” approach by which a biochemical pathway under study is separated or segmented into smaller portions, at least one of which can to a degree of approximation be accurately emulated with a replica microscale and/or nanoscale fluidic implementation whose constituent species, inhibitor(s), catalyst(s) and other reaction agent(s) can be closely controlled and at least one aspect of whose behavior can be measured. Control and measurement information interfaces with a computer that executes algorithms comprising one or more of a control process, control event-script, experiment, data recording, and mathematical model. A model can be used to simulate the actions, behavior, or other aspects of another portion of the biochemical signaling process, pathway, or network. Replica constituents can include enzymes, other proteins, lipids, ions, peptides, and other materials provided under controlled conditions and timing, as well as varying degrees of competitive species, drugs, environmental influences, and substitute or representative molecular crowding. 1. A method for implementing a “breadboard” approach for the study of a biochemical pathway , the method comprising:separating a naturally occurring multiple-stage biochemical process into a plurality of smaller portions, at least one of which can to a degree of approximation be accurately emulated with a fluidic implementation replica;implementing a fluidic implementation replica of at least one of the smaller portions, the replica comprising inputs for reactants, a reaction environment, and provisions for measurement;providing the controlled introduction of a plurality of biochemical materials into the replica, andmaking at least one consuming measurement relating to a resulting biochemical reaction within the replica,wherein the biochemical reaction are controlled by a computer executing an algorithm, andwherein the fluidic implementation replica emulates the at least one the smaller portions of the biochemical ...

GENOMIC SERVICES PLATFORM SUPPORTING MULTIPLE APPLICATION PROVIDERS

Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which genomic sequence reads derived from a biological sample are received. The platform also includes a bioinformatics processing pipeline that comprises a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, and a variant refinement module for producing a set of refined variants associated with the biological sample. A variant imputation module produces a set of imputed variants associated with the user and a variant storage module, operating on a server-less framework, is disposed to receive a query from network infrastructure of a partner application provider and to provide selected ones of the refined or imputed variants m response to the query. 1. A genomic services platform for providing genomic services , the platform comprising:a network interface through which are received genomic sequence reads derived from a biological sample obtained from a user; a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence;', 'a variant calling module operative to identify observed variants in the observed sequence data;', 'a variant refinement module for producing a set of refined variants associated with the user;', 'a variant imputation module for producing a set of imputed variants associated with the user, the variant imputation module being configured to use population reference data in order to produce the set of imputed variants; and', 'a variant storage module, operating on a server-less framework, disposed to receive a query from network infrastructure of a partner application provider and to provide selected ones of the refined or imputed variants in ...

CURATED GENETIC DATABASE FOR IN SILICO TESTING, LICENSING AND PAYMENT

This disclosure relates to methods and systems for a curated genetic variant database and systems and methods for submitting new genetic tests based on the information in the curated database. The methods and systems of the invention further provide for a single curated variant database that allows curation of genetic variants while protecting the proprietary nature of the information submitted to the database. The system and methods also provide for submission of new genetic tests based on genetic variants, conducting genetic tests, and for determining payments to submitters and test developers based on the genetic tests. 1. A system , comprising:a genetic information database; wherein the genetic information database contains genetic variants and estimated effects of the genetic variants;a curation application, wherein the curation application is connected to the genetic information database, and wherein the curation application is accessible by one or more curators and allows access to the genetic information database;wherein the curation application allows the one or more curators to curate information in the genetic information database and allows the one or more curators to provide a curation score for the information in the genetic information database;a submission application; wherein the submission application is connected to the genetic information database; and wherein the submission application is accessible by one or more submitters;wherein the submission application allows the one or more submitters to submit the genetic variants and estimated effects of the geneticvariants to the genetic information database; anda payment application, wherein the payment application is programmed to account for a payment to the one or more curators and the one or more submitters.2. The system of claim 1 , wherein the payment application either accounts for the payment to the one or more curators each time a variant curated by a curator is viewed claim 1 , each time a ...

GENOMIC SERVICES PLATFORM SUPPORTING MULTIPLE APPLICATION PROVIDERS

Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which are received genomic sequence reads derived from a biological sample obtained from a user The platform also includes a bioinformatics processing pipeline including a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, and a variant refinement module for producing a set of refined variants associated with the user. A variant imputation module produces a set of imputed variants associated with the user, and a variant storage module disposed to receive a query from network infrastructure of a partner application provider and to provide selected ones of the refined or imputed variants in response to the query. 1. A genomic services platform for providing genomic services , the platform comprising:a network interface through which are received genomic sequence reads derived from a biological sample obtained from a user; a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence;', 'a variant calling module operative to identify observed variants in the observed sequence data;', 'a variant refinement module configured to produce a set of refined variants associated with the user based on the identified observed variants;', 'a variant imputation module configured to produce a set of predicted genotypes associated with the user based on the population reference genotype data; and', 'a variant storage module configured to:', 'receive a request for genomic information of the user from network infrastructure of a partner application provider via a genomic application programming interface (API), the request supporting provisioning of a genomics service offered ...

GENOMIC SERVICES PLATFORM SUPPORTING MULTIPLE APPLICATION PROVIDERS

Methods, systems and media for providing genomic services are disclosed. In one example, a system for providing genomic services comprises genomic sequencing equipment configured to generate sequence reads based upon a biological sample obtained from a user, and a genomic services platform. The platform includes genomic data storage containing observed sequence data generated by aligning the sequence reads relative to a reference sequence and variants in the observed sequence data derived from the observed sequence data. File storage includes one or more files defining one or more genomic windows respectively associated with each of a plurality of partner application providers or partner applications. A variant storage module is configured to receive a query provided by one of the plurality of partner application providers or partner applications and to fetch, from the genomic data storage, a set of variants associated with reference positions included in a one of the genomic windows associated with the one of the plurality of partner application providers or partner applications. A set of variants are provided to the one of the plurality of partner application providers or partner applications through a genomic API. 1. A system for providing genomic services , the system comprising:genomic sequencing equipment wherein the genomic sequencing equipment is configured to generate sequence reads based upon a biological sample obtained from a user; and genomic data storage containing observed sequence data generated by aligning the sequence reads relative to a reference sequence and variants in the observed sequence data derived from the observed sequence data;', 'file storage including one or more files defining one or more genomic windows respectively associated with each of a plurality of partner application providers or partner applications;', 'a variant storage module configured to receive a query provided by one of the plurality of partner application providers or ...

GENOMIC SERVICES PLATFORM SUPPORTING MULTIPLE APPLICATION PROVIDERS

Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a platform comprises a network interface, in communication with a sequencing laboratory, through which are received genomic sequence reads derived from a biological sample obtained from a user, and a bioinformatics processing pipeline. The pipeline includes a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, a genomic data storage containing at least the observed variants in the observed sequence data, and a variant storage module disposed to receive a query from network infrastructure of a partner application provider and to provide genomic information based on or derived from the observed variants in response to the query. 1. A genomic services platform for providing genomic services , the platform comprising:a network interface, in communication with a sequencing laboratory, through which are received genomic sequence reads derived from a biological sample obtained from a user; and a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence;', 'a variant calling module operative to identify observed variants in the observed sequence data;', 'genomic data storage containing at least the observed variants in the observed sequence data; and', 'a variant storage module disposed to receive a query from network infrastructure of a partner application provider and to provide genomic information based on or derived from the observed variants in response to the query., 'a bioinformatics processing pipeline including2. The platform of claim 1 , wherein the platform further comprises a variant refinement module for producing a set of refined variants associated with the user claim 1 , the variant refinement module being ...

SYSTEM AND METHOD FOR PROCESSING ELECTRONIC MEDICAL AND GENETIC/GENOMIC INFORMATION USING MACHINE LEARNING AND OTHER ADVANCED ANALYTICS TECHNIQUES

Embodiments of the present disclosure relate to a machine-learning system for processing medical information. The system comprises a communications interface configured to access electronic medical data. An automated retrieval processor is configured to analyze the electronic medical data to identify and retrieve relevant electronic data based on predefined search criteria. A learning processor is configured to update and optimize the automated retrieval processor based on received electronic metadata associated with the identified relevant electronic data. Other embodiments relate to a machine-learning method for processing electronic medical information. The method comprises accessing electronic medical data from a public database and/or a private database. In addition, the method comprises analyzing the electronic medical data to identify and retrieve relevant electronic data based on predefined search criteria. Also, the method includes performing adaptive learning based on received electronic metadata associated with the identified relevant electronic data. 1. A machine-learning system for processing medical information , the system comprising:a communications interface configured to access electronic medical data;an automated retrieval processor configured to analyze the electronic medical data to identify and retrieve relevant electronic data based on predefined search criteria; anda learning processor configured to update and optimize the automated retrieval processor based on received electronic metadata associated with the identified relevant electronic data.2. The system of claim 1 , wherein the communications interface is configured to access the electronic medical data from a public database and/or a private database.3. The system of claim 1 , wherein the communications interface is configured to access a real-time medical data feed.4. The system of further comprising a metadata tool configured to add electronic metadata to the identified relevant ...

SYSTEM AND METHOD FOR POLYGENIC PHENOTYPIC TRAIT PREDISPOSITION ASSESSMENT USING A COMBINATION OF DYNAMIC NETWORK ANALYSIS AND MACHINE LEARNING

A method and system comprising receiving genetic and non-genetic data of an individual, calculating a trait predisposition score for the individual, organizing a knowledge base repository using dynamic network analysis of a plurality of genetic variants and of a plurality of phenotypic traits into a heterogeneous knowledge network model, assessing regulatory, catalytic or inhibitory utility of genetic factors by determining existence of said genetic factors within biological pathways, calibrating the phenotypic trait predisposition score for the individual using a machine learning analysis that relates the plurality of genetic variations to the plurality of phenotypic traits, calibrating the heterogeneous knowledge network model using the genetic data and the non-genetic data. 1. A method for Phenotypic Trait Predisposition Assessment Based on the Multiple Genetic Variations in DNA Using a Combination of Dynamic Network Analysis and Machine Learning , comprising:receiving, by a server, genetic and non-genetic data of an individual;calculating, by the server, a trait predisposition score for the individual, wherein the phenotypic trait predisposition score is a reference score;organizing, by the server, a knowledge base repository using dynamic network analysis of a plurality of genetic variants and of a plurality of phenotypic traits into a heterogeneous knowledge network model;assessing, by the server, regulatory, catalytic or inhibitory utility of genetic factors by determining existence of said genetic factors within biological pathways, the biological pathways comprising at least one of metabolic pathways, regulatory networks and signal transduction pathways;calibrating, by the server, the phenotypic trait predisposition score for the individual using a machine learning analysis that relates the plurality of genetic variations to the plurality of phenotypic traits; andcalibrating, by the server, the heterogeneous knowledge network model using the genetic data ...

Method and arrangement for matching mammals by comparing genotypes

A method for determining a matchmaking quality for a first mammal in relation to a plurality of different second mammals by comparing genotypes thereof, comprises steps of providing a first database and second database. The first database comprises genotyping data of known traits and coefficients weighting severity of said traits, and the second comprises genotyping data for at least certain loci common to each of said mammals to be matchmade. In determination of value of the match first results of the coefficients weighting the severities of the traits are determined for each potential breeding pair of the first mammal with each of said plurality of the different second mammals, and second results relating to a diversity are determined for each potential breeding pair of the first mammal with each of said plurality of the different second mammals. A total result determining the matchmaking quality for each potential breeding pair is determined by combining said first and second results for each of said potential breeding pair. 2. A method of for determining said matchmaking quality claim 1 , whereinfirst results of said coefficients weighting the severities of the traits are determined for the potential breeding partners of the first mammal with each of said plurality of the different second mammals by using said first portion of the markers, where a sub-result of the first results relates to a certain genotype and has a certain sub-coefficient, whereupon the first results are determined by summing said sub-coefficients of said sub-results, and second results relating to the diversity are determined by using said second portion of the markers so that if genotype of a certain locus is different for said first mammal than for the potential partner of said different second mammals in the second database, said sub-coefficient for said locus is rewarded and if genotype of said locus is same for both mammals, said sub-coefficient for said locus is not awarded or is ...

METHOD FOR EVALUATING AN IMMUNOREPERTOIRE

Disclosed is a method for amplifying RNA from T and B-cell populations and using the amplified RNA products to evaluate the possible correlation between a normal or abnormal immune response and the development of a disease such as an autoimmune disease, cancer, diabetes, or heart disease. 1. A method for evaluating changes in immune response cell populations and associating those changes with a specific disease , the method comprising the steps of:(a) isolating a subpopulation of white blood cells from at least one human or animal subject;(b) isolating RNA from the subpopulation of cells;(c) amplifying the RNA using RT-PCR in a first amplification reaction to produce amplicons using nested primers, at least a portion of the nested primers comprising additional nucleotides to incorporate into a resulting amplicon a binding site for a communal primer;(d) separating the amplicons from the first amplification reaction from one or more unused primers from the first amplification reaction;(e) amplifying, by the addition of communal primers in a second amplification reaction, the amplicons of the first amplification reaction having at least one binding site for a communal primer; and(f) sequencing the amplicons of the second amplification reaction to identify antibody and/or receptor rearrangements in the subpopulation of cells.2. The method of claim 1 , wherein the product of the second amplification reaction is a polynucleotide comprising the complementarity determining region 3 (CDR3).3. The method of claim 1 , wherein the step of isolating a subpopulation of white blood cells is performed by flow cytometry.4. The method of claim 1 , wherein the subpopulation of white blood cells comprises T cells.5. The method of claim 4 , wherein the T cells are selected from the group consisting of naïve T cells claim 4 , mature T cells and memory T cells.6. The method of claim 1 , wherein the subpopulation of white blood cells comprises B cells.7. The method of claim 6 , wherein the ...

METHOD FOR SELECTING ANTICANCER AGENT BASED ON PROTEIN DAMAGE INFORMATION OF INDIVIDUAL TO PREVENT ANTICANCER AGENT SIDE EFFECTS

The present invention relates to a method and a system for selecting an anticancer agent based on protein damage information of an individual by using individual genome sequencing. The method and the system, according to the present invention, are highly reliable and widely applicable techniques capable of predicting side effects or risks of specific drugs, in other words, anticancer agents, for each individual by performing sequence analysis of an exon part of a gene that codes various proteins involved in pharmacokinetics or pharmacodynamics of anticancer agents. 1. A method for providing information for selecting an anticancer agent using individual genome sequence variation , which comprises:a step of determining one or more gene sequence variation information involved in the pharmacodynamics or pharmacokinetics of an anticancer agent from individual genome sequence information;a step of calculating an individual protein damage score using the gene sequence variation information; anda step of calculating an individual drug score by associating the individual protein damage score with an anticancer agent-protein relation.2. The method for providing information for selecting an anticancer agent using individual genome sequence variation according to claim 1 , wherein the anticancer agent is one or more selected from a group consisting of a thiopurine-based drug claim 1 , a deoxynucleoside analog and a deoxynucleoside analog.3. The method for providing information for selecting an anticancer agent using individual genome sequence variation according to claim 1 , wherein the gene involved in the pharmacodynamics or pharmacokinetics is one or more selected from a group consisting of ABCC1 claim 1 , ABCG2 claim 1 , APEX1 claim 1 , CBR3 claim 1 , ATP7A claim 1 , CBR3 claim 1 , CTH claim 1 , CUL9 claim 1 , CYP1A1 claim 1 , CYP2C9 claim 1 , CYP2D6 claim 1 , CYP4B1 claim 1 , DPEP1 claim 1 , DPEP2 claim 1 , DPYD claim 1 , DRD3 claim 1 , EPHX1 claim 1 , FMO2 claim 1 , FMO3 ...

PATHOLOGY DETERMINATION ASSISTANCE DEVICE, METHOD AND STORAGE MEDIUM

The device for assisting determination of pathology of a polycystic kidney disease according to the present invention has an extraction means for extracting gene mutation information in a region related to polycystic kidney disease using sequence data showing gene sequences of a test subject; an acquisition means for acquiring, using the extracted gene mutation information, medical information corresponding to the extracted gene mutation from a plurality of databases in which gene mutation and medical information are associated with each other; and a list display means for displaying a list containing the extracted gene mutation information and the obtained medical information. 16-. (canceled)7. A pathology determination assistance device for assisting determination of pathology of polycystic kidney disease , comprising:an extraction means for extracting information on gene mutation in a region related to polycystic kidney disease using sequence data showing a gene sequence of a test subject;an acquisition means for acquiring, using the extracted information on gene mutation, medical information corresponding to the extracted gene mutation from a plurality of databases in which gene mutation and medical information are associated with each other; anda list display means for displaying a list containing the extracted information on gene mutation and the obtained medical information.8. The pathology determination assistance device according to claim 7 , wherein the pathology determination assistance device comprises a storage unit in which the databases are stored.9. The pathology determination assistance device according to claim 7 , wherein the information on gene mutation is chromosome position-based information claim 7 , which includes a chromosome number claim 7 , the position of mutation claim 7 , and the kind of the base after mutation.10. The pathology determination assistance device according to claim 8 , wherein the information on gene mutation is chromosome ...

METHOD AND SYSTEM FOR IDENTIFICATION AND CLASSIFICATION OF OPERATIONAL TAXONOMIC UNITS IN A METAGENOMIC SAMPLE

A system and method for identification and classification of operational taxonomic units (OTUs) in a metagenomic sample using short read amplicon sequences has been described. The disclosure enables accurate identification of OTU in a metagenomic sample and provides a framework for easy cross comparison of microbiome community structures sampled across different disconnected metagenomic studies. Instead of using a reference database consisting of full-length marker genes directly for taxonomic classification or OTU-picking, the present disclosure creates customized OTU databases for different hyper-variable regions of a marker gene. These databases consist of reference OTUs obtained through independent clustering of sequences pertaining to different selected hyper-variable regions of the marker gene. In another embodiment, mapping back is also provided facilitating cross comparison between results obtained from different studies that may have utilized different hyper-variable regions. The system results in enhanced accuracy of classification of operational taxonomic units (OTUs) in the metagenomic sample. 1. A method for identification and classification of operational taxonomic units (OTUs) in a metagenomic sample using short read amplicon sequences , the method comprising:{'b': '124', 'collecting the metagenomic sample using a metagenomic sample collection module ();'}{'b': '126', 'sequencing the metagenomic sample using a sequencer ();'}{'b': 104', '106, 'obtaining one of a conventional operational taxonomic unit (OTU) database ()) and a conventional reference sequence database (), wherein the conventional OTU database having a plurality of nucleotide sequences clustered into one or more of conventional operational taxonomic units (OTUs) and conventional taxonomic clades;'}{'b': '110', 'creating, by a processor (), a customized OTU database (OTUX) out of the sequenced metagenomic sample using a plurality of predefined segments of nucleotide sequences from one of ...

PROTEIN IDENTIFICATION METHOD AND SYSTEM

When a terminal sequence to be investigated is specified (S), a corresponding protein is extracted from a database containing known proteins linked with terminal sequences (S). If one protein cannot be uniquely identified (“No” in S), amino-acid residues to be bonded to the target terminal sequences are selected, and new terminal sequences with the selected amino-acid residues respectively added are created for further investigation (S). Each new terminal sequence is examined as to whether or not one protein can be uniquely identified from it, and if not so, another amino-acid residue is added. While such processes are repeated, if it has been found that the protein can be uniquely identified before the sequence length reaches an upper limit, the sequence length is displayed (S). If the sequence length has reached the upper limit without successful identification, a message saying that the protein cannot be identified is displayed (S). 1. A protein identification method for identifying a protein by a terminal sequence which is an amino-acid sequence of a terminal region of the protein , the method comprising:a) an identification candidate extraction step, in which a protein corresponding to a target terminal sequence given as a target to be investigated is searched for and extracted as a protein candidate, using information in which various known kinds of proteins are linked with, at least, their respective terminal sequences;b) an identification result determination step, in which, when only one protein candidate is extracted in the identification candidate extraction step, the candidate is selected as a protein identification result corresponding to the target terminal sequence; andc) an identification possibility prediction step, in which, when a plurality of protein candidates are extracted in the identification candidate extraction step, an extended length of the terminal sequence with which the protein can be uniquely identified is predicted by determining an ...

Dna matching

A method of searching a computer database containing a plurality of stored DNA profiles is provided. The method involves generating a search profile formed of two or more allele identities for each of one or more loci, at least one of the allele identities having a limited range of values, with the search profile being compared against the one or more stored DNA profiles from a database to establish matches between the search and stored profile.

DNA Methylation Landscapes of Post-Traumatic Stress Disorder (PTSD) Susceptibility and Resilience and Novel Therapeutics of PTSD Derived Thereof

Methods regarding DNA methylation signature of post-traumatic stress disorder (PTSD) in brains of susceptible, resilient animals methylated in response to trauma, and S-adensoyl methionine (SAM) treated animals for deriving targets for PTSD therapeutics. Method regarding pathway analysis of the DNA methylation landscape to derive novel targets for therapeutic interventions such as retinoic acid pathway or estrogen receptor pathways. A method of treatment of PTSD comprised of Epigenetic modulators using general DNA methylation modulators such as SAM. A method of treatment of PTSD comprised of retinoic acid or vitamin A and its natural and synthetic analogs such as all-trans-retinoic acid (Tretinoin), 9-cis-retinoic acid (Alitretinoin), and 13-cis-retinoic acid (Isotretinoin) to treat PTSD. A method of treatment of PTSD comprised of a combination of Sadenosylmethionine and retinoic acid or vitamin A and its synthetic and natural analogs such as Tretinoin, Alitretinoin, and Isotretinoin. 1. A DNA methylation signature of post-traumatic stress disorder (PTSD) in brains of susceptible , resilient animals methylated in response to trauma , and S-adensoyl methionine (SAM) treated animals for deriving targets for PTSD therapeutics.2. A pathway analysis of said DNA methylation landscape to derive novel targets for therapeutic interventions such as retinoic acid pathway or estrogen receptor pathways.3. A method of treatment of PTSD comprised of Epigenetic modulators using general DNA methylation modulators such as SAM.4. A method of treatment of PTSD comprised of retinoic acid or vitamin A and its natural and synthetic analogs such as all-trans-retinoic acid (Tretinoin) , 9-cis-retinoic acid (Alitretinoin) , and 13-cis-retinoic acid (Isotretinoin) to treat PTSD.5. A method of treatment of PTSD comprised of a combination of S-adenosylmethionine and retinoic acid or vitamin A and its synthetic and natural analogs such as Tretinoin , Alitretinoin , and Isotretinoin.6. A method ...

Third Generation Sequencing Alignment Algorithm

Methods, software, and systems for aligning a read sequence to a reference sequence are disclosed. In certain embodiments, the methods, software, and systems involve determining similarity of distribution of k-mers between a region of the read sequence and a region of the reference sequence in order to determine whether the region of the read sequence maps to the region of the reference sequence. 2. The method according to claim 1 , wherein steps (a)-(f) are repeated for the read sequence and a different segment of the reference sequence.3. The method according to any one of or claim 1 , wherein the reference sequence segment is a region of a reference sequence obtained from a genome database.4. The method according to any one of or claim 1 , wherein the reference sequence is a read sequence.5. The method according to claim 1 , wherein the reference sequence that is a read sequence is obtained from sequencing the same sample from which the sequence of the read sequence in is obtained.6. The method according to any one of - claim 1 , wherein the length of each of the windows is at least 50 bases.7. The method according to any one of - claim 1 , wherein the length of each of the windows can be any whole number value ranging from 1-10 claim 1 ,000 bases claim 1 , wherein the length is held constant.8. The method according to any one of - claim 1 , wherein the distance d is at least 10 bases long.9. The method according to any one of - claim 1 , wherein the distance d can range from 1-500 bases in length claim 1 , wherein d is held constant.10. The method according to any one of - claim 1 , wherein the k-mer is 2-10 bases in length.11. The method according to claim 10 , wherein the k-mer is 3 bases in length.12. The method according to claim 10 , wherein the k-mer is 4 bases in length.14. The executable software product according to claim 13 , wherein steps (a)-(f) are repeated for the read sequence and a different segment of the reference sequence.15. The executable ...

COMPUTER-IMPLEMENTED METHODS FOR AUTOMATED ANALYSIS AND PRIORITIZATION OF VARIANTS IN DATASETS

Computer-implemented methods for automating identification and prioritization of genomic variants are disclosed. Such methods employ a rule set to analyze information regarding statistical frequency of variants in a dataset and metrics indicating biological relatedness to generate a priority-score indicative of the relevance of each variant in the dataset. The methods perform both variant frequency normalization and universal pairwise variant comparisons across the datasets to automatically calculate the likelihood that each variant is significant to a disease or other biological phenomenon under study. Priority-scores are calculated for the variants based upon such pairwise comparisons, and the results are organized into a priority ranking, which may be used to categorize the results into data subsets for display to a user. 1. A computer-implemented method for automatically identifying and prioritizing variants in a dataset , the method comprising:accessing, by one or more processors, the dataset, wherein the dataset includes genomic sequence data of a target dataset and a control dataset;calculating, by the one or more processors, a frequency-score for each variant in the target dataset, wherein the frequency-score is based upon statistical frequencies with which the respective variant appears in each of the target dataset and the control dataset; performing, by the one or more processors, pairwise comparison between the respective variants of the pair;', 'calculating, by the one or more processors, a relatedness-score for the pair based upon the pairwise comparison; and, 'for each pair of variants in the target datasetcalculating, by the one or more processors, a frequency-corrected relatedness-score for the pair based upon the relatedness-score of the pair and the frequency scores of the respective variants;calculating, by the one or more processors, a control-frequency-score for each variant in the control dataset, wherein the control-frequency-score is based ...

SYSTEMS AND METHODS FOR GENETIC ANALYSIS

The invention relates to using a graph database in genetic analyses to link mutation data to extrinsic data. Entities such as mutations, patients, samples, alleles, and clinical information are individually represented and stored as nodes and relationships between entities are also individually represented and stored. Each node and relationship can be stored using a fixed-size record and nodes can be flexibly invoked to represent any entity without disrupting the existing data. Systems and methods of the invention may be used for obtaining data representing a mutation in an individual and using a node in a graph database to store a description of the mutation. The node has stored within it a pointer to an adjacent node that provides information about a clinical significance of the variant. The graph database can be queried to provide a report of the clinical significance of the mutation. 1. A system for describing genetic information , the system comprising: obtain data representing a mutation in a genome of an individual;', 'use a node in the graph database to store a description of the mutation;', 'store, in the node, a pointer to an adjacent node that provides information about a clinical significance of the mutation; and', 'query the graph database to provide a report of the clinical significance of the mutation in the genome of the individual., 'at least one computer comprising memory coupled to a processor, the system having at least a portion of a graph database stored therein, wherein the system is operable to2. The system of claim 1 , wherein the system is operable to obtain the data representing the mutation by receiving at least one sequence read file that includes the data.3. The system of claim 2 , further operable to represent claim 2 , in the graph database claim 2 , a biological sample from the individual using a sample node and connect the sample node via a pointer to a read file node representing the sequence read file.4. The system of claim 1 , ...

SYSTEMS AND METHODS FOR GENOMIC VARIANT ANNOTATION

A system for annotating genomic variant files includes an application server, an annotation database, a genomic database, and an annotation processing computer system. The genomic database may be graph-oriented. The annotation processing computer system processes can process variant files in batch modes and includes annotation modules designed to improve the speed of the annotation process. The batch modes may include batch transmission, and/or batch annotation. 1. An electronic computer system for the automated annotation of genomic variants , the system comprising:an application server computer system configured to receive one or more variant files from a client computer system different from the application server computer system;an annotation processing computer system different from the application server computer system and the client computer system and configured to receive one or more variant files from the application server computer system;an annotation database accessible by both the application server computer system and the annotation processing computer system;wherein the annotation processing computer system is configured to annotate variants in the variant files received from the application server computer system and store variant annotation results in the annotation database; andwherein the application server computer system is configured to retrieve variant annotation results from the annotation database and deliver retrieved variant annotation results to the client computer system.2. The electronic system of claim 1 , additionally comprising:a genotype database separate from the annotation database;wherein the application server computer system is configured to retrieve variant annotation results from the annotation database and store the retrieved variant annotation results in the genotype database.3. The electronic computer system of claim 2 , wherein the variant annotation results are stored in the genotype database in a graph-oriented ...

SYSTEMS AND METHODS FOR GENOMIC ANNOTATION AND DISTRIBUTED VARIANT INTERPRETATION

A computer-based genomic annotation system, including a database configured to store genomic data, non-transitory memory configured to store instructions, and at least one processor coupled with the memory, the processor configured to implement the instructions in order to implement an annotation pipeline and at least one module filtering or analysis of the genomic data. 1. A computer-based genomic annotation system , comprising:a database configured to store genomic annotation data, the genomic annotation data comprising a plurality of variants, each variant defined at least by one or more genomic locations and a definition of the variation present at the locations, each of the plurality of variants having associated annotations stored in the database, each annotation characterizing a different variant property corresponding to a plurality of predefined annotation categories for each of the plurality of variants;non-transitory memory configured to store instructions, and '(1) receive a variant file including a plurality of variants, each variant defined at least by one or more genomic location and a definition of the variation present at the one or more genomic locations; and (2) generate an annotation file containing annotations corresponding to the plurality of predefined annotation categories for each of the plurality of variants;', 'at least one processor coupled with the memory, the processor configured to comparing the plurality of variants in the received variant file with the plurality of variants stored in the database, and', 'for at least some variants in the variant file that are the same as a variant stored in the database, retrieving annotation information for at least some of the plurality of predefined annotation categories from the database to populate the annotation file., 'wherein producing the annotation file comprises2. The system of claim 1 , wherein for variants in the received variant file that are not the same as any variant stored in the ...

Computer Graphical User Interface With Genomic Workflow

Methods and computer apparatuses are disclosed for processing genomic data in at least partially automated workflows of modules. A method comprises: specifying a source from which nucleic acid sequence(s) are to be obtained; selecting module(s) for processing data, including at least one module for processing the one or more nucleic acid sequences; presenting, in a graphical user interface, graphical components representing the source and the module(s) as nodes within a workspace; receiving, via the graphical user interface, inputs arranging the source and the module(s) as a workflow comprising a series of nodes, the series indicating, for each particular module, that output from one of the source or another particular module is to be input into the particular module; generating an output for the workflow based upon the nucleic acid sequence(s) by processing each module in an order indicated by the series. 1. A method comprising:presenting, in a graphical user interface, graphical components representing a source from which one or more nucleic acid sequences are to be obtained and one or more sets of instructions for processing data, including at least one set of instructions for processing the one or more nucleic acid sequences, wherein the source and the one or more sets of instructions are represented as nodes within a workspace;wherein the source and the one or more sets of instructions are arranged as a workflow comprising a series of nodes, the series of nodes indicating, for each particular set of instructions of the one or more sets of instructions, that output from one of the source or another particular set of instructions is to be input into the particular set of instructions;generating an output for the workflow, wherein the output comprises a set of one or more items of genomic data that are based upon the one or more nucleic acid sequences that are processed by each set of instructions of the one or more sets of instructions in an order indicated by ...

SYSTEM, METHOD AND APPARATUS TO ENHANCE PRIVACY AND ENABLE BROAD SHARING OF BIOINFORMATIC DATA

A system, method and apparatus for enabling individuals to determine their sharing, privacy, and data access preferences and conditions for disclosure of bioinformatic data, including whole genome sequence data over a network. In combination with a privacy preferences repository and policy repository for expressing legal and institutional criteria for accessing such information, a private access bureau enables such privacy requirements to be addressed while simultaneously enabling broad sharing of such data by and with properly authorized parties or applications. Through the use of various forms of metadata, encryption, and globally unique IDs that accompany such data elements, discrete segments of said data can be queried; and where permissible discovered, accessed, analyzed, viewed, linked with other health data and contact details, used, and/or exported based on pertinent privacy laws, institutional policies, and the individual's preferences that are associated with, and dynamically controlled through, an intuitive user interface. 1. A computer implemented method for selectively designating segments of bioinformatic data in an electronic document , the method comprising the steps of:(a) receiving a command by at least one computer from a party wishing to designate such segments identifying at least one portion of an electronic document to be subject to access control;(b) presenting, by said at least one computer, a set of selectable access control directives defining conditions for access to said at least one portion of said electronic document, said selectable access control directives selected and controlled by the holder of privacy rights of said document;(c) receiving, from said party wishing to designate such segments by said at least one computer, selectable access control directives; and(d) imposing access control of said at least one portion by said at least one computer in accordance with said conditions in response to receiving said selectable access ...

Method And Computer System For Assessing Classification Annotations Assigned To DNA Sequences

For assessing classification annotations assigned to DNA sequences stored in a reference database, the DNA sequences are grouped by species (S 1 ) using established classification schemes. Subsequently, a measure of distance between pairs of DNA sequences is determined (S 41 ) by aligning (S 31 ) the respective sequences and determining the measure of distance (S 41 ) based on a score of similarity between the aligned DNA sequences. Determined are one or more centroid sequences (S 42 ) which have the shortest aggregate measure of distance to the other DNA sequences in the respective group (species). Assigned to the DNA sequences (S 5 ) as a quantitative confidence level for their classification annotations is in each case the measure of distance between the respective DNA sequence and the centroid sequence. The assessment and rating of the classification annotations with these confidence levels make it possible to provide to a user a quantitative indication of the degree of representativeness of a DNA sequence for a particular species.

Compatibility mechanisms for devices in a continuous analyte monitoring system and methods thereof

Methods, devices, and kits are provided for determining a compatibility of one or more devices in an analyte monitoring system.

METHODS FOR QUANTITATIVE GENETIC ANALYSIS OF CELL FREE DNA

The invention provides a method for genetic analysis in individuals that reveals both the genetic sequences and chromosomal copy number of targeted and specific genomic loci in a single assay. The present invention further provides methods for the sensitive and specific detection of target gene sequences and gene expression profiles. 1. A method for genetic analysis of cell-free DNA (cfDNA) comprising:(a) treating cfDNA with one or more end-repair enzymes to generate end-repaired cfDNA;(b) ligating one or more adaptors to each end of the end-repaired cfDNA to generate a cfDNA library;(c) amplifying the cfDNA library to generate cfDNA library clones;(d) determining the number of genome equivalents in the cfDNA clone library; and(e) performing a quantitative genetic analysis of one or more target genetic loci in the cfDNA library clones.2. The method of claim 1 , further comprising isolating cfDNA from a biological sample of a subject.3. The method of claim 1 , wherein the cfDNA is isolated from a biological sample selected from the group consisting of: amniotic fluid claim 1 , blood claim 1 , plasma claim 1 , serum claim 1 , semen claim 1 , lymphatic fluid claim 1 , cerebral spinal fluid claim 1 , ocular fluid claim 1 , urine claim 1 , saliva claim 1 , stool claim 1 , mucous claim 1 , and sweat.4. The method of claim 1 , wherein(a) the one or more adaptors comprise a plurality of adaptor species;(b) the one or more adaptors each comprise a primer binding site for amplification of the cfDNA library;(c) the one or more adaptors each comprise one or more unique read codes;(d) the one or more adaptors each comprise one or more sample codes for sample multiplexing; or(e) the one or more adaptors each comprise one or more sequences for DNA sequencing.58.-. (canceled)9. The method of claim 1 , wherein qPCR is performed on the cfDNA clone library and a qPCR measurement is compared to standards of known genome equivalents to determine the genome equivalents of the cfDNA clone ...

SYSTEMS AND METHODS FOR VARIABLE FITTING ON THE BASIS OF MANUAL REVIEW

Systems and methods for variable fitting include communicating one or more descriptions for a system exhibiting a variable value. In response, a response consisting of a first or second indication is received from the user of the disclosed systems and methods. The first and second indications being that the one or more descriptions are respectively considered to be in a first or second class with respect to the variable. The variable value is changed based on the received response. This communicating, receiving, and changing is repeated until an exit condition is considered to exist. 1. A computer-implemented method , comprising: (A) retrieving a value for a variable associated with a system;', '(B) communicating one or more descriptions for the system that each show a value for the variable;', '(C) receiving, responsive to the communicating, a response to the one or more descriptions, the response being either (i) a first indication, the first indication being that the one or more descriptions are considered by a first user to be in a first class with respect to the variable or (ii) a second indication, the second indication being that the one or more descriptions are considered by the first user to be in a second class, distinct from the first class, with respect to the variable;', '(D) changing the value for the variable as a function of the response; and', '(E) repeating the communicating (B), receiving (C), and changing (D) until a terminating state is considered to exist., 'at a computer system having one or more processors, memory and a display;'}2. The computer-implemented method of claim 1 , wherein the changing (D) comprises:increasing the value for the variable, when the response in the previous instance of the receiving (C) is the first indication, anddecreasing the value for the variable, when the response in the previous instance of the receiving (C) is the second indication.3. The computer-implemented method of claim 1 , wherein the variable is a ...

DNA SEQUENCE PROCESSING METHOD AND DEVICE

A DNA sequence processing method and device are used to resolve a prior-art problem of low-efficiency mutation detection on a DNA sample. The method includes: performing alignment computation on each read in the read group according to a reference sequence of a chromosome to obtain an alignment result record of the read relative to the reference sequence; determining a chromosome region in which each read is located; and merging alignment result records of reads located in a same chromosome region into one intermediate result file; determining a target sequence file of each chromosome region according to the N intermediate result files corresponding to the chromosome region; and determining mutation site information of each chromosome region according to the target sequence file of the chromosome region. 1. A DNA sequence processing method , wherein the method is used to process N read groups of a deoxyribonucleic acid (DNA) sample , each read group comprises sequence fragments reads that are obtained after a corresponding sequencing library is used to perform sequencing on the DNA sample , N is a positive integer greater than 1 , and the method comprises: performing alignment computation on each read in the read group according to a reference sequence of a chromosome, to obtain an alignment result record of the read relative to the reference sequence;', 'determining, according to the alignment result record, a chromosome region in which each read is located, wherein the chromosome comprises at least one chromosome region; and', 'merging, into one intermediate result file, alignment result records of reads located in a same chromosome region, wherein, 'performing the following operations on each read group concurrentlythe alignment computation is performed on each read group according to a same reference sequence of a chromosome, chromosome regions comprised in the chromosome are the same, and after the foregoing operations are performed on each read group, each ...

DISCOVERY ROUTING SYSTEMS AND ENGINES

The inventive subject matter provides apparatus, systems, and methods that improve on the pace of discovering new practical information based on large amounts of datasets collected. In most cases, anomalies from the datasets are automatically identified, flagged, and validated by a cross-validation engine. Only validated anomalies are then associated with a subject matter expert who is qualified to take action on the anomaly. In other words, the inventive subject matter bridges the gap between the overwhelming amount of scientific data which can now be harvested and the comparatively limited amount analytical resources available to extract practical information from the data. Practical information can be in the form of trends, patterns, maps, hypotheses, or predictions, for example, and such practical information has implications in medicine, in environmental sciences, entertainment, travel, shopping, social interactions, or other areas. 139-. (canceled)40. A security detection system comprising:a knowledge database programmed to store a plurality of datasets, each dataset comprising at least one descriptor-value pair having a descriptor and an associated value;an analytical engine coupled with the knowledge database, and programmed to identify at least one anomaly in a dataset of the plurality of datasets, wherein the at least one anomaly is associated with a condition and characterizes a descriptor-value pair having a value that meets a qualifier associated with the descriptor at or beyond a predetermined threshold value for the descriptor;a cross-validation engine comprising an association application and a relationship application, coupled with the analytical engine and programmed to designate the at least one anomaly as a significant anomaly by (i) in the association application, cross-referencing the at least one anomaly with one or more other descriptor-value pairs of attributes that are associated with the condition and known to have a value that meets the ...

METHODS AND SYSTEMS FOR PROCESSING GENOMIC DATA

Methods and systems for processing biological sequence data, such as genomic data, are disclosed. In one implementation, a set of biological sequences, such as DNA sequences, may be evaluated and one or more reference sequences may be determined or selected based on the set of biological sequences, which may include iterative determination or selection. The set of biological sequences may be compressed using the one or more reference sequences. Processing may include generating delta representations associated with the biological sequences, as well as generating dictionary information, which may be used for further compression. Metadata may be included in the compressed data. The compressed data may be stored in a compressed data file, which may be in a compressed genomic database or other data storage medium. 1. A computer-implemented method of compressing a plurality of data sequences for use in a system including at least a processor and a memory storing a database of biological sequence data , the method comprising:determining, based upon comparison of the plurality of data sequences prior to compression of the plurality of data sequences, a reference sequence wherein the reference sequence includes data from the plurality of data sequences;processing the plurality of data sequences relative to the reference sequence in order to determine differences between the plurality of data sequences and the reference sequence;creating, using the reference sequence and based upon the differences, a plurality of first delta representations of the plurality of data sequences wherein the creating includes specifying, for each of the differences in ones of the plurality of first delta representations, a corresponding position in the modified reference sequence, an operation, and a value associated with the operation;defining a modified reference sequence;generating, using the modified reference sequence, a plurality of second delta representations of the plurality of data ...

AUTOMATED CLINICAL DOCUMENTATION SYSTEM AND METHOD

A method, computer program product, and computing system for automating a follow-up process is executed on a computing device and includes prompting a patient to provide encounter information via a virtual assistant during a post-visit portion of a patient encounter. Encounter information is obtained from the patient in response to the prompting by the virtual assistant. 1. A computer-implemented method for automating a follow-up process , executed on a computing device , comprising:prompting a patient to provide encounter information via a virtual assistant during a post-visit portion of a patient encounter; andobtaining encounter information from the patient in response to the prompting by the virtual assistant.2. The computer-implemented method of further comprising:processing the encounter information to generate an encounter transcript.3. The computer-implemented method of further comprising:processing at least a portion of the encounter transcript to populate at least a portion of a medical record associated with the patient encounter.4. The computer-implemented method of wherein prompting the patient to provide encounter information via the virtual assistant includes:audibly prompting the patient to provide encounter information via the virtual assistant.5. The computer-implemented method of wherein obtaining encounter information from the patient includes:audibly obtaining encounter information from the patient.6. The computer-implemented method of wherein the encounter information includes one or more of:patient status information;patient medication information; andpatient follow-up information.7. The computer-implemented method of wherein the post-visit portion of the patient encounter includes:a patient follow-up portion of the patient encounter.8. A computer program product residing on a computer readable medium having a plurality of instructions stored thereon which claim 1 , when executed by a processor claim 1 , cause the processor to perform ...

Method using enteric-coated etidronate for treating calcification, hypercalcaemia, and calcinosis of the brain and other organs

Among other things, compositions, kits, and methods for epilepsy therapy using a process for treating calcinosis manifested in Neurocysticercosis, Tuberous Sclerosis Complex, and Sturge-Weber Syndrome; an automated platform for real-time diagnosis and treatment of calcinosis comprising a computer-implemented method for using predictive analytics for administering a novel drug, Kamini™, to human patients generated at least in part from information that has been accumulated automatically from on-line resources.

Compression/Decompression Method and Apparatus for Genomic Variant Call Data

Methods and apparatus for compressing and decompressing genetic information from an individual. In one arrangement, a data compression method generates a compressed representation of at least a portion of an individual's genome by receiving an input file having a representation of the genome as a sequence of variants defined relative to a reference genome. A reference database having a plurality of reference lists of genetic variants from other individuals is accessed. Each reference list has a sequence of genetic variants from a single, phased haplotype. Two mosaics of segments from the reference lists are identified which match the genome to within a threshold accuracy. Each mosaic represents a single one of the two haplotypes of the individual's genome and includes a portion of the sequence of genetic variants from one of the reference lists. The compressed representation is generated by encoding the two mosaics and deviations from the two mosaics. 1. A data compression method for generating a compressed representation of at least a portion of an individual's genome , comprising:receiving an input file comprising a representation of the at least a portion of the individual's genome in the form of a sequence of variants defined relative to a reference genome;accessing a reference database comprising a plurality of reference lists of genetic variants from other individuals, each reference list comprising a sequence of genetic variants from a single, phased haplotype;identifying two mosaics of segments from the reference lists which match the at least a portion of the individual's genome to within a threshold accuracy, each mosaic representing a single one of the two haplotypes of the individual's genome in the at least a portion of the individual's genome for which the compressed representation is to be generated, each of the segments comprising a portion of the sequence of genetic variants from one of the reference lists; andgenerating the compressed ...

EXTENDING ASSEMBLY CONTIGS BY ANALYZING LOCAL ASSEMBLY SUB-GRAPH TOPOLOGY AND CONNECTIONS

Aspects of the present disclosure provide methods, systems, and computer program products for generating one or more extended contigs. Aspects of the exemplary embodiment include receiving input contigs for a genome; generating local assembly subgraphs including the ends of each contig; identifying subgraphs that unambiguously connect two contigs; and generating an extended contig in which the orientation and order of at least two contigs is determined. Extended contigs can include any number of linearly ordered and linked contigs. 1. A method , executed by at least one software component on at least one processor , for producing an extended contig assembly comprising:(a) receiving a contig assembly graph comprising two or more contigs;(b) selecting one or more nodes in the contig assembly graph, wherein the one or more nodes are selected from: nodes corresponding to the end of a contig, nodes present in non-contig-associated regions, nodes at or near ambiguous regions inside a contig, and combinations thereof;(c) obtaining at least one local assembly subgraph comprising sequence reads within a defined distance of the one or more selected nodes;(d) identifying a local assembly subgraph that is connected to only two contigs in the contig assembly graph; and(e) outputting an extended contig assembly graph in which the two contigs are connected.2. The method of claim 1 , wherein the at least one local assembly subgraph is generated by the processor using a local assembly subgraph generator.3. The method of claim 1 , wherein the at least one local assembly subgraph is retrieved from a database.4. The method of claim 1 , wherein identifying a local assembly subgraph that is connected to only two contigs in the contig assembly graph further comprises: characterizing one or more properties of the local assembly subgraph selected from the group consisting of: general complexity measurement of the branching structure inside the local assembly subgraph claim 1 , the ratio of ...

PRIVACY-PRESERVING SIMILAR PATIENT QUERY SYSTEMS AND METHODS

Method including securely calculating, by a processor in electrical communication with a genome registry, an edit-distance between a query private genome and a second private genome, and securely calculating, by the processor, a set difference size between the query genome and the second private genome are disclosed. Systems capable of performing similar patient queries while preserving privacy are also disclosed. 1. A method comprising:securely calculating, by a processor in electrical communication with a genome registry, an edit-distance between a query private genome and a second private genome; andsecurely calculating, by the processor, a set difference size between the query genome and the second private genome.2. The method of claim 1 , further comprising computing claim 1 , by the processor claim 1 , a set of single-character edits from the query genome and a public reference.3. The method of claim 2 , further comprising identifying claim 2 , by the processor claim 2 , preferred clusters by comparing a set of single-character edits with centers of recorded clusters.4. The method of claim 1 , wherein the edit sequence is contained on the genome registry.5. The method of claim 1 , further comprising comparing the set difference size with a predetermined threshold.6. The method of claim 3 , further comprising comparing the set difference size with a predetermined threshold.7. The method of claim 1 , wherein the genome registry is hashed.8. The method of claim 7 , wherein every set element is associated with a separate bucket.9. The method of claim 1 , further comprising square-free calculating claim 1 , by the processor claim 1 , a set difference.10. A system comprising:genomic registry data;a processor; and calculate a query edit sequence from a reference genome and a query genome; and', 'calculate a set difference size from the query edit sequence and a third party edit sequence stored on a server., 'a non-transitory memory having instructions that, in ...

METHOD AND SYSTEM FOR ASSIGNING, ROUTING, AND UNASSIGNING DATA FLOWS OF ULTRASOUND PATCH PROBES

An ultrasound patch probe having ultrasound image acquisition functionality is selectively placed on a patient in communication range of an ultrasound imaging system. A signal processor of the ultrasound imaging system detects a presence of the ultrasound patch probe to establish a connection between the ultrasound patch probe and the ultrasound imaging system. The signal processor assigns the detected ultrasound patch probe to one or both of a patient and an anatomy of the patient. The signal processor maps the ultrasound patch probe to ultrasound image routing parameters based on the assignment. The signal processor routes ultrasound image data acquired by the ultrasound patch probe to one or both of a display area of a display system for presentation of the acquired ultrasound image data and a storage location of a data storage medium for storing the acquired ultrasound image data based on the ultrasound image routing parameters. 1. A method , comprising:detecting, by a signal processor of an ultrasound imaging system, a presence of an ultrasound patch probe to establish a connection between the ultrasound patch probe and the ultrasound imaging system;assigning, by the signal processor, the detected ultrasound patch probe to one or both of a patient and an anatomy of the patient;mapping, by the signal processor, the ultrasound patch probe to ultrasound image routing parameters based on the assignment; androuting, by the signal processor, ultrasound image data acquired by the ultrasound patch probe to one or both of a display area of a display system for presentation of the acquired ultrasound image data and a storage location of a data storage medium for storing the acquired ultrasound image data based on the ultrasound image routing parameters.2. The method of claim 1 , comprising mapping claim 1 , by the signal processor claim 1 , the ultrasound patch probe to a pre-defined set of ultrasound scanning parameters based on the assignment.3. The method of claim 2 , ...

PREDICTING DISEASE BURDEN FROM GENOME VARIANTS

Disclosed herein are analytical methods to predict or determine a subject's phenotype burden and/or genomic load from the subject's genome sequence variants. The disclosed methods may report a dynamically ordered list of genes or genomic regions responsible for each of one or more phenotypes. Also disclosed herein are analytical methods to convert the phenotype burden and/or genomic load into a probability or risk profile or percentile for a certain phenotype or one or more phenotypes among a plurality of phenotypes, which may be compared to a reference population. 1124.-. (canceled)125. A method of prioritizing two or more phenotypes based on a risk score of each of said two or more phenotypes , comprising:(a) obtaining one or more genome sequence variants from one or more genes or genomic regions of a biological sample of a subject; (i) determining a phenotype association score for each gene or genomic region in said one or more genes or genomic regions to provide a plurality of phenotype association scores;', '(ii) combining said plurality of phenotype association scores to provide said risk score for each of said two or more phenotypes;, '(b) determining, using a programmed computer processor, a risk score for each of said two or more phenotypes by(c) prioritizing said two or more phenotypes based on said risk score for each of said two or more phenotypes, thereby providing a list of prioritized phenotypes; and(d) outputting said list of prioritized phenotypes.126. The method of claim 125 , further comprising (e) providing for at least a subset of phenotypes from said list of prioritized phenotypes a dynamically ranked list of genes or genomic regions associated with each phenotype in said subset of phenotypes.127. The method of claim 126 , wherein said dynamically ranked list is ordered based on said phenotype association score.128. The method of claim 125 , wherein said two or more genome sequence variants are determined by high-throughput sequencing.129. The ...

SYSTEMS AND METHODS FOR STRING REPRIORITIZATION

The present disclosure provides methods and systems for reprioritizing a first set of strings based on at least a node annotation to generate a second set of strings. One or more graphical representations comprising machine readable data in annotated nodes may be used to score a first set of strings. To score a first set of strings based on one or more node annotations, a seed node may be selected based on a node annotation corresponding to the first set of strings and a first value may be assigned to the seed node. Information may be propagated from a seed node to neighboring nodes and second values may be assigned to neighboring nodes. A score may be generated from at least a first value and a second value. 1. A computer system for reprioritizing a first set of strings in view of one or more node annotations to generate a second set of strings , comprising: receive (i) a file comprising a first set of strings, wherein the first set of strings includes differences with respect to a reference set of strings, and (ii) one or more graphical representations comprising machine readable data in annotated nodes that are related to one another by one or more edges, where an a given representation of the one or more graphical representations corresponds to each one of the annotated nodes;', selecting a seed node, wherein the seed node is based on a node annotation;', 'assigning a first value to the seed node;', 'propagating information from the seed node across an edge to a neighboring node to generate a second value;', 'generating a score from at least one of the first value and the second value; and, 'score the first set strings, wherein for at least a subset of each of the differences of the first set of strings with respect to the reference set of strings the scoring comprises, 'generate a second set of strings from the score and the first set of strings, wherein the second set of strings is re-prioritized with respect to the first set of strings; and', 'save the second ...

AUTHORIZATION SYSTEM THAT PERMITS GRANULAR IDENTIFICATION OF, ACCESS TO, AND RECRUITMENT OF INDIVIDUALIZED GENOMIC DATA

Systems and methods are provided for controlling dissemination of genomic data. One embodiment is a system that stores genomic data. The genomic data for each individual lists genetic variants determined to exist within that individual. The system receives an access request for a segment of genomic data for an individual, analyzes an authentication token within the request, authenticates the request as belonging to an account for a user based on the authentication token, and reviews authorization directives for the individual that indicate how predefined portions of genomic data are shared. The system also transmits the segment of genomic data in response to determining that the authorization directives permit the account to access the segment of genomic data, and prevents transmission of the segment of genomic data in response to determining that the authorization directives do not permit the account to access the segment of genomic data. 1. A system comprising:a genomic data server that stores genomic data for multiple individuals, the genomic data for each individual listing genetic variants determined to exist within that individual; and an interface that receives an access request for a segment of genomic data for an individual; and', 'a controller that analyzes an authentication token within the request, authenticates the request as belonging to an account for a user based on the authentication token, and reviews authorization directives for the individual that indicate how predefined portions of genomic data are shared,', 'the controller transmits the segment of genomic data in response to determining that the authorization directives permit the account to access the segment of genomic data, and', 'the controller prevents transmission of the segment of genomic data in response to determining that the authorization directives do not permit the account to access the segment of genomic data., 'a genomic authorization server comprising2. The system of wherein:the ...

SECURE COMPUTING SYSTEMS AND METHODS

The present disclosure relates to systems and methods for facilitating trusted handling of genomic and/or other sensitive information. Certain embodiments may use a virtualized execution environment to execute code and/or programs that wish to access and/or otherwise use genomic and/or other sensitive information. In some embodiments, data requests from the code and/or programs may be routed through a transparent data access proxy configured to transform requests and/or associated responses to protect the integrity of the genomic and/or other sensitive information. 120.-. (canceled)21. A method for performing trusted computations on sensitive data performed by a first system comprising a processor and a non-transitory computer-readable storage medium storing instructions that , when executed by the processor , cause the system to perform the method , the method comprising:receiving, from an application executing on a remote system by an interface of the first system, a request to access genomic data set stored within a protected execution environment of the system;transforming the request in accordance with execution context associated with the application to generate a secure request to access the genomic data set;sending the generated secure request to access the genomic data set to a data store storing the genomic data set associated with the protected execution environment;receiving a secure response to the secure request from the data store associated with the protected execution environment;transforming the secure response in accordance with the execution content to generate a response to the request to access the genomic data set; andtransmitting the generated response to the remote system.22. The method of claim 21 , wherein the interface comprises an application programming interface.23. The method of claim 21 , wherein the method further comprises accessing the execution context associated with the application from the protected execution environment.24. ...

FAST AND SECURE RETRIEVAL OF DNA SEQUENCES

Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are identified as being most similar to a query DNA or RNA sequence based on fitting of the retrieved sequence models to the query DNA or RNA sequence. The sequence models may be context tree weighting (CTW) models {S, θ} where Sdenotes the context tree model for the DNA or RNA sequence x stored in the database, and θdenotes parameters of the context tree model S. The fitting may include, for each CTW model {S, θ}, computing the codeword length for the query DNA or RNA sequence y using the CTW model {S, θ. 1. A non-transitory storage medium storing instructions executable by an electronic data processing device to perform a method including:generating a sequences index comprising sequence models for deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sequences stored in a database, the generating including computing the sequence model for each DNA or RNA sequence stored in the database as a finite memory tree source model and parameters for the finite memory tree source model; wherein the sequence models are computed using context tree weighting (CTW); andidentifying one or more DNA or RNA sequences stored in the database as being most similar to a query DNA or RNA sequence based on applying the sequence models to the query DNA or RNA sequence and on determining how well each sequence model fits the query DNA or RNA sequence.2. (canceled)3. The non-transitory storage medium of wherein the identifying includes:computing a query model for the query DNA or RNA sequence as a finite memory tree source model and parameters for the finite memory tree source model; wherein the query model is computed using context tree weighting (CTW); andcomputing a reference value of a compression metric ...

Distributed System Providing Dynamic Indexing And Visualization Of Genomic Data

Systems and methods for dynamic visualization of genomic data are provided in which a genomic visualization system adapts presentation of information content according to scale-relevant annotations within a sequence object. 1. A method of visualizing genomic information , comprising:providing an indexed genomic database that stores a sequence object representative of a genomic region, the sequence object comprising a plurality of scale relevant annotations;coupling a scaling engine with the indexed genomic data storage;using the scaling engine to:adjust scale-relevant information derived from the scale-relevant annotations of the sequence object as a function of a user selected zoom level;dynamically generate a genomic display object for the sequence object, wherein the genomic display object is representative of the scale-relevant information based on the zoom level, wherein dynamic generation comprises an alteration of presented visualization of the sequence object;wherein the scaling engine dynamically downsamples data based on the amount of data required for the genomic region requested;wherein downsampling is accomplished by at least one of a first mechanism that requires no knowledge of underlying data and a second mechanism that requires additional information about the file type; andtransfer the downsampled data to an output device to present the genomic display objects to a user.2. The method of claim 1 , wherein the first mechanism uses a pre-condensed file that is selected based on a number of data points that will be utilized by the output device.3. The method of claim 1 , wherein the second mechanism dynamically summarizes data based on file type information.4. The method of claim 1 , wherein the genomic region is one of the following: a whole genome claim 1 , a chromosome claim 1 , a chromosomal fragment claim 1 , and an allele.5. The method of claim 1 , wherein a bamserver operates as the scaling engine.6. The method of claim 1 , wherein a ...

INTEGRATED SYSTEM FOR NUCLEIC ACID-BASED STORAGE OF DIGITAL DATA

In some embodiments, systems and methods for storing and/or retrieving digital information in a nucleic acid library are provided. In some embodiments, an integrated system comprising a nucleic acid synthesis device, a nucleic acid sequencing device, a computing device, and a nucleic acid library is provided. In some embodiments, a write request that associates a value with a key is received by the system, the system synthesizes nucleic acid molecules associated with the request, and stores the nucleic acid molecules in the nucleic acid library. In some embodiments, a read request for a key is received by the system, and the system sequences nucleic acid molecules from the nucleic acid library that are associated with the key. 1. A system for storing digital information in and retrieving digital information from a nucleic acid library , the system comprising:a nucleic acid synthesis device;a nucleic acid sequencing device;a nucleic acid storage medium configured to store a nucleic acid library; and an external interface configured to receive a read request, the read request including a first key;', 'an address determination engine configured to determine a first address based on the first key;', determine a first primer sequence based on the first address;', 'determine at least one nucleic acid sequence representing the first primer sequence; and', 'provide the at least one nucleic acid sequence representing the first primer sequence to the nucleic acid synthesis device for synthesis of at least one first primer molecule;, 'a sequence generation engine configured to, receive nucleic acid sequence information from the nucleic acid sequencing device representing nucleic acid molecules from the nucleic acid storage medium as amplified using the at least one first primer molecule; and', 'extract a first value from the received nucleic acid sequence information, wherein the first value is associated with the first key., 'a data extraction engine configured to], 'at least ...

BIOINFORMATIC PROCESSING SYSTEMS AND METHODS

The present disclosure relates to systems and methods for facilitating trusted handling of genomic and/or other bioinformatic information. Certain embodiments may facilitate policy-based governance of access to and/or use of bioinformatic information, improved interaction with and/or use of distributed bioinformatic information, parallelization of various processes involving bioinformatic information, and/or reduced user involvement in bioinformatic workflow processes, and/or the like. Further embodiments may provide for memoization processes that may persistently store final and/or intermediate results of computations performed using genomic data for use in connection with future computations. 112-. (canceled)13. A method for performing trusted computations on genomic data performed by a distributed computing system comprising a processor and a non-transitory computer-readable storage medium storing instructions that , when executed by the processor , cause the system to perform the method , the method comprising:receiving first policy information from a stakeholder system articulating one or more first requirements associated with computational results generated using a genomic data set;receiving a first request from a user system to perform a computation by the distributing computer system, the first request comprising a first set of one or more pieces of identification information, the computation comprising analyzing a genomic data set to determine a particular genomic feature of the genomic data set;determining, based on the first set of one or more pieces of identification information, that a result of a prior computation using the first set of one or more pieces of identification information is not stored in a persistent storage associated with the distributed computing system;storing information associated with the first set of one or more pieces of identification information in the persistent storage;generating, based on the first set of one or more pieces ...

METHODS AND MACHINE LEARNING SYSTEMS FOR PREDICTING THE LIKELIHOOD OR RISK OF HAVING CANCER

Embodiments of the present invention relate generally to non-invasive methods and tests that measure biomarkers (e.g., tumor antigens) and collect clinical parameters from patients, and computer-implemented machine learning methods, apparatuses, systems, and computer-readable media for assessing a likelihood that a patient has a disease, relative to a patient population or a cohort population. In one embodiment, a classifier is generated using a machine learning system based on training data from retrospective data and subset of inputs (e.g. at least two biomarkers and at least one clinical parameter), wherein each input has an associated weight and the classifier meets a predetermined Receiver Operator Characteristic (ROC) statistic, specifying a sensitivity and a specificity, for correct classification of patients. The classifier may then be used to assesses the likelihood that a patient has cancer relative to a population by classify the patient into a category indicative of a likelihood of having cancer or into another category indicative of a likelihood of not having cancer. 179-. (canceled)80. A computer implemented method for predicting a likelihood of having cancer in a patient , storing a set of data comprising a plurality of patient records, each patient record including a plurality of parameters and corresponding values for a patient, and wherein the set of data also includes a diagnostic indicator indicating whether or not the patient has been diagnosed with cancer;', 'selecting a subset of the plurality of parameters for inputs into a machine learning system, wherein the subset includes a panel of at least two different biomarkers and at least one clinical parameter;', 'randomly partitioning the set of data into training data and validation data;', 'generating a classifier using a machine learning system based on the training data and the subset of inputs, wherein each input has an associated weight; and', 'determining whether the classifier meets a ...

A novel algorithm for smn1 and smn2 copy number analysis using coverage depth data from next generation sequencing

The disclosure concerns methods and compositions for obtaining reliable copy numbers of highly homologous gene(s) using next generation sequencing. The methods determine whether or not an individual is a carrier of an autosomal recessive gene mutation using a determination of copy number of two genes, in specific embodiments. In at least some cases, an individual is identified whether or not he or she is a carrier or affected for a genetic defect in SMN1, wherein the defect is associated with spinal muscular atrophy.

COMPUTER-BASED SYSTEMS AND METHODS FOR ANALYZING GENOMES BASED ON DISCRETE DATA STRUCTURES CORRESPONDING TO GENETIC VARIANTS THEREIN

A computer-based method for analyzing genetic variants within a plurality of genomes includes submitting a query term to a database storing a plurality of discrete data structures within a memory. Each data structure can uniquely correspond to only one of the genetic variants present within the plurality of genomes, and can include a first data field comprising a unique alphanumeric identifier for the corresponding genetic variant and a second data field comprising a unique alphanumeric identifier for a genome in which the corresponding genetic variant is present. The query term can include a unique alphanumeric identifier for at least one genome and an operation to be performed. The method further can include searching the second data fields of the plurality of data structures stored in the database for matches to the query term that satisfy the operation; and generating an output representing the search result. 1. A computer-based method for analyzing genetic variants within a plurality genomes , the method comprising:submitting a query term to a database storing a plurality of discrete data structures within a memory, each data structure uniquely corresponding to only one of the genetic variants present within the plurality of genomes, each data structure comprising a first data field comprising a unique alphanumeric identifier for the corresponding genetic variant and a second data field comprising a unique alphanumeric identifier for a genome in which the corresponding genetic variant is present, the query term comprising a unique alphanumeric identifier for at least one genome of the plurality of genomes and an operation to be performed on that genome;searching the second data fields of the plurality of data structures stored in the database for unique alphanumeric identifiers that match the query term and satisfy the operation; andgenerating an output representing the result of performing the search.218-. (canceled)19. A computer-based system for analyzing ...

BIOLOGICAL DATABASE INCORPORATING CONTENT-PROVIDER PAYMENT MECHANISM

Systems and methods are used to provide an aggregated genomic information database and compensate contributors. Genomic data and contributor data are received from a contributor client device and stored in an electronic database using a server computer. A linkage between the genomic data and other genomic data stored in the electronic database is determined and the linkage is stored in the electronic database using the server computer. A request for the genomic data from a user client device is received, the genomic data and the linkage are retrieved from the electronic database, and the genomic data and the linkage are sent to the user client device using the server computer. A compensation amount value for the genomic data is calculated and sent to the contributor client device using the server computer. 120-. (canceled)21. A method for generating a biological database , comprising:offering one or more contributing users an opportunity to contribute information related to one or more biological variations;aggregating any information contributed by the one or more contributing users together in the biological database, the information being stored in whole or in part in the biological database or being retrievable in whole or in part from outside the biological database using linking information stored in the biological database;allowing one or more retrieving users to retrieve information retrievable from the biological database; anddetermining a compensation to be distributed to any contributing user having contributed information retrieved by any retrieving user using a compensation engine based on at least a first factor related to the reliability of the contributed information and a second factor related to the popularity of the contributed information.22. The method of claim 21 , wherein the first factor comprises information about a reliability of the contributing user having contributed the contributed information.23. The method of claim 21 , wherein the ...

SYSTEM AND METHOD FOR DRUG TARGET AND BIOMARKER DISCOVERY AND DIAGNOSIS USING A MULTIDIMENSIONAL MULTISCALE MODULE MAP

A new method and system can be implemented to identify, analyze and display hierarchies of condition-specific gene, network or pathway activities or aberrations. Methods are also presented related to biomarker and drug-target identification and diagnosing new patients or samples with diseases or disease subtypes. Further, methods are presented related to predicting patient survival or response to treatment. Finally, methods are presented that can provide information of biological agricultural or medical interest. Methods provided herein include methods of making a multidimensional multiscale module map for identifying, analyzing and displaying hierarchies of network or pathway activities, the multidimensional multiscale map, and systems for discussing genomic features of a subject or sample with the multiscale module map. 1. A method of making a multidimensional multiscale module map for identifying analyzing and displaying hierarchies of network or pathway activities , the method comprising:providing a static multiscale module map;accessing a plurality of measured attributes for a plurality of elements from one or more patients and/or biological samples from at least one condition of interest;assigning a plurality of attributes to a plurality of modules in the static multiscale module map;identifying associations from a plurality of attributes for a plurality of modules; andstoring a database of the most significant associations along with module attributes and the static multiscale module map, thereby generating said multidimensional multiscale module map.2. The method of claim 1 , wherein the assigning is performed by a mapping engine.3. The method of claim 2 , wherein the mapping engine is coupled to the static multiscale module map.4. The method of claim 1 , wherein the identifying is performed by an inference engine.59-. (canceled)10. The method of claim 1 , wherein the static multiscale module map is constructed by automatic analysis of molecular networks to ...

METHOD AND SYSTEM FOR MICROBIOME-DERIVED CHARACTERIZATION, DIAGNOSTICS AND THERAPEUTICS FOR CONDITIONS ASSOCIATED WITH FUNCTIONAL FEATURES

A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome-derived functional features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model. 1. A method for at least one of characterizing , diagnosing , and treating an aminobenzoate-related condition for a subject , the method comprising: [ identifying primers for nucleic acid sequences associated with the aminobenzoate-related condition,', 'amplifying nucleic acid material from the biological samples based on the primers; and, 'determining microorganism nucleic acid sequences, comprising, 'determining alignments of the microorganism nucleic acid sequences to reference sequences associated with the aminobenzoate-related condition;, 'for a set of biological samplesgenerating a microbiome functional diversity dataset based on the alignments;extracting a set of microbiome functional diversity features from the microbiome functional diversity dataset;generating a characterization of the aminobenzoate-related condition based on the set of microbiome functional diversity features;determining a therapy for the subject based on the characterization and a subject biological sample from the subject; andproviding the therapy to the subject, wherein the therapy is operable to modulate microbiome composition to improve a state of the aminobenzoate-related ...

METHOD AND SYSTEM FOR MICROBIOME-DERIVED CHARACTERIZATION, DIAGNOSTICS AND THERAPEUTICS FOR CONDITIONS ASSOCIATED WITH FUNCTIONAL FEATURES

A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome-derived functional features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model. 1. A method for at least one of characterizing , diagnosing , and treating an aminobenzoate-related condition for a subject , the method comprising:providing a set of sampling kits to a population of subjects, each sampling kit of the set of sampling kits comprising a sample container, wherein the sample container is operable to receive a biological sample from a collection site;receiving an set of biological samples from the set of sampling kits;identifying a primer for a nucleic acid sequence associated with the aminobenzoate-related condition;with a bridge amplification substrate of a next generation sequencing platform of a sample processing system, determining a set of microorganism nucleic acid sequences based on the set of biological samples and the primer;generating a microbiome functional diversity dataset for the population of subjects based on the set of microorganism nucleic acid sequences;generating a characterization of the aminobenzoate-related condition based on the microbiome functional diversity dataset;determining a therapy for the subject based on the characterization and a biological sample from the subject, wherein the therapy is ...

METHOD AND SYSTEM FOR MICROBIOME-DERIVED CHARACTERIZATION, DIAGNOSTICS AND THERAPEUTICS FOR CONDITIONS ASSOCIATED WITH FUNCTIONAL FEATURES

A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome-derived functional features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model. 1. A method for characterizing a gastric cancer condition , the method comprising:receiving an aggregate set of samples from a population of subjects; [ identifying a set of primers for nucleic acid sequences associated with the gastric cancer condition,', 'amplifying nucleic acid material from the aggregate set of sample samples based on the set of primers; and, 'determining microorganism nucleic acid sequences, comprising, 'determining alignments of the microorganism nucleic acid sequences to reference sequences associated with the gastric cancer condition, including aminobenzoate-related condition;, 'for the aggregate set of samplesgenerating a microbiome feature dataset for the population of subjects based upon the alignments;generating a characterization model of the gastric cancer condition from the microbiome feature dataset;based upon the characterization model, generating a therapy model that determines a therapy for correcting the gastric cancer condition; andat an output device associated with the subject, providing the therapy to a subject diagnosed with the gastric cancer condition based upon the characterization model and the therapy model.2. ...

PIPELINE FOR RATIONAL DESIGN AND INTERPRETATION OF BIOMARKER PANELS

A new pipeline for the rational design and interpretation of biomarker panels is provided. The pipeline includes: generating the maximally informative marker set from biomarker databases; selecting an optimal biomarker panel based on the desired accuracy, economic, and experimental constraints; and interpreting the assay results by a statistically robust matching to reference data. The pipeline can also be used to identify biological samples, including cell types and progenitor cells. 1. A method for identifying a biological sample comprising:identifying a plurality of biomarkers that are indicia of the identity of the biological sample;ranking the identified biomarkers from most-informative to least-informative to generate a ranked biomarker set;selecting a biomarker panel using the ranked biomarker set and determining the size and contents of the biomarker panel;using the biomarker panel to assay the biological sample to generate a biomarker assay output; andcomparing the biomarker assay output to reference data for the biomarkers in the biomarker panel to rank the biomarkers in the biomarker assay output from best-match to least-match as compared with the reference data to identify the biological sample.2. The method of claim 1 , further comprising:interpreting the results of the comparison to identify the biological sample.3. The method of claim 2 , further comprising:determining a statistical probability value that the identification of the biological sample is correct.4. The method of claim 1 , wherein selecting the biomarker panel further comprises a series of simulations that determine the size and contents of the biomarker panel providing the level of accuracy claim 1 , economy claim 1 , and/or throughput tailored to the specifications of an end-user.5. The method of claim 1 , wherein ranking of the plurality of biomarkers further comprises a selection algorithm that identifies a subset of biomarkers that distinguish one cell type from another in the ...

Long-Term Data Storage Service for Wearable Device Data

Methods and apparatus for storing data about biological entities are provided. A computing device can receive a plurality of data items about a biological entity from a plurality of sources. The computing device can verify each data item of the plurality of data items using the computing device by at least: determining a source of the data item from among the plurality of sources, determining a provenance for the data item associated with the source of the data item, and verifying that the data item is associated with the biological entity based at least on the provenance for the data item associated with the source of the data item. After verifying that a particular data item is associated with the biological entity, the computing device can store the particular data item in a data log associated with the biological entity. 1. A method , comprising:receiving, at a computing device, a plurality of data items about a biological entity from a plurality of sources, wherein the plurality of sources comprises a wearable device being worn by the biological entity and the plurality of data items comprises a data item that includes physiological data obtained by one or more sensors of the wearable device; determining a source of the data item from among the plurality of sources,', 'determining a provenance for the data item associated with the source of the data item, and', 'verifying that the data item is associated with the biological entity based at least on the provenance for the data item; and, 'verifying each data item of the plurality of data items using the computing device by at leastafter verifying that a particular data item is associated with the biological entity, storing the particular data item in a data log associated with the biological entity using the computing device.2. The method of claim 1 , wherein the physiological data comprises at least one of cardiac data claim 1 , pulmonary data claim 1 , or analyte data.3. The method of claim 1 , wherein ...

Systems and Methods for Annotating Biomolecule Data

Systems, methods, software and computer-usable media for annotating biomolecule-related data are disclosed. In certain exemplified embodiments, the biomolecules can be nucleic acids and the data can be sequence-related data. In various embodiments, systems can include one or more public or private biological attributes (e.g., annotation information databases, data storage devices and systems, etc.) sources, one or more genomic features data sources (e.g., genomic variant tools, genomic variant databases, genomic variant data storage devices and systems, etc.), a computing device (e.g., workstation, server, personal computer, mobile device, etc.) hosting an annotations module and/or a reporting module, and a client terminal. 1. A system for annotating genomic features , comprising:a client device;a first data source configured to store genomic features data associated with one or more genomic sequence positions;a second data source configured to store biological attributes data; [ receive genomic features data from the first data source,', 'search the second data source to identify relevant biological attributes associated with the genomic features data, and', 'annotate the genomic features data with the identified biological attributes, and, 'an annotation component configured to, 'an analytics component configured to parse the annotated genomic features data to ascertain statistical trends within the annotated genomic features data; and, 'an annotations module communicatively connected with the client device, the first data source and the second data source, comprisinga reporting module communicatively connected to the client device and the annotations module, the reporting module configured to generate a report summarizing the annotated genomic features data and the ascertained statistical trends.2. The system claim 1 , as recited in claim 1 , wherein the annotations module further includes a filtering component configured to filter the annotated genomic features ...

Bipartite Graph Structure

A bipartite graph structure is utilized to better store data. The bipartite graph structure may be used in a biochemical database to efficiently store a variety of molecules and processes that might occur between the molecules. Molecules are represented as molecule nodes, which may have metadata fields including a molecule name, a molecule type, a molecular formula, a sequence, a molecular charge, a set of molecular properties, and a set of component molecules. Processes operating on the molecules are represented by process nodes, which may have metadata fields including a process name, a set of process roles, a set of process properties, and a set of sub-processes. Edges, called roles, each associate a molecule node with a process node and represent the role the associated molecule plays in the associated process. The roles may contain metadata identifying the role type and the stoichiometry coefficient of the molecule in the process. 1. A system for storing biochemical information comprising:a non-transitory computer readable storage medium; a plurality of molecule nodes, wherein each molecule node represents a molecule in a biochemical environment, and wherein each molecule node includes a plurality of molecule metadata fields describing the molecule;', 'a plurality of process nodes, wherein each process node represents a process occurring in a biochemical environment, and wherein each process node includes a plurality of process metadata fields including at least a roles field, wherein the roles field defines the roles of molecules in the process; and', 'a plurality of edges, wherein each edge associates a molecule node to a process node, and wherein each edge characterizes a role of a molecule represented by the associated molecule node in a process represented by the associated process node, wherein the edge includes the stoichiometric coefficient of the molecule in the process., 'a processor executing instructions to configure the non-transitory computer ...

MULTI-DIMENSIONAL MAPPING OF BINARY DATA TO DNA SEQUENCES

Systems and methods for multi-dimensional mapping of binary data DNA sequences are described. In one embodiment, the method may include determining a current level of a first DNA base from a sequence of DNA bases based at least in part on a read process of the sequence, determining a current level of a second DNA base after the first DNA base and a current level of a third DNA base after the second DNA base, and decoding binary data from the sequence based at least in part on the determined current level of the first DNA base, the determined current level of the second DNA base, and/or the determined current level of the third DNA base. 1. A deoxyribonucleic acid (DNA) storage system comprising: determine a current level of a first DNA base from a sequence of DNA bases based at least in part on a read process of the sequence;', 'determine a current level of a second DNA base after the first DNA base and a current level of a third DNA base after the second DNA base based at least in part on the read process and a set of possible DNA base pairs permitted to occur after the first DNA base according to an encoding scheme that does not allow homopolymers to occur in adjacent DNA bases; and', 'decode binary data from the sequence based at least in part on the determined current level of the first DNA base, the determined current level of the second DNA base, and the determined current level of the third DNA base., 'a DNA reader for reading sequences of DNA bases, the DNA reader being configured to2. The DNA storage system of claim 1 , wherein the set of possible DNA base pairs permitted to occur after the first DNA base includes nine possible combinations of DNA base pairs based at least in part on the encoding scheme not allowing homopolymers.3. The DNA storage system of claim 2 , wherein the nine possible combinations of DNA base pairs map to nine nodes of a signal constellation diagram.4. The DNA storage system of claim 3 , wherein the DNA reader is further configured ...

COMPUTING TECHNOLOGIES FOR IMAGE OPERATIONS

A method comprises: receiving, via a processor, an image depicting a tissue; quantifying, via the processor, the image based on: segmenting, via the processor, the image into a plurality of segments; identifying, via the processor, a plurality of histological elements in the segments; forming, via the processor, a network graph comprising a plurality of nodes, wherein the histological elements correspond to the nodes; measuring, via the processor, a feature of the network graph; performing, via the processor, a transformation on the image based on the feature; determining, via the processor, a non-parametric feature of the image based on the transformation; saving, via the processor, the non-parametric feature onto a database. 1. A method comprising:receiving, via a processor, an image depicting a tissue; segmenting, via the processor, the image into a plurality of segments;', 'identifying, via the processor, a plurality of histological elements in the segments;', 'forming, via the processor, a network graph comprising a plurality of nodes, wherein the histological elements correspond to the nodes;', 'measuring, via the processor, a feature of the network graph;', 'performing, via the processor, a transformation on the image based on the feature;', 'determining, via the processor, a non-parametric feature of the image based on the transformation;', 'saving, via the processor, the non-parametric feature onto a database., 'quantifying, via the processor, the image based on2. The method of claim 1 , wherein the image is a whole slide image.3. The method of claim 1 , wherein the segment depicts at least one of a nucleus claim 1 , a cell claim 1 , or a gland.4. The method of claim 3 , wherein the quantifying comprises performing claim 3 , via the processor claim 3 , a morphometric process on the at least one of the nucleus claim 3 , the cell claim 3 , or the gland claim 3 , wherein the identifying is based on the morphometric process.5. The method of claim 1 , wherein ...

WEB SEARCH AND INFORMATION AGGREGATION BY WAY OF MOLECULAR NETWORK

A molecular network-based web search and information aggregation system and a process for creating a synthetic molecular network are disclosed. The amount of information and data available through the Internet is growing rapidly, yet current search through natural language-based keyword and page rank algorithm or directory search often cannot provide satisfactory relevant results. The process creates the synthetic molecular network according to a set of rules and chemistry knowledge. The synthetic molecular network is structured such that molecular information can be aggregated in ways that conform to contemporary graphing theory and chemistry rules. In this way, the molecular network-based web search and information aggregation system reduces reliance on natural language by leveraging strong relational associations between molecules that do not correlate to a set of natural language keywords. 1. A non-transitory computer readable medium storing a program which , when executed by at least one processing unit of a computing device , builds a molecular network that is structured according to a set of molecular mapping rules which make it easier for a machine or a computer to process information aggregated as a result of performing a web search via the molecular network , said program comprising sets of instructions for:retrieving a set of data from a registered molecule database;determining whether the set of data comprises information identifying a molecule;when the set of data comprises information identifying the molecule, creating a node representing the molecule;when the set of data does not comprise information identifying the molecule, determining whether the set of data comprises information specifying a synthetic chemical relationship between two molecules;when the set of data comprises information specifying the synthetic chemical relationship between two molecules, creating an edge representing the synthetic chemical relationship between the two molecules; ...