814results about "Bioinformatics" patented technology

Some of these new methods harness distributed computing capabilities to integrate biometric abstraction processes, wireless network connectivity, and specialized software for mediation, to produce a unified result set. A mediator that enables rapid health care support is used in a computer system having a database of information to be shared with authorized requesters, under privacy rules or other pre-defined constraints. The methods, using specialized software for mediation, are preferably enabled to process a securely transmitted remote data request as a query to verify or identify an individual, whether it is sent via a network that is wireless in any part, or not. Upon receiving a remote request, typically sent by a requesting application other than one operated by the individual who is the subject of the request, the mediator uses the individual's transformed biometric data of the request to rapidly advance query resolution, under all query preprocessing rules, and query results post-processing rules, that apply.

Orthoses with microprocessor control placed around the joint of a patient are used to perform and to monitor isometric, range-of-motion, proprioception and isotonic exercises of the joint. A variety of improved hardware elements result in an orthosis that is easier to use and interacts more efficiently with the controller to allow the monitoring of a greater range of motions while holding down cost and provide suitable accurate evaluation of the exercises. Efficient ways of programming the exercises, monitoring the exercises and evaluating the exercise provide a comprehensive program for the rehabilitation of an injured or weakened joint.

A method of processing a signal, including taking a signal formed from a plurality of source signal emitters and expressed in an original domain, decomposing the signal into a mathematical representation of a plurality of constituent elements in an alternate domain, analyzing the plurality of constituent elements to associate at least a subset of the constituent elements with at least one of the plurality of source signal emitters, separating at least a subset of the constituent elements based on the association and reconstituting at least a subset of constituent elements to produce an output signal in at least one of the original domain, the alternate domain and another domain.

Systems, methods and computer readable media for performing a domain-specific metasearch, and obtaining search results therefrom. A metasearch engine capable of accessing generic, web-based search engines and domain-relevant search engines is provided to receive one or more queries inputted by a user, and to search for documents on at least one the generic, web-based search engines and domain-relevant search engines which are relevant to the queries. Raw data search results are fetched in the form of text documents. Relevant data including semantic information are extracted from the raw data search results, and converted to a local format. The relevant data having been converted to the local format may be visualized as a network visualization. Additionally or alternatively, the raw data search results may be ranked and / or filtered based on the linking of the relevant data. Visualization of the raw data having been ranked and / or filtered may be performed in addition to, or alternative to visualization of the network.

This invention relates to a method, system and apparatus for the management of comprehensive and cumulative genetic and health assessment databases in relation to animals worldwide. More specifically, the invention is directed to methods and systems that are used to determine animal health care, well-being and nutrition.

The present invention provides a structure-based methodology for efficiently generating and screening protein libraries for optimized proteins with desirable biological functions, such as antibodies with high binding affinity and low immunogenicity in humans. In one embodiment, a method is provided for constructing a library of antibody sequences based on a three dimensional structure of a lead antibody. The method comprises: providing an amino acid sequence of the variable region of the heavy chain (VH) or light chain (VL) of a lead antibody, the lead antibody having a known three dimensional structure which is defined as a lead structural template; identifying the amino acid sequences in the CDRs of the lead antibody; selecting one of the CDRs in the VH or VL region of the lead antibody; providing an amino acid sequence that comprises at least 3 consecutive amino acid residues in the selected CDR, the selected amino acid sequence being a lead sequence; comparing the lead sequence profile with a plurality of tester protein sequences; selecting from the plurality of tester protein sequences at least two peptide segments that have at least 10% sequence identity with lead sequence, the selected peptide segments forming a hit library; determining if a member of the hit library is structurally compatible with the lead structural template using a scoring function; and selecting the members of the hit library that score equal to or better than or equal to the lead sequence. The selected members of the hit library can be expressed in vitro or in vivo to produce a library of recombinant antibodies that can be screened for novel or improved function(s) over the lead antibody.

The present invention provides a structure-based methodology for efficiently generating and screening protein libraries for optimized proteins with desirable biological functions, such as antibodies with high binding affinity and low immunogenicity in humans. In one embodiment, a method is provided for constructing a library of antibody sequences based on a three dimensional structure of a lead antibody. The method comprises: providing an amino acid sequence of the variable region of the heavy chain (VH) or light chain (VL) of a lead antibody, the lead antibody having a known three dimensional structure which is defined as a lead structural template; identifying the amino acid sequences in the CDRs of the lead antibody; selecting one of the CDRs in the VH or VL region of the lead antibody; providing an amino acid sequence that comprises at least 3 consecutive amino acid residues in the selected CDR, the selected amino acid sequence being a lead sequence; comparing the lead sequence profile with a plurality of tester protein sequences; selecting from the plurality of tester protein sequences at least two peptide segments that have at least 10% sequence identity with lead sequence, the selected peptide segments forming a hit library; determining if a member of the hit library is structurally compatible with the lead structural template using a scoring function; and selecting the members of the hit library that score equal to or better than or equal to the lead sequence. The selected members of the hit library can be expressed in vitro or in vivo to produce a library of recombinant antibodies that can be screened for novel or improved function(s) over the lead antibody.

Computer-implemented methods, programs and apparatus for generating a library design for a combinatorial library of materials. A library design includes a set of sources representing components to be used in preparing the combinatorial library, destinations replying arrangements of cells and mappings, defining one or more distribution patterns for assigning components to cells in the destination arrangement or arrangements. Mappings include gradients and sets of user-defined equations, and are used to calculate the amount of on components to be assigned to a cell or cells in an arrangement. A library design can also include one or more process parameters defined to vary over time or across a plurality of destination cells. The invention outputs a data file defining the library design, including electronic data representing the sources, the destinations and the mapping, in a format suitable for implementing manually or using automated material handling apparatus.

A system and method for processing and storing personal information in a secure manner is described. In particular, a system and method for processing, splitting and storing genomic information or portions thereof in a secure electronic format is disclosed. An individual's genomic sequence is digitized and a splitting algorithm applied to fragment and randomise the digitized genomic information into at least two separate datasets. One dataset is retained by the individual and the second dataset is stored on a central server as a secure database record. Each dataset in isolation presents uninformative data and it is only when both datasets are combined, using a reconstruction algorithm to recombine the separate dataset data for an individual that the digitized data is capable of being presented into a useable and informative format.

The present invention provides users with access to Internet-accessible databases via one portal of entry, such that queries need not be repeated multiple times in order to obtain needed information. Advantageously, the present invention will harness a systematic dynamic query profiler, document scoring, and display of retrieved documents via a knowledge-based system that facilitates user editing. Thus, the present invention will aid users so that less of their time and effort are required in order to obtain precisely the desired information for which they are searching.

Methods, computer systems, and computer program products for maintaining a stem cell registry comprising information about a plurality of stem cell units. A donor is enrolled in the stem cell registry. A stem cell unit from the donor is characterized. Information about the stem cell unit, obtained by the characterizing, is recorded in the stem cell registry. Computer readable media comprising a plurality of data records. One or more respective data records in the plurality of data records comprises (i) a collection identifier number that uniquely corresponds to a stem cell donation, (ii) a cord blood cell count associated with the stem cell donation, and (iii) a placenta blood cell count associated with the stem cell donation. Additional computer readable media comprising a plurality of data records. One or more respective data records in the plurality of data records comprises (i) a cord blood cell count associated with a stem cell donation, (ii) a placenta blood cell count associated with the stem cell donation, and (iii) an indication of at least two stem cell transplant units in the stem cell donation.

The present invention is related to databases and the exchange of scientific information. Specifically the invention discloses a laboratory data management system including a knowledge base that stores characteristics of laboratory reagents, experiment subjects, tissues and cells. The invention also includes an experiment input module that accepts input of parameters of an experiment and data from a knowledge base module. Further, the invention includes a protocol creator connected to the knowledge base module and the experiment input module that creates a laboratory protocol for an experiment based on data supplied from the knowledge base module and the experiment input module. The invention also includes methods to use the described system.

Disclosed systems, methods, and computer readable media can detect an association between semantic entities and generate semantic information between entities. For example, semantic entities and associated semantic collections present in knowledge bases can be identified. A time period can be determined and divided into time slices. For each time slice, word embeddings for the identified semantic entities can be generated; a first semantic association strength between a first semantic entity input and a second semantic entity input can be determined; and a second semantic association strength between the first semantic entity input and semantic entities associated with a semantic collection that is associated with the second semantic entity can be determined. An output can be provided based on the first and second semantic association strengths.

The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides.

Orthoses with microprocessor control placed around the joint of a patient are used to perform and to monitor isometric, range-of-motion, proprioception and isotonic exercises of the joint. A variety of improved hardware elements result in an orthosis that is easier to use and interacts more efficiently with the controller to allow the monitoring of a greater range of motions while holding down cost and provide suitable accurate evaluation of the exercises. Efficient ways of programming the exercises, monitoring the exercises and evaluating the exercise provide a comprehensive program for the rehabilitation of an injured or weakened joint.

A system for helping a chemist to identify pharmacophoric mechanisms, based on a set of input data representing many chemical compounds. Given an input data set defining for each compound a feature characteristic and an activity characteristic, a computer agglomeratively clusters representations of the molecules based on their feature characteristics. The result of this process is a multi-domain pyramid structure, made up of a number of nodes each representing one or more molecules. For each node, the computer identifies a representative feature set (such as a largest substructure common among the molecules in the node) and a representative activity level (such as an average of the activity levels of the molecules in the node). The computer then provides as output to a chemist a description of all or part of the pyramid. This process thus converts a large set of raw data into an understandable and commercially useful form, which can assist the chemist in developing beneficial new pharmaceuticals.

A method for creating an amalgamated bioinformatics database from at least a first database and a second database is presented. Concepts are identified in a first 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 first 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 first 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 first set of concepts and the second set of concepts is identified and a record is generated in the amalgamated bioinformatics database.

Systems and methods are provided for collecting, preparing, and / or analyzing a biological sample. A sample collection site may be utilized with one or more sample processing device. The sample processing device may be configured to accept a sample from a subject. The sample processing device may perform one or more sample preparation step and / or chemical reaction involving the sample. Data related to the sample may be sent from the device to a laboratory. The laboratory may be a certified laboratory that may generate a report that is transmitted to a health care professional. The health care professional may rely on the report for diagnosing, treating, and / or preventing a disease in the subject.

A method of processing a signal, including taking a signal formed from a plurality of source signal emitters and expressed in an original domain, decomposing the signal into a mathematical representation of a plurality of constituent elements in an alternate domain, analyzing the plurality of constituent elements to associate at least a subset of the constituent elements with at least one of the plurality of source signal emitters, separating at least a subset of the constituent elements based on the association and reconstituting at least a subset of constituent elements to produce an output signal in at least one of the original domain, the alternate domain and another domain.

The present invention provides a methodology for efficiently generating and screening protein libraries for optimized proteins with desirable biological functions, such as improved binding affinity towards biologically and / or therapeutically important target molecules. The process is carried out computationally in a high throughput manner by mining the ever-expanding databases of protein sequences of all organisms, especially human. In one embodiment, a method is provided for constructing a library of antibody sequences based on the amino acid sequence of a lead antibody. The method comprises: providing an amino acid sequence of the variable region of the heavy chain (VH) or light chain (VL) of a lead antibody; identifying the amino acid sequences in the CDRs of the lead antibody; selecting one of the CDRs in the VH or VL region of the lead antibody; providing an amino acid sequence that comprises at least 3 consecutive amino acid residues in the selected CDR, the selected amino acid sequence being a lead sequence; comparing the lead sequence with a plurality of tester protein sequences; and selecting from the plurality of tester protein sequences at least two peptide segments that have at least 15% sequence identity with the lead sequence, the selected peptide segments forming a hit library. The hit library of antibody sequences can be expressed in vitro or in vivo to produce a library of recombinant antibodies that can be screened for novel or improved function(s) over the lead antibody.

The present invention relates to systems and methods for searching an information directory in such a manner that it is easy to search, drill down, drill up and drill across an information directory using multiple independent hierarchical category taxonomies of the directory.

An instrumentation interface application that obtains information from an instrument directory and generates a graphic user interface populated based on the information. The information for a given instrument may be formatted in a manner so as to allow the interface application to interpret the information to be displayed in a certain manner. By delegating the such details of the instrument information to a directory instead of the interface application, the interface application can be utilized more effectively for relatively large biological laboratories that have many instruments of different types. The graphic user interface generated in such a manner can be used to monitor and control a variety of different aspects of the laboratory, including instrument management, sample management, and study-related management.

The present invention provides methods for rapid forensic analysis of mitochondrial DNA by amplification of a segment of mitochondrial DNA containing restriction sites, digesting the mitochondrial DNA segments with restriction enzymes, determining the molecular masses of the restriction fragments and comparing the molecular masses with the molecular masses of theoretical restriction digests of known mitochondrial DNA sequences stored in a database.

The present invention is related to databases and the exchange of scientific information. Specifically the invention disclosed a unified scientific database that allows researchers to easily share their data with other researches. The present invention also allows for the ease of data collection, annotation, storage, management, retrieval and analysis of scientific data through and into the database. In addition, it allows for archival storage and retrieval of data collected directly from laboratory instruments to ensure data consistency for patent and other purposes. It also allows for ease of sharing data between laboratories in remote locations. The present invention also supports the automated creation of experimental protocols.

A personal health monitor, including: (a) a physiological data input device operative to gather physiological data; (b) a detachable module that is detachably connected to a multi-purpose personal data accessory, operative to transmit the physiological data to the multi-purpose personal data accessory; and (c) the multi-purpose personal data accessory, whereas the multi-purpose personal data accessory is adapted to execute health monitoring software such as to enable the multi-purpose personal data accessory to receive the physiological data, process the physiological data to provide processed physiological data and control a long range transmission of the processed physiological data to a remote entity.

The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides.

A device, in particular a sample preparation device for the quantitative analysis of a drug and / or metabolite profile in a biological sample, which includes an insert for such a device being impregnated with at least one internal standard, to the internal standard itself, and to a kit comprising the device. Further, the invention also relates to an apparatus containing the device, and to a method for the quantitative analysis of a drug and / or metabolite profile in a biological sample employing the device.

Methods, systems and computer program products are provided for storing, organizing and / or manipulating cohort based information associated with a research study. Project information associated with a first project is received at an interface of a computer database environment. The project information associated with the first project includes cohort information associated with one or more cohorts of the first project and patient information associated with members of the one or more cohorts of the first project. A first virtual project drawer is generated associated with the first project to be stored in the computer database environment. The first virtual project drawer includes the project information associated with the first project, at least one cohort file and / or at least two cohort member files.

An apparatus and method analyzes a metabolic profile in a biological sample. The apparatus includes an input unit for inputting the drugs and / or metabolites to be screened; a controlling unit for determining a parameter set for metabolites preparation and for mass spectrometry analysis depending on the input of the kind of metabolites to be screened; a treatment unit for preparing the metabolites to be screened depending on the determined parameter set; a mass spectrometer for performing mass spectrometry analysis on prepared metabolites depending on the parameter set; a database for storing results of analyzing and parameter sets for metabolite preparation and for mass spectrometry analyses; and an evaluation unit for evaluating the results of mass spectrometry by use of reference results stored in the database to output an analysis of the metabolites profile.

A system and method of integrating diverse sources of data and data streams is presented. The method can include selecting a scenario based on a topic, creating a multi-relational directed graph based on the scenario, identifying and converting resources in accordance with the scenario and updating the multi-directed graph based on the resources, identifying data feeds in accordance with the scenario and updating the multi-directed graph based on the data feeds, identifying analytical routines in accordance with the scenario and updating the multi-directed graph using the analytical routines and identifying data outputs in accordance with the scenario and defining queries to produce the data outputs from the multi-directed graph.