570results about "Cheminformatics programming languages" patented technology

Described herein are methods and systems useful for characterizing clinical outcomes of a subject. Provided herein includes computer-assessed methods, medical information systems, and computer-readable instructions that can aid an end-user in diagnosis, prognosis, and treatment of a clinical outcome.

Systems and methods are used to store an electronic record of all product ion spectra of all detectable compounds of a sample. A plurality of product ion scans are performed on a tandem mass spectrometer one or more times in a single sample analysis across a mass range using a plurality of mass selection windows. All sample product ion spectra of all detectable compounds for each mass selection window are produced. All sample product ion spectra for each mass selection window are received from the tandem mass spectrometer using a processor. All sample product ion spectra for each mass selection window are stored as an electronic record of all detectable compounds of the sample using the processor. The electronic record is used to characterize compounds known at the time the electronic record is stored or to characterize compounds that became known after the electronic record was stored.

Innovative undo / redo operations can be applied to separate objects or parts of objects within multi-object data, without having to undo and redo along a rigid chronological sequence of recorded operations. In one implementation, a user selects an object, or part of an object, and innovative undo / redo techniques enable the user to apply undo and redo operations to only the selected object or part, while skipping undo and redo operations for other objects. The undo / redo operations can also be applied in parallel to multiple objects. A graphical user interface (GUI) provides linear or hierarchical representations of operations applied to each object and displays undo / redo controls for each object.

Abstract of Disclosure A computer-based system is described that provides users with the ability to develop high-fidelity digital quantitative representations of physical and chemical phenomena, and to employ an optimization-based approach to control associated physiochemical processes. The system includes a computational environment, intuitive user interface(s), integrated software libraries, analytical tools, and visualization / rendering engine that together provide an integrated framework for nanoscale modeling, analysis, simulation, and synthesis. Additionally, the system includes an optimal linear control synthesis methodology that incorporates a first order dynamic mathematical representation (of the conceptual molecular system) suitable for applying various pragmatic control system techniques including optimization of structured singular values, linear quadratic performance functions, Lyapunov criteria, or similar, for the purposes of nanoscale fabrication and molecular assembly.

The invention is an integrated, data-centric hazard communication system. The system has an authoring module and a means for disseminating hazard information about a material and its components, decomposition products and related materials. The authoring module decompiles material data, associates the decompiled data with hazard information, and recompiles material data associated with hazard information to provide hazard information about the material, its components, decomposition products of the material, and substances related to the material. The system can be a general purpose computer programmed with computer instructions to perform these functions. Computer software for performing these functions is also presented.

Systems and methods are used to store an electronic record of all product ion spectra of all detectable compounds of a sample. A plurality of product ion scans are performed on a tandem mass spectrometer one or more times in a single sample analysis across a mass range using a plurality of mass selection windows. All sample product ion spectra of all detectable compounds for each mass selection window are produced. All sample product ion spectra for each mass selection window are received from the tandem mass spectrometer using a processor. All sample product ion spectra for each mass selection window are stored as an electronic record of all detectable compounds of the sample using the processor. The electronic record is used to characterize compounds known at the time the electronic record is stored or to characterize compounds that became known after the electronic record was stored.

A chemical information system having a graphical user interface that allows manipulation of multiple databases having related material and information. The system includes a server and multiple workstations communicating with the server. The databases reside on the server, which may include multiple servers.

The present application is directed to the use of computerized data processing to plan, perform, and assess the results of high-throughput screening of multicomponent chemical compositions and solid forms of compounds. Systems utilized include databases of molecular descriptors and related compounds and their properties as determined empirically and through simulation, along with multidimensional visualization tools. Methods include methods for determining chemical compositions by performing steps including selecting a plurality of combinations of values of experimental parameters that can be varied by an automated experiment apparatus, determining a set of experimental results, and determining a second plurality of combinations of values based on the set of experimental results. Additional methods include selecting values of parameters that produce a composition, the values being relatively far from areas of rapid change or boundaries between solid forms.

An olfaction processor (OLP) (100) that generates RAW data (35) including content data (139d) relating to chemical substances is provided. The OLP (100) includes a generator (130) that generates the RAW data (35). The chemical substances include at least one of compounds, molecules, and elements. The generator (130) includes a conversion unit (131) that converts intensity variations, which show detected chemical substances included in data from at least one sensor that detects an amount that changes due to presence of at least one of the chemical substances, to the content data (139d) by mapping onto a frequency space where a plurality of frequencies have been respectively assigned to a plurality of specified chemical substances.

The present invention is a pocket-sized, portable computing apparatus that performs frequently used laboratory calculations, provides a look-up function for commonly used data and procedures, and provides note-taking and data capture for record-keeping. The present invention displays data in a form that a chemist finds most convenient and manipulates this data with functions a chemist typically utilizes in his work. In addition, the present invention provides a user interface that is compatible with traditional methods for formula manipulations and chemistry workflows and that increases the efficiency of the user in performing laboratory tasks.

A method for non-targeted complex sample analysis which involves the following steps. A first step involves providing a data base containing identifying data of known molecules. A second step involves introducing a complex sample containing multiple unidentified molecules into a Fourier Transform Ion Cyclotron Mass Spectrometer to obtain data regarding the molecules in the complex sample. A third step involves comparing the collected data regarding the molecules in the complex sample with the identifying data of known molecules in order to arrive at an identification through comparison of molecules in the sample.

The invention provides methods, apparatus, and systems for performing high-throughput preparation and screening of salts and polymorphs of drug candidates. The invention is directed towards enhancing the pre-formulation discovery process used for drug development. In particular, processes that determine suitable salts and processes that discover substantially every polymorph that can form from a particular drug candidate are provided. The processes are performed using several apparatuses that are specifically configured to carry-out various steps in a high-throughput characterization process. One such apparatus is configured for synthesizing a plurality of library members based on, for example, a library model generated by a computer system. Another apparatus may filter the synthesized solution to provide a substantially pure mixture that can be subjected to salt or polymorph testing. Yet another apparatus may be used to crystallize mixtures on a substrate such that the crystallized mixture can be screened by one or more screening devices.

This invention relates to computer-based methods, systems, and databases for visualizing chemical structure relatedness.

The database is populated with target chemicals, corresponding listings of reagent chemicals, corresponding listings of equipment and corresponding listings of procedures. The database is then searched in response to user identification of a target chemical. In response, a listing is displayed of reagent chemicals that are used to synthesize the target chemical, equipment that is used to synthesize the target chemical, and a procedure that is used to synthesize the target chemical by reacting the reagent chemicals in the equipment according to the procedure. An icon-based reaction editor and / or context-sensitive Boolean query option generators may be provided. A reaction template may be used to perform predictive chemistry. A reaction relay may be used to graphically display related chemicals and procedures using a hub and spoke arrangement.

A stochastic algorithm has been developed for predicting the drug-likeness of molecules. It is based on optimization of ranges for a set of descriptors. Lipinski's “rule-of-5”, which takes into account molecular weight, logP, and the number of hydrogen bond donor and acceptor groups for determining bioavailability, was previously unable to distinguish between drugs and non-drugs with its original set of ranges. The present invention demonstrates the predictive power of the stochastic approach to differentiate between drugs and non-drugs using only the same four descriptors of Lipinski, but modifying their ranges. However, there are better sets of 4 descriptors to differentiate between drugs and non-drugs, as many other sets of descriptors were obtained by the stochastic algorithm with more predictive power to differentiate between databases (drugs and non-drugs). A set of optimized ranges constitutes a “filter”. In addition to the “best” filter, additional filters (composed of different sets of descriptors) are used that allow a new definition of “drug-like” character by combining them into a “drug like index” or DLI. In addition to producing a DLI (drug-like index), which permits discrimination between populations of drug-like and non-drug-like molecules, the present invention may be extended to be combined with other known drug screening or optimizing methods, including but not limited to, high-throughput screening, combinatorial chemistry, scaffold prioritization and docking.

The invention discloses a method and a device for identifying isomerism graph and property corresponding to a molecular space structure, and machine equipment. The method comprises the following steps: carrying out feature description containing a topological structure on a heterogeneous graph to generate feature information; through sampling the isomerism graph and the feature information, generating a feature vector, corresponding to a key node, on a topological structure contained in the isomerism graph; performing aggregation processing on the feature vectors to generate graph representation vectors corresponding to the isomerism graphs; and according to the graph representation vector, performing classification processing on the isomerism graph to obtain a classification prediction result. Therefore, the identification of the graphical representation corresponding to the heterogeneous graph, such as the molecular spatial structure, can be realized through the neural network, the analysis and processing performance related to the isomerism graph is effectively improved, the neural network is not limited to the classification and identification of network data any more, and the application scene is greatly expanded.

A system to produce validated weighted relations between drugs and adverse drug reactions (ADRs). At least one processor to monitor social media for links between drugs and ADRs; extract a relation between a drug and an ADR using named entity recognition to provide a weighted relation between the drug and the ADR, the weight based on confidence of the link between the drug and the ADR in social media. The at least one processor to use domain knowledge of ontologies of drug names and / or ADRs to refine the weighted social media relation; quantify the weighted social media relation by using drugs and ADR links extracted from research publications and / or from clinical trial reports and provide a research weight for the relation; and / or quantify the weighted social media relation by using internet search engine and searching for the drug and the ADR, numbers of hits quantify internet weight for the relation.

The database is populated with target chemicals, corresponding listings of reagent chemicals, corresponding listings of equipment and corresponding listings of procedures. The database is then searched in response to user identification of a target chemical. In response, a listing is displayed of reagent chemicals that are used to synthesize the target chemical, equipment that is used to synthesize the target chemical, and a procedure that is used to synthesize the target chemical by reacting the reagent chemicals in the equipment according to the procedure. An icon-based reaction editor and / or context-sensitive Boolean query option generators may be provided. A reaction template may be used to perform predictive chemistry. A reaction relay may be used to graphically display related chemicals and procedures using a hub and spoke arrangement.

A method of acquiring and compiling data obtained on a mass spectrometer system, comprises: (a) generating a multiplexed mass spectrum comprising a superposed plurality of product-ion mass spectra comprising a plurality of product-ion types, each product-ion mass spectrum corresponding to fragmentation of a respective precursor-ion type, each precursor-ion type and each product ion type having a respective mass-to-charge (m / z) ratio; (b) decomposing the multiplexed product-ion mass spectrum so as to recognize relative abundances of previously-observed product-ion mass spectra within the multiplexed product-ion mass spectrum, the decomposing employing a mass-spectral library having a plurality of entries corresponding to respective product ion mass spectra previously-observed on said mass spectrometer system; (c) recognizing an additional contribution to the multiplexed mass spectrum that is neither attributable to random variation nor to any previously-observed product-ion spectrum; and (d) storing at least one new entry in the mass-spectral library relating to the recognized additional contribution.

Systems and methods are described that provide regulatory data associated with chemical products. Methods and systems are provided for identifying constituents of the chemical products and for obtaining regulatory data and other information associated with the chemical products. Regulatory data and other chemical data can be obtained from various sources, including government agencies and other regulatory authorities in plural jurisdictions, states and countries. Included in the regulatory data is information that governs handling, shipping, selling, storing, use and disposal of the chemical products. Systems and methods are described that provide improved and automate access to relevant regulatory data.

A hydroprocessing catalyst has been developed. The catalyst is a crystalline transition metal tungstate material or metal sulfides derived therefrom, or both. The hydroprocessing using the crystalline transition metal tungstate material may include hydrodenitrification, hydrodesulfurization, hydrodemetallation, hydrodesilication, hydrodearomatization, hydroisomerization, hydrotreating, hydrofining, and hydrocracking.

A structure-generating method for generating a structure candidate of a new material including: by a structure-generating processor: performing machine learning on a machine learning model, wherein the machine learning model is configured to provide a result based on a descriptor of a material, a physical property of the material, and a structure of the material; and generating a structure candidate of the new material based on the result of the machine learning, wherein the new material has a target physical property, and wherein the descriptor of the material, the physical property of the material, and the structure of the material are stored in a database.

A method and a system determine that product information acquired from an electronic catalog includes a product identifier and chemical structure information that is associated with the product identifier. A substance identifier and a quality identifier for a chemical product are derived from product information for a chemical product, and a product identifier for the chemical product is derived from the substance identifier and the quality identifier.

To provide a molecular information providing system that allows the molecular information to be shared by providing high precision information without depending on the format of atomic arrangement notation from a terminal unit.The molecular information providing system of the invention has the terminal units to including molecular structure input / output means, and a molecular information providing apparatus connected via a network to the terminal units and including a database storing a molecular structure, an intermediate representation generated from the molecular structure, and a characteristic decided depending on the molecular structure. The molecular information providing apparatus comprises a coordinate system transforming part for calculating the principal axes of inertia from an atomic arrangement notation specifying the molecular structure, and registering in the database an intermediate representation that is a coordinate transformation of the atomic coordinates into a coordinate system in the directions of the principal axes of inertia, and a retrieval executing part for retrieving the molecular structure stored in the database, employing the intermediate representation.

A remote microarray analysis system, method and apparatus for use in the remote analysis of a chemical compound microarray supported on a substrate is disclosed. Pixel image data is received from a remote location including image data that depicts (a) a calibration scale associated with the substrate and (b) the microarray. A transformation action of said pixel data corresponding to the calibration scale is determined and the received image data corresponding to at least the microarray is adjusted by applying the transformation action. The adjusted image of the microarray is compared with a database of stored microarray pixel data to extract information from said image.

The present invention relates to methods and apparatus to monitor and potentially prevent occurrences of lung cancer in patients. The invention includes apparatus and methods to determine a patient's pre-disposition or propensity to acquire lung cancer. Also included are apparatus and methods to monitor for patient biomarkers and for environmental agents, to warn and to take action to reduce exposure to environmental agents and to increase patient screening for the occurrence of lung cancer.