Ebay, Incorporated

X Development LLC

Incyte Pharmaceuticals, Inc.

Google Inc.

Incyte Genomics, Inc.

Frank D Russo

Nate L Lyman

Jason Donald Thompson

Peter A Covitz

Joe Don Heath

Stephanie F Berry

Tod M Klingler

Cathryn E Sabatini

Luuk Van Dijk

Steve Chien

James Aspinall

Finnegan Southey

Quang Duong

Alex George Koleszar

Paul Donnelly

Lee Crawford

Yvonne R Boldt

Rachel J Wright

Jennifer L Hillman

Janice K Au-Young

Jeffrey J Seilhamer

Ingrid E Akerblom

Timothy J Maslyn

Guy Schory

Stephen Kenneth Lobo

Stephen Richard Thomas

Nicholas Casavant

Christina M Altus

Nicholas Ruggero

Yu Tanouchi

Tod M Klinger

Jana Hartman

Techniques for simulating networks using dynamics-based constraints are disclosed.

Simulations networked activity using dynamics-based constraints on reusable network component

Real-time busyness information is for a public place is computed in a privacy-sensitive way, and provided for display in relation to historical busyness information. An aggregate amount of real-time location information available for a particular public place is measured (), and used to determine () whether the public place is privacy-qualified. If the public place is privacy-qualified, real-time busyness information is computed () for the public place based on the real-time location information. Further, it is determined () whether the computed real-time busyness information is accuracy-qualified, based on a comparison of the real-time busyness information to historical busyness information. If both qualifications are met, the real-time busyness information is output () for display or to another application.

Realtime busyness for places

A method for matching production of FBA metabolism to supply and demand within a larger production network is described herein. An objective function of FBA metabolism is modified to include an upstream supply generated in upstream sub-units, as well as a downstream demand generated within downstream sub-units in the production network. FBA metabolism and the upstream and downstream sub-units are iteratively solved with updated initial conditions, producing a time series solution to the production network.

Modified FBA in a production network

Methods, systems, and apparatuses, including computer programs encoded on a computer storage medium, can be implemented to perform certain actions. The actions can include maintaining biological data related to multiple biological systems in a first format in a data repository, receiving a first selection of a biological system of the multiple biological systems for constructing a model that simulates a behavior of the biological system, retrieving a subset of data of the biological data that is associated with the first selection of the biological system, receiving a second selection of a modeling technique of the multiple modeling techniques for constructing the model, compiling the subset of biological data into configuration data of a second format that is specific to the modeling technique and that is different from the first format, and generating the model using the modeling technique and the configuration data.

Biological modeling framework

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.

Bipartite graph structure

A method for allocating resources among multiple sub-models in a simulation of a biological cell is described herein. The method receives an initial state dataset including initial aggregate resources in a plurality of sub-models, which make up a whole cell model. The method calculates, at a first time step, an outcome of each of the sub-models, which includes a local production, a local consumption and local net value of at least one resource shared between at least two sub-models. The method calculates a subsequent state dataset based on the outcome of each of the sub-models. The subsequent state dataset includes subsequent aggregate resources, the local production, the local consumption and local net value. The method determines, at a second time step, a second outcome of each of the plurality of sub-models based on the subsequent aggregate resources and the local production, local consumption and local net value.

Dynamic coordinating framework for model cell simulations

A system is described for constructing a biological simulation using inputs from a knowledge base data structure and one or more templates. The knowledge base data structure comprises a set of entries representing distinct molecules and chemical reactions specific within the cell. Each template defines a sub-model program specification and a set of sub-model parameters to further characterize the sub-model specification. A graphical user interface is presented on a display for a user to view and select a templates and to assign information from the knowledge base to the selected template. From the graphical user interface, the user selects multiple templates to be included in the simulation and information from the knowledge base generally describing the cell. Based on the information selected from the graphical user interface, a compiler generates a simulation configuration data file comprising computer code capable of being executed by a simulation engine.

Data structure, compilation service, and graphical user interface for rapid simulation generation

Systems and methods for passive dynamic geofencing on a mobile device are discussed. For example, a method for passive dynamic geofencing can include operations such as monitoring a first parent geofence and a first plurality of child geofences; detecting crossing a boundary of the first parent geofence into a second parent geofence; loading the second parent geofence and a second plurality of child geofences encompassed by the second parent geofence; and monitoring the second parent geofence and the second plurality of child geofences.

Passive dynamic geofencing for mobile devices

A method for simulating a biochemical environment utilizes a heterogeneous process model, which evaluates both a flux balance analysis and one or more detailed models each on a different but overlapping sets of molecules in the biochemical environment. The heterogeneous process model evaluates the flux balance analysis based on a stoichiometric matrix, a flux vector including initial internal exchange flux values, and an objective function. The heterogeneous process model evaluates the one or more detailed models based on an initial set of molecule concentrations and a plurality of detailed model parameters. The results are then used to update the exchange fluxes and molecules concentrations. The process is repeated thereby integrating the results of the flux balance analysis with the one or more detailed models.

Heterogeneous method for modelling a biochemical environment

Various implementations monitor a parent geofence that geographically encompasses a plurality of child geofences, each respective child geofence of the child geofences associated with a respective physical location within the parent geofence. One or more implementations receive location data that indicates a current location of a mobile device. In turn, the current location can be used to determine that the mobile device has entered a particular child geofence of the plurality of child geofences. In response to determining that the mobile device has entered the particular child geofence, one or more implementations select an application configuration for a mobile application on the mobile device, where the application configuration corresponds to the particular child geofence. One or more implementations transmit the application configuration to the mobile device effective to alter a functionality of the mobile application at the mobile device based on the current location.

Configuring mobile device applications based on location

A method for analyzing a bipartite graph data structure to condense reaction pathways of a metabolic network is described herein. A cell's metabolic network is structured as a bipartite graph, with molecule nodes representing the molecules within metabolism and edges connecting molecule nodes representing chemical reactions or processes. Molecule nodes within the bipartite graph are categorized according to the number of edges leading into and out of each node. If the structure of the bipartite graph indicates that the molecule node does not contribute to flux value solutions of a mathematical model of the metabolic network, then the node and its connected reaction pathway is blocked or removed from the bipartite graph. Thus the complexity of the bipartite graph may be reduced, and crucial nodes and pathways identified.

Method for analyzing and optimizing metabolic networks

Growing community of inventors

Redwood City, CA, United States of America

Frank D Russo