Abstract: 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 (410), and used to determine (420) whether the public place is privacy-qualified. If the public place is privacy-qualified, real-time busyness information is computed (440) for the public place based on the real-time location information. Further, it is determined (450) 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 (470) for display or to another application.

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

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

Abstract: 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 (410), and used to determine (420) whether the public place is privacy-qualified. If the public place is privacy-qualified, real-time busyness information is computed (440) for the public place based on the real-time location information. Further, it is determined (450) 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 (470) for display or to another application.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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 (410), and used to determine (420) whether the public place is privacy-qualified. If the public place is privacy-qualified, real-time busyness information is computed (440) for the public place based on the real-time location information. Further, it is determined (450) 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 (470) for display or to another application.

Abstract: 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.

Abstract: 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.

Abstract: 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 (410), and used to determine (420) whether the public place is privacy-qualified. If the public place is privacy-qualified, real-time busyness information is computed (440) for the public place based on the real-time location information. Further, it is determined (450) 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 (470) for display or to another application.

Abstract: 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.

Abstract: Embodiments include simulating the behavior of enzymatic reactions in silico in place of or in addition to running in vitro experiments. The in silico simulations may involve varying the initial concentrations of the reactant while setting the rate of change of concentration each form of an enzyme to be at steady state, which may aid in realistically representing the kinetics of the reaction. Some embodiments may allow for modeling enzymatic reactions so as to obtain mathematical relationships between the reaction rate and initial concentration of a reactant. Some embodiments may determine rate constants for microscopic steps within the enzymatic reactions. In addition, some embodiments may include optimizing for a plurality of initial reactant concentrations simultaneously rather than optimizing for one initial reactant concentration at a time, in order to generate a velocity versus concentration curve and to determine the catalytic rate constant kcat and Michaelis constant Km.

Abstract: Embodiments include simulating the behavior of enzymatic reactions involving multiple substrates binding with an enzyme. Some embodiments may allow for modeling the reactions without requiring known values for kinetic rate constants for microsteps of the reaction. Embodiments may include computer-implemented methods. Methods may include initializing an initial free energy profile for a reaction. The initial free energy profile may include a plurality of initial waypoints. The methods may include generating a plurality of rate equations, each rate equation representing a component step of the plurality of component steps. Methods may include simulating an in silico behavior of the reaction. Simulating may include generating concentrations of the substrates using the plurality of rate equations.

Abstract: The present disclosure relates to modeling biological systems and biochemical processes. In order to accurately model these systems and processes, the behavior at the boundary of models of the system and processes is important. Some embodiments include representing rates of change of concentrations of molecules at the boundaries of models as dynamic and responsive rather than static and invariant. The rates of change of the concentrations of molecules may be modeled as proportional controllers. In some embodiments, the proportional controllers may be saturable. Using responsive boundaries reduces model complexity, thereby increasing computational speed and efficiency. Additionally, the responsive boundaries may more accurately and realistically depict the behavior of components within a system compared to other boundary modeling techniques. Alternatively or additionally, some embodiments may include using a result of a model with responsive boundaries to engineer or alter a biological system.

Abstract: 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.

Abstract: The present disclosure relates to general and scalable techniques for modeling in silico the kinetics of systems of connected biochemical reactions. Particularly, aspects of the present disclosure are directed to deconstructing a reaction into a plurality of component steps, translating each component step into a set of rate equations to obtain a standard mathematical construct or model representing each component step, numerically integrating across the standard mathematical constructs or models using a system of ordinary differential equations to determine a contribution of each component step to a rate of change of molecules within reaction, and deriving a in silico behavior of a system utilizing the reaction based on the contribution of each component step to the rate of change of the molecules within the reaction. The standard mathematical constructs or models may be parameterized based on an energy profile for the reaction inferred from machine-learning approaches.

Abstract: The present disclosure relates to general and scalable techniques for modeling in silico the kinetics of systems of connected biochemical reactions. Particularly, aspects of the present disclosure are directed to deconstructing a reaction into a plurality of component steps, translating each component step into a set of rate equations to obtain a standard mathematical construct or model representing each component step, numerically integrating across the standard mathematical constructs or models using a system of ordinary differential equations to determine a contribution of each component step to a rate of change of molecules within reaction, and deriving a in silico behavior of a system utilizing the reaction based on the contribution of each component step to the rate of change of the molecules within the reaction. The standard mathematical constructs or models may be parameterized based on an energy profile for the reaction inferred from machine-learning approaches.

Abstract: 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.

Abstract: 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.