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公开(公告)号：US11024403B2
公开(公告)日：2021-06-01
申请号：US15876962
申请日：2018-01-22
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
IPC: G01N33/48 , G01N33/50 , G16B5/00 , G16C20/10 , G06F16/332 , G06F16/901
Abstract: 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.
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公开(公告)号：US10657179B2
公开(公告)日：2020-05-19
申请号：US15694506
申请日：2017-09-01
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
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.
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3.发明授权公开(公告)号：US11380420B1
公开(公告)日：2022-07-05
申请号：US15973415
申请日：2018-05-07
Applicant: X Development LLC
Inventor： Frank Russo , Jason Thompson , Nicholas Casavant , Yu Tanouchi
IPC: G06F3/0484 , G16B5/00 , G06F8/41 , G06N5/02 , G16B45/00 , G06F3/04847
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.
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公开(公告)号：US10453551B2
公开(公告)日：2019-10-22
申请号：US15177047
申请日：2016-06-08
Applicant: X Development LLC
Inventor： Chirath Thouppaurachchi , Ian Peikon , Jason Thompson , Tammo Spalink
Abstract: The behavior and/or internal activities of a microorganism can be simulated using a model of the microorganism. Such simulations can be used to determine the efficacy of treatments, disinfectants, antibiotics, chemotherapies, or other methods of interacting with the microorganism, or to provide some other information about the microorganism. Systems and methods are provided herein for fitting, refining, or otherwise improving such models in an automated fashion. Such systems and methods include performing whole-cell experiments to determine a correspondence between the predictions of such models and the actual behavior of samples of the microorganism. Such systems and methods also include, based on such determined correspondences, directly assessing determined discrete sets of properties of the microorganism and/or of constituents of the microorganism and updating parameters of the model corresponding to the properties of the discrete set such that the overall accuracy of the model is improved.
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公开(公告)号：US20200242168A1
公开(公告)日：2020-07-30
申请号：US16844615
申请日：2020-04-09
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
IPC: G06F16/901 , G16B5/00 , G16B50/00 , G16C20/90 , G16B45/00
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.
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Patent Agency Ranking
公开(公告)号：US20190073450A1
公开(公告)日：2019-03-07
申请号：US15694500
申请日：2017-09-01
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
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.
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公开(公告)号：US09927441B1
公开(公告)日：2018-03-27
申请号：US15223062
申请日：2016-07-29
Applicant: X Development LLC
Inventor： Jason Thompson , Jonathan Ross
IPC: C12N15/115 , G01N33/68
CPC classification number: G01N33/6803
Abstract: A method for determining concentrations of target proteins in a protein sample can involve: (i) contacting the protein sample with an aptamer library to form a mixture; (ii) allowing the aptamers in the aptamer library to bind to the target proteins in the protein sample; (iii) removing the aptamers that have not been bound to a target protein in the mixture; and (iv) measuring the concentration each aptamer bound to proteins in the mixture. The concentration of a particular protein in the protein sample can be derived from the measurements of the concentrations of the aptamer or aptamers bound to that particular protein in the mixture.
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公开(公告)号：US20170357748A1
公开(公告)日：2017-12-14
申请号：US15177047
申请日：2016-06-08
Applicant: X Development LLC
Inventor： Chirath Thouppaurachchi , Ian Peikon , Jason Thompson , Tammo Spalink
CPC classification number: G16B5/00 , C12M41/14 , C12M41/36 , C12M41/46 , C12M41/48 , C12Q1/02 , C12Q1/025 , C12Q3/00 , G01N33/5005 , G01N33/5097 , G01N35/00871 , G01N35/0099 , G01N2035/0097
Abstract: The behavior and/or internal activities of a microorganism can be simulated using a model of the microorganism. Such simulations can be used to determine the efficacy of treatments, disinfectants, antibiotics, chemotherapies, or other methods of interacting with the microorganism, or to provide some other information about the microorganism. Systems and methods are provided herein for fitting, refining, or otherwise improving such models in an automated fashion. Such systems and methods include performing whole-cell experiments to determine a correspondence between the predictions of such models and the actual behavior of samples of the microorganism. Such systems and methods also include, based on such determined correspondences, directly assessing determined discrete sets of properties of the microorganism and/or of constituents of the microorganism and updating parameters of the model corresponding to the properties of the discrete set such that the overall accuracy of the model is improved.
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公开(公告)号：US20190228130A1
公开(公告)日：2019-07-25
申请号：US15876962
申请日：2018-01-22
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
Abstract: 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.
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公开(公告)号：US10192010B1
公开(公告)日：2019-01-29
申请号：US15164125
申请日：2016-05-25
Applicant: X Development LLC
Inventor： Jonathan Ross , Jason Thompson
Abstract: An example method may include identifying (i) a first group of reactions that corresponds to a first set of precursors and a first set of reaction products and (ii) a second group of reactions that corresponds to a second set of precursors and a second set of reaction products. No precursor in the first set of precursors is also in the second set of precursors, no reaction product in the first set of reaction products is also a precursor in the second set of precursors, and no reaction product in the second set of reaction products is also a precursor in the first set of precursors. The method may also include executing a first processing thread to iteratively calculate respective quantities of the precursors in the first set of precursors and executing a second processing thread to iteratively calculate respective quantities of the precursors in the second set of precursors.
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