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    BIPARTITE GRAPH STRUCTURE
    1.
    发明申请
    BIPARTITE GRAPH STRUCTURE 审中-公开

    公开(公告)号：WO2019045853A8

    公开(公告)日：2019-03-07

    申请号：PCT/US2018/039129

    申请日：2018-06-22

    Applicant: X DEVELOPMENT LLC

    Inventor： THOMPSON, Jason ,  RUSSO, Frank

    IPC: G06F19/28 ,  G06F19/12

    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.

    BIPARTITLE GRAPH STRUCTURE
    2.
    发明申请
    BIPARTITLE GRAPH STRUCTURE 审中-公开

    公开(公告)号：WO2019045853A1

    公开(公告)日：2019-03-07

    申请号：PCT/US2018/039129

    申请日：2018-06-22

    Applicant: X DEVELOPMENT LLC

    Inventor： THOMPSON, Jason ,  RUSSO, Frank

    IPC: G06F19/28 ,  G06F19/12

    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.

    DYNAMIC COORDINATING FRAMEWORK FOR MODEL CELL SIMULATIONS
    3.
    发明申请
    DYNAMIC COORDINATING FRAMEWORK FOR MODEL CELL SIMULATIONS 审中-公开

    公开(公告)号：WO2020050967A1

    公开(公告)日：2020-03-12

    申请号：PCT/US2019/046990

    申请日：2019-08-19

    Applicant: X DEVELOPMENT LLC

    Inventor： RUSSO, Frank ,  THOMPSON, Jason ,  RUGGERO, Nicholas

    IPC: G16B5/30 ,  G16B50/00

    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.

    SIMULATING LIVING CELL IN SILICO
    4.
    发明申请
    SIMULATING LIVING CELL IN SILICO 审中-公开
    在硅片上模拟活细胞

    公开(公告)号：WO2017214379A1

    公开(公告)日：2017-12-14

    申请号：PCT/US2017/036526

    申请日：2017-06-08

    Applicant: X DEVELOPMENT LLC

    Inventor： THOUPPAURACHCHI, Chirath ,  PEIKON, Ian ,  THOMPSON, Jason ,  SPALINK, Tammo

    IPC: C12M1/36 ,  C12M1/34

    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.

    Abstract translation: 可以使用微生物模型模拟微生物的行为和/或内部活性。 这种模拟可用于确定治疗，消毒剂，抗生素，化学疗法或与微生物相互作用的其他方法的效力，或提供关于微生物的一些其他信息。 本文提供了用于以自动方式拟合，精炼或以其他方式改进这些模型的系统和方法。 此类系统和方法包括进行全细胞实验以确定这些模型的预测与微生物样品的实际行为之间的对应关系。 基于这样确定的对应关系，这样的系统和方法还包括直接评估微生物和/或微生物成分的确定的离散性质集合，并且更新与离散集合的性质对应的模型的参数，使得总体准确度 的模型得到了改进。

    METHOD FOR ANALYZING AND OPTIMIZING METABOLIC NETWORKS
    5.
    发明申请
    METHOD FOR ANALYZING AND OPTIMIZING METABOLIC NETWORKS 审中-公开

    公开(公告)号：WO2019143434A1

    公开(公告)日：2019-07-25

    申请号：PCT/US2018/066036

    申请日：2018-12-17

    Applicant: X DEVELOPMENT LLC

    Inventor： THOMPSON, Jason ,  RUSSO, Frank

    IPC: G16B5/00 ,  G16C20/10

    CPC classification number: G16B5/00 ,  G06F16/3328 ,  G06F16/9024 ,  G16C20/10

    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.

    HETEROGENEOUS METHOD FOR MODELLING A BIOCHEMICAL ENVIRONMENT
    6.
    发明申请
    HETEROGENEOUS METHOD FOR MODELLING A BIOCHEMICAL ENVIRONMENT 审中-公开

    公开(公告)号：WO2019045852A1

    公开(公告)日：2019-03-07

    申请号：PCT/US2018/039127

    申请日：2018-06-22

    Applicant: X DEVELOPMENT LLC

    Inventor： THOMPSON, Jason ,  RUSSO, Frank

    IPC: G06F19/12

    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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