公开(公告)号：US11183273B2

公开(公告)日：2021-11-23

申请号：US15694500

申请日：2017-09-01

Applicant: X Development LLC

Inventor： Jason Thompson ,  Frank Russo

IPC: G16C10/00 ,  G16C20/10 ,  G16B5/00 ,  G16B50/00 ,  G06F17/13 ,  G06F17/18

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.

公开(公告)号：US20190073433A1

公开(公告)日：2019-03-07

申请号：US15694506

申请日：2017-09-01

Applicant: X Development LLC

Inventor： Jason Thompson ,  Frank Russo

IPC: G06F17/30 ,  G06F19/00 ,  G06F19/28 ,  G06F19/26

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.