公开(公告)号：US20220036964A1

公开(公告)日：2022-02-03

申请号：US16942222

申请日：2020-07-29

Applicant: X Development LLC

Inventor： Frank Russo ,  Andreas Hoenselaar

IPC: G16B5/20 ,  G06F30/20

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.

公开(公告)号：US20190236243A1

公开(公告)日：2019-08-01

申请号：US15885463

申请日：2018-01-31

Applicant: X Development LLC

Inventor： Frank Russo

IPC: G06F19/12 ,  G06F17/16

CPC classification number: G16B5/00 ,  G06F17/16 ,  G06F2217/16

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.

公开(公告)号：US20230082983A1

公开(公告)日：2023-03-16

申请号：US18048718

申请日：2022-10-21

Applicant: X Development LLC

Inventor： Frank Russo

IPC: G16B5/00 ,  G06F17/16

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.

公开(公告)号：US11508459B2

公开(公告)日：2022-11-22

申请号：US15885463

申请日：2018-01-31

Applicant: X Development LLC

Inventor： Frank Russo

IPC: G16B5/00 ,  G06F17/16 ,  G06F111/10

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.

公开(公告)号：US11456053B1

公开(公告)日：2022-09-27

申请号：US15648901

申请日：2017-07-13

Applicant: X Development LLC

Inventor： Frank Russo ,  Jason Donald Thompson

IPC: G16B5/00

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.

公开(公告)号：US20220139494A1

公开(公告)日：2022-05-05

申请号：US16949495

申请日：2020-10-30

Applicant: X Development LLC

Inventor： Frank Russo

IPC: G16B5/00

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.

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.

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

IPC: G06F19/00 ,  G06F17/18 ,  G06F17/13

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.