US 11,456,053 B1Granted

Biological modeling framework

AssigneeX Development LLC

InventorsFrank Russo, Jason Donald Thompson

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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.

Claims20

Dependent claims

A method performed by one or more computers, the method comprising:

maintaining biological data related to a plurality of biological systems in a data repository;
receiving, via one or more user interfaces, a first selection of a biological system of the plurality of biological systems for generating a model that simulates a behavior of the biological system, wherein the model is a computational model;
retrieving a subset of data of the biological data from multiple entries in the data repository, wherein the biological data is associated with the first selection of the biological system, and wherein the data repository specifies reactions of multiple biological objects represented in the multiple entries, and wherein at least one of the multiple biological objects corresponds to at least part of the biological system;
receiving, via the one or more user interfaces, a second selection of a modeling technique of a plurality of modeling techniques for generating the model;
determining that the data repository lacks at least some other biological data for simulating the behavior of the biological system using the model, wherein the at least some other biological data comprises a listing of the reactions that are active for a set of conditions, wherein the set of conditions comprises temperature or nutrients in media;
in response to the determination, performing in silico experiments over a range of conditions in the set of conditions;
predicting the at least some other biological data using the performed in silico experiments, wherein the at least some other biological data predicted comprises uptake of components or growth rates;
compiling the subset of data with the predicted at least some other biological data into configuration data that is specific to the modeling technique;
generating the model using the modeling technique and the configuration data;
simulating the behavior of the biological system by executing the model;
and
outputting one or more results from executing the model in the data repository.

9 more elements

A non-transitory computer-readable storage medium coupled to one or more processors and having instructions stored thereon which, when executed by the one or more processors, cause the one or more processors to perform operations comprising:

maintaining biological data related to a plurality of biological systems in a first format in a data repository;
receiving, via one or more user interfaces, a first selection of a biological system of the plurality of biological systems for generating a model that simulates a behavior of the biological system, wherein the model is a computational model;
retrieving a subset of data of the biological data from multiple entries in the data repository, wherein the biological data is associated with the first selection of the biological system, and wherein the data repository specifies reactions of multiple biological objects represented in the multiple entries, and wherein at least one of the multiple biological objects corresponds to at least part of the biological system;
receiving, via the one or more user interfaces, a second selection of a modeling technique of a plurality of modeling techniques for generating the model;
determining that the data repository lacks at least some other biological data for simulating the behavior of the biological system using the model, wherein the at least some other biological data comprises a listing of the reactions that are active for a set of conditions, wherein the set of conditions comprises temperature or nutrients in media;
in response to the determination, performing in silico experiments over a range of conditions in the set of conditions;
predicting the at least some other biological data using the performed in silico experiments, wherein the at least some other biological data predicted comprises uptake of components or growth rates;
compiling the subset of data with the predicted at least some other biological data into configuration data that is specific to the modeling technique;
generating the model using the modeling technique and the configuration data;
simulating the behavior of the biological system by executing the model;
and
outputting one or more results from executing the model in the data repository.

9 more elements

A system, comprising:

one or more processors;
and
a computer-readable storage device coupled to the one or more processors and having instructions stored thereon which, when executed by the one or more processors, cause the one or more processors to perform operations comprising:
maintaining biological data related to a plurality of biological systems in a data repository;
receiving, via one or more user interfaces, a first selection of a biological system of the plurality of biological systems for generating a model that simulates a behavior of the biological system, wherein the model is a computational model,;
retrieving a subset of data of the biological data from multiple entries in the data repository, wherein the biological data is associated with the first selection of the biological system, and wherein the data repository specifies reactions of multiple biological objects represented in the multiple entries, and wherein at least one of the multiple biological objects corresponds to at least part of the biological system;
receiving, via the one or more user interfaces, a second selection of a modeling technique of a plurality of modeling techniques for generating the model;
determining that the data repository lacks at least some other biological data for simulating the behavior of the biological system using the model, wherein the at least some other biological data comprises a listing of the reactions that are active for a set of conditions, wherein the set of conditions comprises temperature or nutrients in media;
in response to the determination, performing in silico experiments over a range of conditions in the set of conditions;
predicting the at least some other biological data using the performed in silico experiments, wherein the at least some other biological data predicted comprises uptake of components or growth rates;
compiling the subset of data with the predicted at least some other biological data into configuration data that is specific to the modeling;
generating the model using the modeling technique and the configuration data;
simulating the behavior of the biological system by executing the model;
and
outputting one or more results from executing the model in the data repository.

12 more elements

Dependencies are inferred from the claim text.