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Engineering Genetic Circuits: Abstraction Methods · LearnSpace
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Engineering Genetic Circuits: Abstraction Methods

Курс от University of Colorado Boulder
Средний≈ 18 чАнглийский
О курсеНавыкиПрограммаПреподаватели

О курсе

This course introduces how to perform abstraction of genetic circuit models. The first module teaches reaction-based abstraction methods that apply steady-state approximations to reduce the complexity and improve the analysis time of these models. The second module describes piecewise approximations to simplify non-linear reaction-based models of genetic circuits. The third module presents Markov chain models and methods for analyzing them. The fourth module provides methods to abstract models even further using state-based abstraction methods. Finally, the fifth module demonstrates methods, such as infinite-state stochastic model checking, to determine the likelihood that a genetic circuit hazard will cause circuit failure. This course can also be taken for academic credit as ECEA 5935, part of CU Boulder’s Master of Science in Electrical Engineering.

Навыки, которые вы освоите

Markov ModelMathematical ModelingSimulationsElectrical and Computer EngineeringVerification And ValidationHazard AnalysisFailure AnalysisBiological EngineeringProcess ModelingEngineering Analysis

Программа курса

5 модулей · 88 учебных материалов

01Reaction-based Abstraction22 материалов

Basic Abstractions

Course Updates and Accessibility SupportЧтениеNon-Credit Students: Welcome and Where to Find HelpЧтениеOptional Reading Materials ЧтениеOverviewВидео

Учитесь у экспертов

Chris Myers

Professor

Lukas Buecherl

PhD at the University of Colorado, Boulder

Engineering Genetic Circuits: Abstraction Methods
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≈ 18 ч

5 модулей

Язык: Английский

Субтитры: Узбекский, Казахский

Часть программы вашего университета
Irrelevant Node EliminationВидео
Production-Passage-Time ApproximationВидео
Michaelis-Menten EquationВидео
Enzymatic Approximation TransformationВидео
Engineering Genetic Circuits Chapter 5 (Section 5.1 and 5.2)Чтение
Enzymatic ApproximationЗадание

Operator Site Reduction

Models for Repression and ActivationВидеоOperator Site Reduction DerivationВидеоOperator Site Reduction TransformationВидеоStatistical Thermodynamical Model OverviewВидеоStatistical Thermodynamical Model ExampleВидеоEngineering Genetic Circuits Chapter 5 (Section 5.3 and 5.4)ЧтениеOperator Site ReductionЗадание

Additional Abstractions and Examples

Dimerization ReductionВидеоApplication to the Phage Lambda ModelВидеоStoichiometry AmplificationВидеоEngineering Genetic Circuits Chapter 5 (Section 5.5 to 5.8)ЧтениеReaction-based Abstraction of a Genetic Toggle Switch Взаимная проверка
02Piecewise Models18 материалов

Logical Encoding

Logical Encoding OverviewВидеоHill FunctionsВидеоCritical Thresholds, Intervals, and Regulatory DomainsВидеоEngineering Genetic Circuits Chapter 6 (Section 6.1)ЧтениеLogical EncodingЗадание

Piecewise Linear Differential Equations

Piecewise Linear Differential Equations OverviewВидеоPiecewise Linear Differential Equations SolutionsВидеоBlack, White, and Transparent BoundariesВидеоLabeled Hybrid Petri NetsВидеоEngineering Genetic Circuits Chapter 6 (Section 6.2)ЧтениеPower Linear Differential EquationsЗадание

Stochastic Finite State Machines

Stochastic Finite State Machines OverviewВидеоReaction SplitizationВидеоGuarded CommandsВидеоTransition Rate GenerationВидеоStochastic FSM SimulationВидеоEngineering Genetic Circuits Chapter 6 (Section 6.3)Чтение
03Markov Chain Analysis18 материалов

Markov Chains

Markov Chains IntroductionВидеоDiscrete-Time Markov ChainsВидеоSteady-State DistributionsВидеоComputing Steady-State Distributions: Direct MethodsВидеоComputing Steady-State Distributions: Iterative MethodsВидеоEngineering Genetic Circuits Chapter 6 (Section 6.4)Чтение Introduction to the Numerical Solution of Markov Chains Chapter 1-3 (Optional)ЧтениеDTMC QuizЗадание

Steady-State Distribution Analysis

Continuous-Time Markov ChainsВидеоEmbedded Markov ChainВидеоPhage Lambda ExampleВидеоSteady-State Distribution AnalysisЗадание

Transient Analysis

Transient SolutionsВидеоUniformizationВидеоTruncation ErrorВидеоTransient Analysis Algorithm and ExampleВидеоIntroduction to the Numerical Solution of Markov Chains Chapter 8 (Optional)ЧтениеTransient Analysis QuizЗадание
04State-based Abstraction14 материалов

Abstraction for Genetic Circuits

Overview of Abstraction WorkflowВидеоGenetic Toggle Switch ExampleВидеоAutomated Abstraction Methodology for Genetic Regulatory NetworksЧтениеAbstraction MethodЗадание

Stochastic Model Checking

State-Based AbstractionВидеоTransition Rate CalculationsВидеоPropertiesВидеоMarkov Chain AnalysisВидеоExamplesВидеоStochastic Model Checking of Genetic CircuitsЧтениеStochastic Model CheckingЗадание

Qualitative Logical Models

Qualitative Logical Models OverviewВидеоEngineering Genetic Circuits Chapter 6 (Sections 6.5 and 6.6)ЧтениеQuiz Qualitative Logic ModelsЗадание
05Infinite-state Stochastic Model Checking Case Study16 материалов

Genetic Circuit Hazards

Genetic Circuit FailuresВидеоAutomatic Model GeneratorВидеоFunction HazardsВидеоAddressing Genetic Circuits HazardsВидеоGenetic Circuit Dynamics: Hazard and Glitch AnalysisЧтениеGenetic Circuits HazardsЗадание

Stochastic Simulation

Continuous Stochastic LogicВидеоComputational Prediction of Glitch LikelihoodВидеоModel PredictabilityВидеоLaboratory EvaluationВидеоStochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINAЧтениеHazard Simulation Using iBioSimВзаимная проверка

STAMINA

Infinite-State Stochastic Model Checking ВидеоSTAMINA ResultsВидеоSTAMINA 2.0: Improving Scalability of Infinite-State Stochastic Model CheckingЧтениеHazard Verification Using STAMINAВзаимная проверка
Stochastic FSMЗадание