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Engineering Genetic Circuits: Modeling and Analysis · LearnSpace
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Engineering Genetic Circuits: Modeling and Analysis

Курс от University of Colorado Boulder
Средний≈ 25 чАнглийский
О курсеНавыкиПрограммаПреподаватели

О курсе

This course gives an introduction to how to create genetic circuit models. These models leverage chemical reactions represented using the Systems Biology Markup Language (SBML). The second module introduces methods to simulate these models using ordinary differential equation (ODE) methods. The third module teach stochastic simulation methods. The fourth module introduces several variations of the stochastic simulation algorithm. Finally, the fifth module introduces genetic technology method that leverage computational analysis for selecting parts and verifying their performance.   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

Simulation and Simulation SoftwareMathematical ModelingSimulationsDifferential EquationsBiological EngineeringNumerical AnalysisBiochemistryBiotechnologyProcess ModelingAlgorithmsEngineering AnalysisMathematical Software

Программа курса

5 модулей · 138 учебных материалов

01Genetic Circuit Models35 материалов

Introduction

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

Учитесь у экспертов

Chris Myers

Professor

Lukas Buecherl

PhD at the University of Colorado, Boulder

Engineering Genetic Circuits: Modeling and Analysis
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Обучение на Coursera

≈ 25 ч

5 модулей

Язык: Английский

Субтитры: Узбекский, Казахский

Часть программы вашего университета
Laws of ThermodynamicsВидео
Law of Mass ActionВидео
Engineering Genetic Circuits - Chapter 1 (Section 1.1)Чтение
Chemical Reaction Model BasicsЗадание

Genetic Models

Genetic Circuit ModelsВидеоSystem Biology Markup LanguageВидеоEngineering Genetic Circuits - Chapter 1 (Section 1.7.4)ЧтениеSBML Level 3: An Extensible Format for the Exchange and Reuse of Biological ModelsЧтениеGenetic Circuit Models Using SMBLЗадание

Intelligent Biological Simulator (iBioSim)

OverviewВидеоProject Management ВидеоCreating a ModelВидеоSpeciesВидеоPromotersВидеоCompartments ВидеоModulesВидеоEventsВидеоEvent ExamplesВидеоUnit Definitions ВидеоModel EditorВидеоConstraints, Parameters, and VariablesВидеоReactionsВидеоSBML Mathematical FormulasВидеоiBioSim FunctionsВидеоRulesВидеоConstraints ВидеоModel Editor PreferencesВидеоiBioSim 3: A Tool for Model-Based Genetic Circuit DesignЧтениеiBioSim TutorialЧтениеiBioSim Demo VideoЧтениеGenetic Toggle Switch ModelВзаимная проверка
02Genetic Circuit Analysis (ODEs)20 материалов

Classical Chemical Kinetic Models

OverviewВидеоClassic Chemical Kinetic ModelВидеоODE Model ExampleВидеоEngineering Genetic Circuits Chapter 3 (Section 3.1)ЧтениеChemical Kinetic ModelsЗадание

ODE Simulation Methods

Differential Equation SimulationВидеоEuler's MethodВидеоRunge-Kutta MethodВидеоAdaptive Stepsize ControlВидеоEngineering Genetic Circuits Chapter 3 (Section 3.2)ЧтениеODE Simulation Using iBioSimВзаимная проверкаODE Simulation MethodsЗадание

Qualitative ODE Analysis

Qualitative ODE AnalysisВидеоSaddle-Node ExampleВидеоTranscritical Bifurcation ExampleВидеоPitchfork Bifurcation ExampleВидеоTwo-Dimentional ODE ModelВидеоSpatial MethodsВидеоEngineering Genetic Circuits Chapter 3 (Sections 3.3 and 3.4)
03Stochastic Analysis29 материалов

Stochastic Chemical Kinetics

IntroductionВидеоStochastic Chemical Kinetic ModelВидеоBiomolecular Reaction ChannelВидеоMonomolecular ReactionsВидеоTrimolecular ReactionsВидеоJump Markov ProcessesВидеоEngineering Genetic Circuits Chapter 4 (Sections 4.1 and 4.2)ЧтениеStochastic Chemical KineticsЗадание

Stochastic Simulation Algorithms

IntroductionВидеоDerivation of Gillespie's Stochastic Simulation AlgorithmВидеоImplementation of Gillespie's SSAВидеоGillespie's SSA ExamplesВидеоEngineering Genetic Circuits Chapter 4 (Section 4.3)ЧтениеStochastic Simulation Using iBioSimВзаимная проверка

Alternative Stochastic Simulation Algorithms

Gillespie's First Reaction MethodВидеоGibson/Bruck's ImprovementsВидеоComposition and RejectionВидеоTau LeapingВидеоExplicit Tau-Leaping Simulation AlgorithmВидеоEngineering Genetic Circuits Chapter 4 (Sections 4.4 and 4.5)Чтение

Additional Stochastic Simulation Topics

The Chemical Langevin EquationВидеоThe Reaction Rate EquationВидеоStochastic Petri NetsВидеоPhage Lambda ModelВидеоSpatial GillespieВидеоEngineering Genetic Circuits Chapter 4 (Sections 4.6 to 4.9)Чтение
04SSA Variations25 материалов

Hierarchical SSA (hSSA)

Population-Based ModelsВидеоThe Hierarchical Stochastic Simulation AlgorithmВидеоHierarchical Simulation ExampleВидеоRuntime Comparison between hSSA and SSAВидеоArray Package for Tracking Cellular PopulationsВидеоPopulation of Repressilator Circuits Using ArraysВидеоPopulation of Genetic Toggle Circuits Using ArraysВидеоHierarchical Stochastic Simulation Algorithm for SBML Models of Genetic CircuitsЧтениеEfficient Analysis of Systems Biology Markup Language Models of Cellular Populations using ArraysЧтениеHierarchical SSA (hSSA)Задание

Weighted SSA (wSSA)

Motivation and BackgroundВидеоImportant SamplingВидеоUnderlying Mathematics of the wSSAВидеоThe weighted stochastic simulation algorithm ВидеоAn Efficient and Exact Stochastic Simulation Method to Analyze Rare Events in Biochemical SystemsЧтениеWeighted SSA (wSSA)Задание

Incremental SSA (iSSA)

Introduction and MotivationВидеоIncremental Stochastic Simulation AlgorithmВидеоMarginal Probability Density EvolutionВидеоMean PathВидеоMedian PathВидеоAdaptive Time StepВидеоMultiple Paths
05Genetic Circuit Technology Mapping29 материалов

Introduction to Genetic Technology Mapping

IntroductionВидеоCrosstalkВидеоSignal MismatchВидеоRoadblockingВидеоGenetic Context EffectsВидеоAutomation and Computer Aided DesignВидеоLibrary CreationВидеоExisting Technology MappingВидеоTechnology Mapping of Genetic Circuits: From Optimal to Fast SolutionsЧтениеIntroduction to Genetic Technology MappingЗадание

Cello's Technology Mapping

Overview of CelloВидеоGenetic Gate AssignmentВидеоImpact of Gate Isolation and Gate and Gate LibraryВидеоCello Circuit ExamplesВидеоAnalysis of Circuit FailuresВидеоGenetic Circuit Design AutomationЧтение

iBioSim's Technology Mapping

Overview of iBioSim's Technology MappingВидеоDAG RepresentationВидеоPartitioning and DecompositionВидеоMatching and CoveringВидеоTechnology Mapping's CostВидеоDirected Acyclic Graph-Based Technology Mapping of Genetic Circuit ModelsЧтение

Verification of Genetic Circuit Designs

Model GenerationВидеоRule 30 ExampleВидеоSequential Genetic CircuitsВидеоDesign of Asynchronous Genetic CircuitsЧтениеVerification of Genetic Circuit DesignsЗадание
Чтение
Qualitative ODE AnalysisЗадание
Stochastic Simulation MethodsЗадание
Alternative Stochastic Simulation AlgorithmsЗадание
Additional Stochastic Simulation TopicsЗадание
Видео
An Incremental Stochastic Simulation Algorithm for Genetic CircuitsЧтение
Incremental SSA (iSSA)Задание
Cello's Technology MappingЗадание
iBioSim's Technology MappingЗадание