CS620 : Modelling and Simulation

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Course Info

Course Category

Bioinformatics

Course Level

Undergraduate

Credit Hours

3

Pre-requisites

N/A

Instructor

Prof. Dr. Muaz Naizi
PhD
COMSATS University Islamabad

Course Contents

Introduction, when simulation is the appropriate tool, when it is not, Advantages and Disadvantages, Disadvantages of Simulation, Areas of application, Military applications, System and Environment, System Concepts, Components of a system, Discrete and Continuous, Model of a system, Types of Models, Discrete Event Simulation, Steps in a sim. Study: Planning, Steps in a sim. Study: Conceptualization, Steps in a sim. Study: Data Collection and Model Translation, Steps in a sim. Study: Verification and Validation, Steps in a sim. Study: Experimental Design, Steps in a sim. Documentation, Steps in a sim. Study: Logs & Reports, Steps in a sim. Study: Phases Overview, Simulation Case Studies: Basic steps, Basics of a Spreadsheet Simulation: Simulating Randomness, Simulating a Coin Toss, Simulating a Random Service Time, Simulating a Random Arrival Time, Framework for Spreadsheet Simulation, Framework Simulation Table Design, Framework using Discrete event simulation: General Idea, Framework using Discrete event simulation – I, Framework using Discrete event simulation – II, Framework using Discrete event simulation – III, Framework using Discrete event simulation – IV, Event Scheduling Time advance algo, Event Scheduling Time advance algo-II, Event Scheduling Time advance algo-III, Event Scheduling Time advance algo-IV, World views – I, World views – II, Manual Simulation, Manual Simulation-II, Manual Simulation-III, Statistical Models in Sim, Review of Terms-I, Review of Terms-II, Review of Terms-III, Review of Terms- IV, Useful models – I, Useful models – II, Why Agent-Based Modeling? , A Thought Experiment , Complex Systems and Emergence , Understanding Complex Systems and Emergence, Example 1: Integrative Understanding, Example 2: Differential Understanding, Agent-Based Modeling as Representational Infrastructure for Restructuration’s, Example:, Predator-Prey Interactions, Example: Forest Fires, What Is Agent-Based Modeling?, Ants , Creating the Ant Foraging Model, Results and Observations from the Ant Model, What Good Is an Ant Model?, What Is Agent-Based Modeling?, Agent-Based Models vs. Other Modeling Forms, Randomness vs. Determinism, When Is ABM Most Beneficial? Trade-offs of ABM, What Is Needed to Understand ABM?, Explorations, Beginner NetLogo Explorations, Ants and Other Model Explorations, Concept Explorations, NetLogo Explorations, Creating Simple Agent-Based Models, Life -I, Life-II, Life-III, Heroes and Cowards-I, Heroes and Cowards-II, Heroes and Cowards-III, Simple Economy-I, Simple Economy-II, Simple Economy-III, Model Explorations , Model Designing Examples, NetLogo Explorations, NetLogo Explorations-II, Exploring and Extending Agent-Based Models , The Fire Model, First Extension: Probabilistic Transitions, Second Extension: Adding Wind, Third Extension: Allow Long-Distance Transmission, Advanced Modeling Applications, The Diffusion-Limited Aggregation (DLA) Model, First Extension: Probabilistic Sticking, Second Extension: Neighbor Influence, Third Extension: Different Aggregates, Advanced Modeling Applications , The Segregation Model, Description of the Segregation Model, First Extension: Adding Multiple Ethnicities, Second Extension: Allowing Diverse Thresholds, Third Extension: Adding Diversity-Seeking Individuals, Advanced Urban Modeling Applications, The El Farol Model, First Extension: Color Agents That Are More Successful Predictors, Second Extension: Average, Min, and Max Rewards, Third Extension: Histogram Reward Values, Advanced Modeling Applications , Creating Agent-Based Models, Designing Your Model, Choosing Your Questions, A Concrete Example, Choosing Your Agents, Choosing Agent Properties, Choosing Agent Behavior Choosing Parameters of the Model, Summary of the Wolf Sheep Simple Model Design, Examining a Model, Multiple Runs, Predator-Prey Models: Additional Context, Advanced Modeling Applications, The Components of Agent-Based Modeling, Agents, Properties & Behaviors, Collections of Agents, The Granularity of an Agent, Agent Cognition, Other Kinds of Agents , Environments, Spatial Environments, Network-Based Environments, Special Environments , Interactions, Observer/User Interface, Schedule, Analyzing Agent-Based Models, Types of Measurements, Modeling the Spread of Disease , Statistical Analysis of ABM: Moving beyond Raw Data, The Necessity of Multiple Runs within ABM, Using Graphs to Examine Results in ABM, Analyzing Networks within ABM, Environmental Data and ABM, Correctness of a Model , Verification, Communication, Describing Conceptual Models, Verification Testing, Beyond Verification, Sensitivity Analysis and Robustness, Verification Benefits and Issues, Validation , Macrovalidation vs. Microvalidation, Face Validation vs. Empirical Validation, Validation ,Benefits and Questions & VOMAS, Replication, Replication of Computational Models: Dimensions and Standards, Benefits of Replication, Recommendations for Model Replicators , Recommendations for Model Authors, Complex Adaptive Systems, History, Complexity , Adaptation, System Approach, Modeling of CAS, Agent-based, Complex Network Based, Cognitive Agent-based Computing Framework , More models, Bernoulli Distribution, Binomial Distribution, Poisson Distribution, Uniform Distribution, Exponential Distribution, Triangular Distribution, Characteristics of Queueing Systems, The Calling Population, System Capacity, The Arrival Process, Queue Behavior and Queue Discipline, Service Times and the Service Mechanism, Queueing Notation, Long-Run Measures of Performance of Queueing Systems, Properties of Random Numbers, Properties of Random Numbers, Generation of PseudoRandom Numbers, Tests for Random numbers, Random Variate Generation, Inverse Transform Technique, Acceptance Rejection Technique, Other topics in Randomness, Data Collection, Identifying the Distribution with Data, Histograms, Selecting the Family of Distributions, Quantile-Quantile Plots, Parameter Estimation ,Preliminary Statistics: Sample Mean and Sample Variance, Evolution of computer systems architectures, Evolution of database systems, Evolution of operating systems, Evolution of computer networks, Need for performance evaluation, Role of performance evaluation in computer engineering, Overview of performance evaluation methods, Performance metrics and evaluation criteria, Comparison of Two System Designs, Independent Sampling with Equal Variances, Independent Sampling with Unequal Variances, Common Random Numbers (CRN), Confidence Intervals with Specified Precision, Comparison of Several System Designs ,Bonferroni Approach to Multiple Comparisons, Bonferroni Approach to Selecting the Best, Bonferroni Approach to Screening, Metamodeling, Simple Linear Regression ,Testing for Significance of Regression ,What Does Optimization via Simulation Mean?, Why is Optimization via Simulation Difficult? , Using Robust Heuristics ,An Illustration: Random Search, introduction to Perf. Eval, Events, Measurements (sampling), Intervals, Response, Independence, Randomness, Workloads, Problems encountered in model development and use, A case study, Introduction to Software Reliability, Definitions and Software Reliability Model, Software Reliability Growth Modeling, Imperfect Debugging Modeling, Imperfect Debugging Model with Perfect, Imperfect Debugging Model for Introduced Faults, Software Availability Modeling, Model Description, Software Availability Measures, Application of Software Reliability Assessment, Optimal Software Release Problem, Statistical Software Testing-Progress Control, Optimal Testing-Effort Allocation Problem, Introduction to Formal Modeling, Basic notation-I, Basic notation-II, Classical Petri nets-I, Classical Petri nets-II, Timed Petri nets-I, Timed Petri nets-II, Priority-based, Colored, Generalized Petri Nets, Formal Spec. using Z, Basic Concepts of Z, State charts use in Z, Sets, Making a Counter Using Z-Init Schema and Basic Definitions, Making a counter - Querying the Counter, Changes in the counter, Class Enrollment example basics, Basic Set definitions of class enrollment example, Initialization of class example, Enrollment schema, Certificate receipt schema, Free Type Definitions for class enrollment, Writing Z using LaTeX/LyX-I, Writing Z using LaTeX/LyX-II, Writing Z using LaTeX/LyX-III, Writing Z using LaTeX/LyX-IV