Jan 17 |
First class - overview of course
- What is simulation?
- What is modeling?
- What is computer modeling?
- What is computer simulation?
Homework
- Banks: read chapters 1 & 2
- Grimm: read chapters 1 & 2
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Jan 19 |
Overview of NetLogo
- Guest lecture by Ryan Kennedy
Homework
- Install and experiment with NetLogo on your computer or OIT account
- Assignment given in class
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Jan 24 |
Lecture
- A simulation ontology
- A simulation workflow
- Differences between analytical, numberical, and simulation models
- Simulation structures
- Network of servers, queues and other activities
- Cellular automata
Homework
- Visit cellular automata web site demoed in class. Review and experiment with the applet.
- Read
- Chapters 3, 4 & 5 in Banks
- Chapter 3 in Grimm
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Jan 26 |
Guest Lecture: Prof. Frank Collins
- Project teams formed
- Preliminary formulation of project one
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Jan 31 |
Lecture
- Discussion of project one
- Probability distributions
- Discrete distributions
- Continuous distributions
- Cummulative distributions
- Expectation
- Bernoulli distrubutions
- Binomial distributions
- Geometric distributions
- Negativee binomial distributions
- Poisson distributions
Homework
- Visit web site with applets for distributions, play and develop an intution for each
- Additional distributions
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Feb 2 |
Lecture
- Discussion of project one
- Analogs of stochastic engineering scenarios in the biological context
- Continuous probability distributions; see web site
Homework
- Pencil & paper problems due Feb 16: Banks, pp. 194-199, ex 3, 4, 5, 6, 14, 15, 19, 25, 26, 33, 38, 43
- Read in Banks: Chapters 7 & 8
- Review article, Life is lognormal
- Review materials on RePast here
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Feb 7 |
Lecture
- Discussion of project one
- Repast
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Feb 9 |
Lecture
- Discussion of project one: demos
- Continuous probability distributions; see web site
- Empirical
- Many many more distributions. For example, see here.
Homework
- Project one due on Feb 21
- Submitted online on a web page
- Applet
- Link ot the .nlogo file
- Short write up: discussion, limitations, intepretation, analysis, potential improvements/extensions
- Project two: port model of project one to Repast: due date TBD
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Feb 14 |
News: new beta release of NetLogo Lecture
- Project demos
- Complete discussion of probability distributions
- Discuss homework due Thursday
- Start discussion of Theory of Random-Number Generation
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Feb 16 |
Lecture
- Project demos
- Discussion of homework assignment
Homework
- Reminder: programming project one due. See Feb 9 lecture notes.
- Read in Banks: Chapters 7 & 8
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Feb 21 |
News:
- Simulation PhD sholarship available (Australia) (here)
- Test 1 will be on March 2 on all material covered or assigned for prior class.
Lecture
- Homework due today ... discussion. Email URL's to instructor and TA
- Long tails
- Pseudo Random Number generation
- Theory
- Linear congruential methods
- Examples
- Problems with generators
- Testing generators
Homework
- Computer scientists: Start building version of project one in RePast: due TBD
- Biologists: start designing next simulation
- Read articles:
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Feb 23 |
News
- Post-doctoral position available for agent based modeling of infection transmission (here)
- A. aegypti
intron size (here) ... what kind of distribution is this?
Lecture
- Random numbers in NetLogo (demo)
- Class projects
- Testing random number generators
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Feb 28 |
Lecture
- Is this distribution normally distributed?
- More on testing random number generators for uniformity and independencee
- Kolmogorov-Smirnov test
- Chi-Squared test
- Runs tests
- 2-tuple, 3-tuple, n-tuple tests
- Autocorrelation
- Features of good generators
- Long period generators (here)
- Random variate generation
- Inverse transform technique
Homework
- Test 1 on all material covered in class prior to exam
- RePast implementations due Mar 23
- Schedule one hour meeting with Dr Madey and Dr. Collins to discuss project 1
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Mar 2 |
Test 1
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Mar 7 |
Lecture
- Random variate generation
- Inverse transform method continued
- Input modeling
Homework
- Reminder: RePast implementations due Mar 23
- Read Chapters 9 and 10 in Banks
- Starting with the NetLogo random number demo, using the inverse transform method, add the random distributions: Triangular, Weibull, and "Empirical
Continuous" (due Mar 28 - email URL to TA and instructor).
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Mar 9 |
News/Interest
Lecture
- Guest speaker - Dr. Jeanne Romero-Severson, Department of Biological Sciences, University of Notre Dame
- Exam items
- Demo of next NetLogo homework
- Input Modeling
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Mar 14, 16 |
Spring Break |
Mar 21 |
News
- Simulation projects for remainder of semester
- Each computer science student is expected to be the lead developer on a primary project and a secondary developer on a second project
- Your current project can continue as your primary or secondary project
- Each simulalation project will require a "conference style" research paper by the end of the semester. Each paper will be invited for submittion to the Swarm Conference to be held at Notre Dame
this summer
- Prof. David Severson will visit class to present another simulation problem
- Test 2 in the course will be given on Tuesday, April 4
Lecture
- Quantile-quantile plots for input modeling
- Goodness-of-fit tests
- Chi-squared
- Kolmogorov-Smirnov
- Verification and Validation
Homework
- Reminder: RePast implementations due
Mar 23 March 30
- Reminder: Netlogo implementation of Triangular, Weibull, and "Empirical Continuous" random number generators due Mar 28. One from every computer science student!. (demo)
- Review articles here
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Mar 23 |
News
Lecture
- Discussion of verification and validation
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Mar 28 |
News
- Seminar on analysis and inference on simulation results - Steven Bankes (at University of Michigan)
Lecture
- Discussion of homework due Thursday (Repast implementation of project 1)
- Final project 1 demos ... schedule
- More on Verification & Validation
Homework
- Submit a proposal (1-2 pages) in research article format of your primary simulation project for the rest of the course.
- Identify any other contributing CSE students
- Identify your biologist collaboarator/consultant
- Describe the biological question(s) that will be investigated
- Describe your proposed simulation design and development
- Due Tuesday, April 4
- Test 2, Tuesday, April 4 ... on all material covered up to prior class. Same format as test 1.
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Mar 30 |
Guest Lecture
- Professor David Severson
Department of Biological Sciences
University of Notrer Dame
"Population replacement in the mosquito Aedes aegypti using a meiotic drive system"
- Articles related to this project here
Other course business
- Discussion of exam 2
- Review rendom number generation programming
- Discussion of RePast assignment due today
- Discussion of next project
Lecture
- Output analysis for a single model
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Apr 4 |
In class test |
Apr 6 |
Guess Lecture
- Discuss project proposals
- Ryan Kennedy
- Paper presentation on Verification and Validation studies
- Paper (pdf)
- Slides
- Output analysis
Homework
- Due April 18: submit a Gantt Chart plan for your final course project
- Read chapters 11 & 12 in Banks
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Apr 11 |
Lecture
- Output analysis
- Interpretation of "cost-effectiveness" figure (gif)
- Discussion of role of simulation in the scientific method (slides)
- Review presentation on "Agent-based Simulations of In Vitro Multicellular Tumor Spheroid Growth"
Homework
- Final project deliverables
- Conference quality research paper
- Copy of simulation(s) (including source)
- Documentation/User Guide
- Images/figures that could be used in a poster
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April 13 |
Lecture
- Completion of chapter 11
- Replication issues
- Confidence analysis on output
- Little bit of Chaos theory
- Logistic map
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April 18 |
Course business:
- Final exam
- Send digital copies of proposal (if you submitted a paper copy)
News
- Final release of NetLogo 3.1 (more)
Lecture
- Discuss test 2
- Project status reports
- Gantt Charts
- Questions on output analysis
- Voronoi Diagrams
- Comparison and evaluation of multiple systems (designs, hypothesis, etc.)
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April 20 |
Trivia:
Lecture:
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April 25 |
More trivia
Business
- Final exam
Course Sect Instructor Exam Start End Bldg Room
40239 01 Madey 5/8/2006 10:30AM 12:30PM DBRT311
- Project deliverables due date
Lecture
- Project reports
- GIS demo
- Discussions of Grimm & Railsback
- Chapter 2
- Chapter 3
- Chapter 4
Homework
- Read Grimm & Railsback: Chapters 4-6
- Submit an initial draft of your final report by Monday, May 1
- Title
- Authors
- Abstract
- Text and/or outline
- Introduction: what is the question, what are hypotheses, literature (agent-based and biological)
- Description of simulation approach
- Results: preliminary or outline
- References
- Figures
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April 27 |
News
- Bug discovered in NetLogo (Brandon Rich) (here)
Lecture
- Project status reports
- Discussions of Grimm & Railsback
Chapter 2
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May 2 |
News
- Two job openings for computer scientists in multi-agent-based systems (including modeling fine-grained emergent systems) (here)
Lecture
- Project reports
- Draft papers - discussion
- Chapter 3
- Pattern-oriented modeling
- Data mining used to discover patterns
- Correlations, regression analysis
- Association rules
- Clusters
- Classification
- Temporal, time-series relationships
- Spatial-temporal relationships
- Network structure, link relationships
- Cause and effect relationships
- Feedback relationships
- Logistic map
- Lotka-Voltera
- Course wrap-up (Concept Map)
- TCEs
Homework
- Decide, in consultation with your biology collaborator, if a poster and abstract will be submitted to the 10th Annual Swarm Modeling Conference to be held this summer at Notre Dame (June 23-34). See here for more info. These are encouraged! If yes, a set of slides and poster (file) should also be submitted as part of your final project. Note, this is something you can add to your resume/CV.
- All deliverables due, Friday, May 12th, at 9:00 am.
- Project presentations will be given during the final exam period, Monday, May 8, 10:30-12:30. Budget for 10 minutes plus questions.
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