Notes

• 6/8/10

  • System dynamics

    • Vensim

    • Goal modeling

    • Agent Sheets

• 6/9/10

  • Resources

  • EXCEL

• 6/10/10

  • Nancy Darling

  • Chris Martin

  • Rich Salter

  • John - Norovirus model

• 6/11/10

6/8/10

System dynamics

Vensim

HAVE=HAD+CHANGE

BREAK

Goal modeling

Example 1: Population of bunnies

Showed 2 models for population of bunnies. One was used a carrying capacity variable. The other used competition. When both models were graphed on the same chart, user can use the slide function to adjust competition and carry capacity until the curves overlay. Then the same models predict the same output.

example is not on website but will be later.

Example 2: Pharmaceutical Drugs

Pharma.mdl

Video from part of the lecture.

Agent Sheets

Master tools: http://shodor.org/talks/oberlin

went over rabbits/wolves/grass in interactive activities found on shodor site.

If you can draw concept map of interconnections then you have a model and Vensim and Stella allow you to create a model of the concept map.

In agent modeling the idea is not to create a concept map but rather to 'tell a story.' These are then modeled in Netlogo or AgentSheets. Built on 'if .. then.. else' scenarios.

e.g. in rabbit/wolf/grass model you would model grass eating as 'grass will be eaten if the bunny is hungry and ... and ... '

Went over examples using Agent Sheets program.

Opened file named 'Voting'

Opened file named 'predatorprey'

TEST: WHile running if a Frog-prince is next to 1 princess then there is a_______ chance the Frog-prince will chnage into a Real-prince. The princesses move randomly in the Forest; the frog-prince hops, and any Real-prince moves randomly in the Forest.

NOUNS (Agents)

Prince

Frog-prince - green

Real-prince - blue

Princess - pink

Forest - brown rectangle

VERBS (Behaviors)

Move

hop

change

Looked at Ecoli model, tree burning model - shows how to update each agent at each timestep.

If you want a different size, create a new Sheet and import the Agents from the smaller sheet.

4:09pm Demo NetLogo which requires, unlike Agent Sheets, the writing of actual code or at least what looks like code.

Goto netlogo

Open Termites from Files>>Models Library>>Biology>>Termites

Many great simulations that can be used. They are well documented and easy to use. Creating models might not be as easy as creating them from scratch in other packages.

6/9/10

In Vensim PLE: To create unit consistency enter units in the one that has the most complicated units. In the other entities you should click on the 'units' button and the program should autofill.

There is also a 'Units check' under the 'Models' menu.

Simple Function and Bunny Comparison were added to the list of models in http://shodor.org/talks/oberlin/vensim

_________________________

Resources

NSDL.org - Science Literacy Maps

EXCEL

Example files located at: http://www.shodor.org/talks/oberlin/excel/

Developer tools may not be turned on. If you don't have View>>Toolbars>>Forms you are not set up as a developer. Turning this on is different depending on which version of Excel you are on. I did not see how to turn it on.

Changing names of individual cells, ranges of cells or whole columns. We can then use that name as a reference.

Forms can allow one to use scrollbars to control in the spreadsheet to control values in a cell. Slider bars and graph updating are finicky i.e. they can vary across platforms and versions.

Went over models that are modeling similar concepts to those that we did in Vensim.

Function Model (Snake2.xls)

Pharmacology Dosing (Pharma.xls) If statements are used in calculation

Modeling something over and over again.

Iteration - circular reference requires that you shut off the automatic update (Control in Preferences - on mac-Excel>>Preferences>>Calculation : set iteration to manual) MAC: APPLE+= to iterate PC: F9 to iterate

Game of Life (GameOfLife2.xls) - uses conditional formatting to color cell white or black

Laplace Equation (PULSE.xls)

Computer Assisted Algebra system - (MatLab, MathCad, Mathematica): Dan Warner demoed Sage from sagemath.org

Demo file is located at: https://clemix.clemson.edu:34567/home/pub/41/ (it is called Oberlin_Sage_Intro)

(note you will need to accept an SSL certificate and then create an account. Finally if you want to edit it yourself you will need to "edit a copy").

Video of Dan Warner's presentation.

6/10/10

Nancy Darling

Chris Martin

Web pages used in Chris Martin's presentation:

http://www.eveandersson.com/pi/monte-carlo-circle

http://en.wikipedia.org/wiki/Buffon%27s_needle

http://mste.illinois.edu/reese/buffon/buffon.html

http://mste.illinois.edu/reese/buffon/bufjava.html

http://www.cut-the-knot.org/ctk/August2001.shtml

http://mathworld.wolfram.com/MonteCarloIntegration.html

http://www.obitko.com/tutorials/genetic-algorithms/tsp-example.php

Rich Salter

http://nova.oberlin.edu

John - Norovirus model

6/11/10

• • http;//www.computationalscience.org

  • Login ---> Create new account

  • NCSI "bread crumb"

  • Workshops ---> Register for Oberlin

  • "details" ---> surveys a) Friday b) Post

National Computational Science Initiative

sc10.supercomputing.org/ Nov 13-19, 2010 - International Conference for High Performance Computing, Networking, Storage and Analysis - Education program

www.teragrid.org in Pittsburgh TeraGrid '10 August 2-5th, 2010

Computational Legal Studies blog - maintained by University of Michigan grad students in Complex Systems

Random notes:

• • Magnify screen while demonstrating in front of the class

    • Mac - Cntl and use 2 fingers to zoom in on something

    • PC - ZoomIt utility (this can be run from the web). Find it by googling 'zoomit'

Place in North Carolina where one can visit Shodor and stay?? ShoRedon - remote research facility

Shodor can still work with you. Contact them and they can videoconference in or use iChat.