Materials from 2010 CBBE workshop at NC A&T

Day 1, Monday, July 19

• Session 1 - Modeling Intro - Population growth models

  • Presentation
  • Models
    • AgentSheets introductory tutorial, M&M population model and model building tutorial
    • Excel tutorial and workbook analyzing data, and validating AgentSheets simulation
    • Vensim tutorials 1 and 2 for building models of population growth
    • R script demonstrating Euler method of numerical integration of a simple exponential growth curve in R

• Session 2 - Modeling enzyme kinetics with MatLab SimBiology

  • Michaelis-Menten Presentation
  • MatLab Presentation
  • MatLab Right triangle script
  • MatLab Micahelis-Menten model script

• Session 3 - Modeling photosynthesis with Vensim

  • Presentation
  • Vensim model building tutorial
  • Vensim model
  • R script implementing this model using two forms of numercial integration

• Session 4 - Water transport "root to shoot" model

  • Presentation
  • Model description and MatLab scripts

Day 2, Tuesday, July 20

• Session 1 - Probability Intro - Modeling Molecular Evolution

  • PowerPoint
    • Slide presentation on introductory probability and modeling molecular evolution
  • Excel
    • Coin toss workbook exploring probability
    • Two nucleotide sequences for analysis in Excel

• Session 2 - Jukes-Cantor Model of Molecular Evolution

  • AgentSheets Jukes-Cantor AgentSheets model (you can run the applet version in your browser here)
  • Excel Jukes-Cantor Excel model
  • R scripts
    • Jukes-Cantor R model
    • testing script

  • Session 3 - Molecular Phylogenetics

    • Reading phylogenetic trees presentation
    • Excel MEGA 4 software walkthrough

  Related Materials

  • MatLab Parallel Coputing Intro
  • Analysis of high-throughput sequencing data with R and Bioconductor

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