Time: Wednesday, July 14, 9:00 am - noon
Place: Bioinformatics Computer Core Lab (Rm 104), Life Sciences Bldg
Organizers: Tarynn M. Witten
Audience: Primarily 1st year students

Topics of session

• Understand the underlying concepts of the three scenarios motivating this research simulation.
• Understand the basic ideas behind mathematical modeling/computer simulation.
• Understand the basics of the Maple programming language for solving differential equations (Maple4Students) and be aware of other similar symbolic programming languages such as Mathematica.
• Understand some of the basics derivatives and differential equations and the construction of simple differential equations mathematical models.

Resources of session

• Notes: None. You will get them as we go in class.
  
• Papers: Look through the papers. Do not let the mathematics scare you. Just get a sense of what the papers are attempting to address.
• ControllingInfectiousDiseaseOutbreaks.pdf – Addresses factors that make make an infectious disease outbreaks controllable
• EbolaVirusAndPublicHealth.pdf – Examines the basic reproductive number of Ebola and the effects of public health measures
• EmergencyResponseToSmallpox.pdf – Examines the emergency response to a smallpox attack and the case for mass vaccination.
• ModelingTheSARSEpidemic.pdf – Looks at how epidemiologists handled modeling the SARS outbreak.
• TransmissionAndControlOfSARS.pdf – Looks at how to model the transmission dynamics of severe acute respiratory syndrome (SARS).
• TransmssionDynamicsOfSARSinHongKong.pdf – Examines the SARS modeling problem as applied to Hong Kong outbreak.
• Epidemic-networks2.pdf – Examines modeling the spread of an epidemic through social network structures
• LessVaccineMoreMeasles.pdf – Looks at the interaction between vaccination and measles spread.
• PandemicInfluenza.pdf – Looks at how epidemiologists think about pandemics.
• SimpleModelComplexEpidemics.pdf – Examines the changes in patterns of epidemic outbreak and how the temporal dynamics is modeled.
• GeneRegulatoryNetworks.pdf – Examines creating and modeling complex gene regulatory networks.
• InSilcoEcoli.pdf – Looks at how to model some basic metabolic dynamics of E. coli.
• ModelingDrugTolerance1.pdf and ModelingDrugTolerance2.pdf – Examines how to construct a mathematical model of drug tolerance.
• HodgkinHuxleyNeuralModels.pdf – Examines the basic Hodgkin-Huxley model of neural behavior
• Programs:
• There are a number of programs we will use today. When you get into class, download the file Day1Programs.zip. Save it to the desktop.
• Create a desktop folder called MapleModelingPrograms. Move the zip file into the new folder and change the extension then unzip the files. You should have 12 files.
• Links:
• Maple – Maplesoft Home Page
• Maple4Students – More on Maple for students
• Mathematica – Steve Wolfram’s Home Page for Mathematica

Before coming to the session

• Look through each of the scenarios and think about the questions asked at the end of each scenario. Scenario1, Scenario2, Scenario3
• Read over some of the papers related to at least one of the scenarios
• Visit the Maple/Maple4Students websites

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