VCU Bioinformatics and Bioengineering Summer Institute
Virginia Commonwealth University
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Research Simulation
Making a Model of Bacterial Mutation

Time: Thursday, July 15, 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 four scenarios motivating this research simulation.
  • Continue to develop the basic ideas behind mathematical modeling/computer simulation and to move to more complex models of biological systems.
  • Continue to understand the basics of the Maple programming language for solving differential equations (Maple4Students) and extend that knowledge into systems of differential equations.
  • Understand modeling basics behind some multivariate differential equations models such as the Delbruck-Luria model, the Scenario4 aging immune system model, Hodgkin-Huxley model for the neuron, and the cyclical neutropenia model.
  • Be introduced to some of the more sophisticated modeling concepts such as chaos, attractors, and stochasticity.

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.
    • AgeRelatedChangesInLymphocytes.pdf – Examines the effects of aging on the immune system. This review aims to provide an overview of age-related changes in lymphocyte development and function and discusses current controversies in the field of aging research.
    • AlteredHumanBCellsAndAging.pdf – Examines the memory B-cell concentration, which was positively correlated with memory T-cell concentrations in healthy elderly volunteers, nursing-home residents, and healthy young adults.
    • PharmacokineticsOfNaphthaleneInRats.pdf – Examines the problem of making a physiologically based pharmacokinetic model for inhalation and intravenous administration of naphthalene in rats and mice. Pay particular attention the last pages that look at the modeling aspects.
    • PharmacokineticsOf2-MethoxyaceticAcidInRats.pdf – Addresses the problem of dosimetry models that accurately predict chemical disposition in animals for the purposes of improved exposure-response assessment. Make sure to look at Figure 2 and related discussion in this paper.
    • CyclicalNeutropeniaModeling.pdf – Examines the problem of modeling the production and regulation of circulating blood neutrophil numbers.
    • FelineLeukemiaVirusPropagation.pdf – Examines the problem of modeling density-dependent dynamics and the dispersal of individuals. It uses the domestic cat-feline leukemia virus as an example of a micro-parasite and host system. It attempts to predict the disease dynamics between the two populations.
    • MammalPredatorPreyModels.pdf – Looks at how to model different size predator-prey species.
    • MeaslesModeling.pdf – Examines the problem of whether or not you can use a discrete-time vs. a continuous-time model to model the behavior of measles.
    • ModelingInfectionDueToNeisseria.pdf – Examines the problem of modeling invasive meningococcal disease, an important cause of morbidity and mortality in young children and adolescents. Pay particular attention to the differential equation model system in the Materials and Methods Section of this paper.
    • ModelingMeningitisEpidemiology.pdf – Looks at the problem of modeling infectious diseases transmitted by asymptomatic carriers. It looks at this problem as applied to meningitis.
    • ModelingInfluenzaTypeA.pdf – Examines modeling the influenza A drift in antigenic properties and how that affects the spread of the disease.
    • TuberculosisModeling.pdf – One third of the world’s population is estimated to be infected with the bacterium causing tuberculosis, resulting in nearly 3 million deaths per year. This paper looks at modeling a TB epidemic. Pay particular attention to Section 3, equations 1-10.
    • HodgkinHuxleyNeuralModels.pdf – Examines the basic Hodgkin-Huxley model of neural behavior
  • Programs:
    • When you get into class, download the file CD8DifferentialEquations-BBSI2004.mws.mw. Save it to the desktop folder you created on Day 1 (Note: to save the file above, right click the link and choose "Save Target As..")
    • Open up Maple so that it is ready to be used.
  • Links:

Before coming to the session

  • Review the scenarios, this time in more detail and think about models of drugs in more detail. Look at the two pharmacokinetics articles in the article list above for more help.
  • Review at least one of the articles from Day 1. Pick one of the four scenarios and look at two papers related to that scenario. Be prepared to discuss what you have learned as it applies to what you read and the idea of developing the model of your chosen scenario.
  • Read at least one of the modeling articles from the Day 2 article list and be prepared to discuss it in class.
  • Make sure that you have altered the Maple program to include the density dependent factor in the growth. You should be prepared to demonstrate your solution in class.
  • Using the Maple material you have, write a simple program to solve one of the systems of differential equations in any particular paper.

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