Paul Macklin's Math Cancer Lab Website

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Recent news

Friday, Sep 9th, 2016
Coarse-graining discrete cell cycle models: Introduction One observation that often goes underappreciated in computational biology discussions is that a computational model is often a model of a model of a model ... [read more]

Tuesday, Aug 30th, 2016
Some quick math to calculate numerical convergence rates: I find myself needing to re-derive this often enough that it’s worth jotting down for current and future students. Introduction A very common task in our ... [read more]

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Resources

Please find below numerous resources for those interested in mathematical modeling and cancer biology (from the perspective of a modeler). You may also want to look at the open source software page.

Tutorials

Dundee Summer School 2010

Here is a series of 4 talks I gave ranging from basic biology for mathematical modelers, agent model formulation and analysis, patient-specific calibration, and numerical method with simulation results.

Many of these results are in press; I try to indicate the relevant papers and book chapters where possible. As I continue to update my website, I will include better links to the publishers' websites.

  1. Lecture 1: Basic biology for modelers There is an expanded version available in this book chapter.
  2. Lecture 2: An agent-based cell model, with analysis and application to breast cancer (DCIS). This is currently published in this book chapter, this book chapter, this book chapter, and this journal article.
  3. Lecture 3: Parameter estimation and patient-specific calibration. This is currently published in this book chapter, this book chapter, this book chapter, and this journal article.
  4. Lecture 4: Numerical method and simulation results. This is currently published in this book chapter, this book chapter, this book chapter, and this journal article.

Biology and Pathology for Modelers

Here are a few primers that may be helpful for new modelers and students.

  1. Basic ductal carcinoma in situ (DCIS) pathobiology for modelers