Paul Macklin's Math Cancer Lab Website

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Recent news

Sunday, Sep 3rd, 2017
Common problems and solutions: Here, we document common problems and solutions in compiling and running PhysiCell projects. Compiling Errors I get the error “clang: error: unsupported option ‘-fopenmp’” when I compile ... [read more]

Thursday, Aug 31st, 2017
Running the PhysiCell sample projects: Introduction In PhysiCell 1.2.1 and later, we include four sample projects on cancer heterogeneity, bioengineered multicellular systems, and cancer immunology. This post will walk you through ... [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