PhysiCell: an opensource framework for multicell modeling,

Professor: Heber Lima Rocha e Aneequa Sundus (University of Indiana at Bloomington)

Horarios: Segunda 14/02 a Quarta 16/02 de 14:00h às 15:30h

  1. Class 1:
    • Introduction to agent-based modeling and PhysiCell: Learning about the motivation for agent-based modeling, briefly survey on agent-based modeling techniques, introduce (and contextualize) PhysiCell, and show recent examples of PhysiCell-powered investigations.
    • Working with Projects in PhysiCell: Learn how to work with sample (and template) projects in PhysiCell: populating/depopulating sample projects, compiling, editing settings, running, viewing results, and clearing data.
    • PhysiCell First Dive: Learn about cells, phenotype, and cell definitions in PhysiCell. Introduce the basic, intermediate, and advanced modeling workflows. Run through the basic workflow and explore data in a Jupyter notebook.
  2. Class 2:
    • Introduction to Cell Phenotype in PhysiCell: A detailed exploration of cell phenotype in PhysiCell.
    • A complete example: Run through a complete project in the intermediate modeling workflow: start with the template project, customize the model with the graphical model builder, and run.
    • Introduction to Custom Variables, Parameters, Microenvironment, and C++ searches: Work with custom cell variables, custom simulation parameters, microenvironment boundary setup, and searches (in C++ project source code).
  3. Class 3:
    • Functions in PhysiCell: Learn about custom C++ cell functions to 'encode' cell behavioral rules and hypotheses. Use the full modeling workflow to simulate oxygen-dependent birth, death, and motility. Lots of handy C++ tidbits.
    • Chemical Communication in PhysiCell: Learn about chemical cell-cell communication. Run through the full modeling workflow with examples based on quorum sensing in cell colonies.