# 2021 PhysiCell Workshop and Hackathon These resources were originally developed for the 2021 Virtual PhysiCell Workshop and Hackathon, taking place July 25-31, 2021. For a full agenda, please see [agenda.md](https://github.com/physicell-training/ws2021/blob/main/agenda.md). ## Setup Materials To arrive prepared, all workshop participants should work through the pre-workshop materials prior to Monday, July 25th. ### MacOS Setup * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_macOS_setup.pdf) * Video: [click here](https://www.youtube.com/watch?v=mv_phTdanws) ### Windows Setup * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Windows_setup.pdf) * Video: [click here](https://www.youtube.com/watch?v=Jp3ZOMt761M) ## PhysiCell Virtual Course ### Session 0: Introduction to agent-based modeling and PhysiCell Learn about the motivation for agent-based modeling, briefly survey agent-based modeling techniques, introduce (and contextualize) PhysiCell, and show recent examples of PhysiCell-powered investigations. **(approx 40 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session0.pdf) * Video: [click here](https://youtu.be/RWI0SKX49eo) ### Session 1: 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. **(approx 20 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session1.pdf) * Video: [click here](https://youtu.be/fP7-n_RlITU) ### Session 2: 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. **(approx 60 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session2.pdf) * Code: [click here](https://github.com/physicell-training/ws2021/tree/main/code/Session_2) * Video: [click here](https://youtu.be/fSpyhVry3eU) ### Session 3: Introduction to Cell Phenotype in PhysiCell (Part 1) Start a detailed exploration of cell phenotype in PhysiCell. **(approx 40 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session3.pdf) * Video: [click here](https://youtu.be/EqqEQWRaoak) ### Session 4: Introduction to Cell Phenotype in PhysiCell (Part 2) Finish a detailed exploration of cell phenotype in PhysiCell. **(approx 50 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session4.pdf) * Video: [click here](https://youtu.be/Kb47UeMrTjY) ### Session 5: 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. **(approx 85 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session5.pdf) * Code: [click here](https://github.com/physicell-training/ws2021/tree/main/code/Session_5) * Video: [click here](https://youtu.be/YpQV65CJdGw) ### Session 6: 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). **(approx 20 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session6.pdf) * Video: [click here](https://youtu.be/Fvd3aQ63fK4) ### Session 7: 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. **(approx 80 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session7.pdf) * Code: [click here](https://github.com/physicell-training/ws2021/tree/main/code/Session_7) * Video: [click here](https://youtu.be/ygK7THTN_QU) ### Session 8: 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. **(approx 60 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session8.pdf) * Code: [click here](https://github.com/physicell-training/ws2021/tree/main/code/Session_8) * Video: [click here](https://youtu.be/tu3gUseGY8g) ### Special Session: PhysiBoSS enables multiscale simulations of signalling pathways A special guest lecture by Arnau Montagud (Barcelona Supercomputing Center) on PhysiBoSS, which integrates MaBoSS Boolean networks in PhysiCell agents. **(approx 65 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_PhysiBoSS.pdf) * Video: [click here](https://youtu.be/2w2-Q-gvO4U) ### Session 9: Contact testing and pressure Learn about testing for contact with other cells and a nondimensionalized mechanical pressure. **(approx 15 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session9.pdf) * Video: [click here](https://youtu.be/RwzWBBXkEEg) ### Session 10: Contact examples Learn about contact interaction functions, including standardized functions for spring-like cell-cell adhesion. See an example inspired by developmental biology where cells aggregate and link to form "worms" that travel collectively up chemical gradients. In the special contact functions, linked cells use a signal that diffuses across cell junctions to determine if they are head, middle, or tail cells. **(approx 50 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session10.pdf) * Code: [click here](https://github.com/physicell-training/ws2021/tree/main/code/Session_10) * Video: [click here](https://youtu.be/_k4BdLm5LTU) ### Session 11: Intracellular Modeling Part 1 Learn about integrating intracellular ODE-based signaling models in PhysiCell agents, using libRoadrunner. **(approx 55 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session11.pdf) * Video: [click here](https://youtu.be/w3gdgFSwtms) ### Session 12: Intracellular Modeling Part 2 Continue learning about intracellular modeling, including tips on using COPASI to generate PhysiCell-compatible SBML. **(approx 90 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session12.pdf) * Video: [click here](https://youtu.be/lMtG44cJejM) ### Session 13: Sharing models via nanoHUB Learn about converting PhysiCell projects to cloud-hosted, "zero-install" models on nanoHUB. **(approx 25 min)** * Slides: [click here](https://github.com/physicell-training/ws2021/blob/main/pdfs/PhysiCell_ws2021_Session13.pdf) * Video: [click here](https://youtu.be/lTQCRWzJnyI)