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UCI-sysbio-2022

This repository collects notes, handouts, and other materials from the PhysiCell curriculum at the UCI Systems Biology Short Course (June 13, 2022.) See more at https://ccbs.uci.edu/education/fasb-sc/

Preparation

The majority of the PhysiCell session will be run using online web models, with optional work on C++ for the more advanced part of the session.

NanoHub registration

Participants should create a nanoHUB account in advance at https://nanohub.org/register. I suggest using the Google login option.

NanoHub model

Our session will use the pc4learning web app. For best results, use a fast connection.

GitHub

Participants not familiar with GitHub may want to use their very convenient desktop client. Get it at https://desktop.github.com/

Slides and Materials

By Sunday (June 12th), full slides and materials will be available here on GitHub at https://github.com/physicell-training/UCI-sysbio-2022.

I suggest cloning the whole repository with GitHub. Then you'll have a copy of all slides and code. Moreover, you can easily check for and download any updates.

C++ setup

The last part of the session will extend our web-based models to add C++ functions for more model dynamics. To participate in this part of the session, run our setup tutorials found at https://github.com/PhysiCell-Training/ws2021

Slides

The live slides for the session are available here: UCI-sysbio-2022 live version

I also give extended slides here: UCI-sysbio-2022 extended version. The slides include:

  • additional mathematical detail
  • complete the Part II online example
  • complete the Part III C++ extension

Source code

Full source code for the example is available at: https://github.com/physicell-training/UCI-sysbio-2022/tree/main/code/PhysiCell