GUI Overview

• Code tab:                the custom code (C++)
• Config Basics tab: input parameters common to all models (e.g., domain grid, simulation time, choice/frequency of outputs)
• Microenvironment tab:   microenvironment parameters that are model-specific
• User Params tab:            user parameters that are model-specific
• Out: Cell Plots tab:           output display of the cells
• Out: Substrate Plots tab: output display of the substrates

Clicking the 'Run' button will use the specified parameters and start a simulation. When clicked, it creates an "Output" widget that can be clicked/expanded to reveal the progress (text) of the simulation. When the simulation generates output file(s), they can be visualized in the appropriate output tabs. The "Max" count in each output tab will be dynamically updated as those output files are generated by the running simulation. When the "Run" button is clicked, it toggles to a "Cancel" button that will terminate (not pause) the simulation.

Introduction

This app demonstrates how you can model run an intracellular model along with PhysiCell. It uses libRoadrunner to read/process a SBML file that represents the intracellular model and also to solve the SBML model. In this particular model, our SBML contains a set of ODEs.

This model and cloud-hosted demo are part of a course on computational multicellular systems biology created and taught by Dr. Paul Macklin in the Department of Intelligent Systems Engineering at Indiana University. It is also part of the education and outreach for the IU Engineered nanoBIO Node and the NCI-funded cancer systems biology grant U01CA232137. The models are built using PhysiCell: a C++ framework for multicellular systems biology [1].

Basic instructions

Modify the parameters in the "Config Basics" and "User Params" tabs. Click the "Run" button once you are ready.

To view the behavior of the cells , click the "Cell Plots" tab, and slide the bar to advance through simulation frames. Note that as the simulation runs, the "Max" field (maximum frame number) will increase, so you can view more simulation frames.

To view the changing substrate fields, click the "Substrate Plots" tab, choose a substrate from the drop-down menu, and slide through the saved times. Note that as the simulation runs, the "max" field (maximum frame number) will increase, so you can view more simulation frames.

Note that you can download full simulation data for further exploration in your tools of choice.

Researchers should cite this work as follows:

• Randy Heiland (2020), "PhysiCell model with SBML intracellular model," https://nanohub.org/resources/pc4sbml. (DOI: 10.21981/BT3F-7151).

  BibTex | EndNote

1. Jupyter notebooks
2. nanobio applications
3. NanoBio Node at Indiana
4. PhysiCell