Bridging Scales

This is the code base for the publication: Bridging scales: A hybrid model to simulate vascular tumor growth and treatment response by Duswald, Lima, Oden, and Wohlmuth (2023) available here.

Software Stack and Depndencies

• BioDynaMo. To install, consult the BDM dev-guide. Install the latest master as described in the link. Following the dev-guide allows us to easily upgrade and extend BioDynaMo if necessary.

Running the simulations

Building on the BioDynaMo platform, the commands to running the simulations assume a functional installation of BioDynaMo and are

source <path>/thisbdm.sh  # source biodynamo 
bdm build                 # compile application code
bdm run                   # execute application code
bdm view                  # open results in ParaView

Reproducing the results of the publication

Reproducing the results of the different experiments of the publication requires setting the correct parameters but also minimal changes to code, i.e., possibly adding a few lines of code to adequately set the initial conditions. This process it automated in a second repository that can be found at TobiasDuswald/bdm-angiogenesis-reproducer. Please consult the README.md of that repository for further instructions.