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.
- 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.
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 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.