Setting up a simulation and running it is done with the BioDynaMo command line interface (CLI). Open a new terminal and execute:
This command must be executed whenever you want to use BioDynaMo in a new terminal!
<installation-directory> will be
$HOME/biodynamo-vX.Y.Z, where X.Y.Z is the version number
A basic BioDynaMo workflow looks as follows:
To create a new project run the following command:
biodynamo new <enter_name>
This command creates a new Git repository for you with the name specified
<enter_name> placeholder. You will see a folder appear with the same
name, containing some template files to get you started.
If you wish to have your Github account linked to your project you can
--github option to the command.
biodynamo assist command requires
The provided template files in your newly created folder can be used as a
starting point for your simulation. The
src directory contains the files with
the source code that defines the simulation. You can edit and add the code that
describes your model in this folder.
Building the simulation and running it can be done with the command:
All your source code will be compiled and linked against the BioDynaMo libraries, and an executable file will be created and run. It is at this point you might encounter compilation errors. You will need to fix them before the simulation can actually run.
There are some demos in the installation. They can be listed with the command:
Each of these demos can be copied out to a directory and executed with two
biodynamo demo <name> [target] cd <destination> # as printed out by the previous command biodynamo run
For example, to run the demo
cell_division, we can do:
biodynamo demo cell_division /tmp cd /tmp/cell_division biodynamo run
It can happen that you encounter an error or issue that you cannot solve on your own. Or you might be convinced that there is a bug in BioDynaMo. For such occasions we have provided you with BioDynaMo assistance:
This command will create a folder called
debug in which debug information will be collected.
A git branch will be created and uploaded to Github. Send the link to this branch to us,
so we can take a look at the issue. Check out Contact on how to contact us.