The Angiogenesis project is a Chaste add-on with functionality for modelling blood flow, angiogenesis and nutrient and drug transport in micro-vessels as described in the paper here source:chaste/projects/Angiogenesis/paper/chaste_angiogeneis_plos_cb.pdf. Click on the images below to see some example applications. Detailed installation instructions are below.
- Image(source:/chaste/projects/Angiogenesis/test/tutorials/images/haematocrit.png, 20%, align=centre, border=1, link=PaperTutorials/Angiogenesis/BloodFlow)
The project can be used directly as a typical C++ Chaste project or else as a Python package (with some extra dependencies). First, Chaste dependencies need to be built from source following the [wiki:InstallGuides/InstallGuide]. The project only supports the development version of Chaste. This can be obtained by doing:
using subversion. The project code itself can be obtained by doing:
The Angiogenesis project code needs to be included in the main Chaste source. This can be done with a symbolic link:
The C++ libraries can be built using either the standard Chaste Scons build system (see [wiki:ChasteGuides/DeveloperBuildGuide]) or the new [wiki:ChasteGuides/CmakeBuildGuide] (preffered). For CMake, first create a build directory outside the source tree and proceed as:
The will build the C++ library and all tests. To avoid building tests do:
as the final command.
A conda Python package for Linux is currently under development. In the meantime this package needs to be built from source as a PyChaste module. First, build PyChaste following the instructions [wiki:PaperTutorials/PyChaste]. Then, follow the above C++ instructions to build the Angiogenesis project, but with the additional CMake flag `-DBUILD_ANGIOGENESIS_PYTHON=ON`. The final steps should look like:
The Python package `angiogenesis` will be in `$BUILD_DIR` under `Chaste/projects/Angiogenesis/python`. The finished package should be copied into the `chaste/projects` module of PyChaste.
The source and test code are in the `src` and `test` folders respectively. Unit tests can be built and run using the Chaste CMake framework [wiki:ChasteGuides/CmakeBuildGuide]. It is recommended that the [wiki:PaperTutorials/Angiogenesis/BuildVesselNetwork] are followed. To run the first tutorial do:
To run all C++ tests and tutorials do:
The Python source and tests are in the `src/python` and `test/python` folders. The [wiki:PaperTutorials/Angiogenesis/PythonBuildVesselNetwork] should be followed next.
To run the Python tutorial do:
To run all Python tests do:
A full list of tutorials is given at the bottom of this page.