This is the TOPAS-nBio extension repository, a Monte Carlo simulation framework for (sub-) cellular radiobiology.
TOPAS-nBio is described here: https://topas-nbio.readthedocs.io/. This page includes a class documentation and the license.
TOPAS-nBio is an extension of OpenTOPAS (TOol for PArticle Simulations), which can be obtained from https://OpenTOPAS.github.io. The TOPAS documentation can be found at https://opentopas.readthedocs.io/.
The TOPAS-nBio package was described in Schuemann et al., Radiation Research, 2019, 191(2), p.125. This reference should be cited for all work using the TOPAS-nBio package.
We encourage contribution of user-developed extensions that fit within the TOPAS-nBio scheme. If you would like to contribute code, please contact the developers.
Note
The main difference in installing for Debian/Ubuntu and MacOS is the installation paths.
Tip
Users can install multiple extensions by either:
-
Copy all the Extension directories into a common global directory, or
-
Using the
\;between directory paths e.g., (and see below):-DTOPAS_EXTENSIONS_DIR=/MyProject1Extensions/\;/MyProject2Extensions/
Follow installation for Debian/Ubuntu procedures after and including step 8.4. Then:
$ cd $HOME/Applications/
Clone the repository:
$ git clone https://github.com/topas-nbio/TOPAS-nBio.git
Return to the OpenTopas-build directory:
$ cd $HOME/Applications/TOPAS/OpenTOPAS-build
Repeat cmake command by including the TOPAS_EXTENSIONS_DIR variable as follows (don't miss the -D):
$ cmake ../OpenTOPAS -DCMAKE_INSTALL_PREFIX=../OpenTOPAS-install -DTOPAS_EXTENSIONS_DIR=$HOME/Applications/TOPAS-nBio
Build:
$ make -j8 install
Follow installation for MacOS procedures after and including step 7.4. Then:
$ cd /Applications
Clone the repository:
$ git clone https://github.com/topas-nbio/TOPAS-nBio.git
Return to the OpenTopas-build directory:
$ cd /Applications/TOPAS/OpenTOPAS-build
Repeat cmake command by including the TOPAS_EXTENSIONS_DIR variable as follows (don't miss the -D):
$ cmake ../OpenTOPAS -DCMAKE_INSTALL_PREFIX=../OpenTOPAS-install -DTOPAS_EXTENSIONS_DIR=/Applications/TOPAS-nBio
Build:
$ make -j8 install
Run the demos. For some demos, a pause before quit is enabled, then, write exit at the terminal prompt.
Linux:
$ source rundemos.csh
Mac:
$ source rundemos.csh