TOPAS-nBio

This is the TOPAS-nBio extension repository, a Monte Carlo simulation framework for (sub-) cellular radiobiology.

The current version 2.0 is a legacy version. A new version will be released within this month and be based on OpenTOPAS: https://opentopas.github.io/index.html

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/index.html. The OpenTOPAS documentation can be also found there.

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.

General information

0. Pre-requisites:

   TOPAS installed with recommended OS system, c++ and cmake versions, see the OpenTOPAS website.

1. We recommend having a global directory for extensions named topas_extension and move in TOPAS-nBio there

   Linux: mkdir ~/topas_extensions

   Mac: mkdir /Applications/topas_extensions

2. Unzip TOPAS-nBio directory in topas_extensions and navigate to the topas directory

   Linux: cd ~/topas Mac: cd /Applications/topas

3. Unzip the Geant4Headers.zip

   Linux: unzip -e Geant4Headers.zip Mac: unzip -e Geant4Headers.zip

4. Build the extensions

   Linux: cmake ./ -DTOPAS_EXTENSIONS_DIR=~/topas_extensions/TOPAS-nBio make -j4 Mac: cmake ./ -DTOPAS_EXTENSIONS_DIR=/Applications/topas_extensions/TOPAS-nBio make -j4

5. 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