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TOPAS-nBio extension repository, for documentation and license see: https://topas-nbio.readthedocs.io/

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TOPAS-nBio

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 TOPAS (TOol for PArticle Simulations), which can be obtained from www.topasmc.org. The TOPAS documentation can be found at https://topas.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.

General information

  1. Pre-requisites:

    TOPAS installed with recommended OS system, c++ and cmake versions, see topas https://topas.readthedocs.io/en/latest/getting-started/install.htm

  2. 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

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

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

  4. Unzip the Geant4Headers.zip

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

  5. 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

  6. 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

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TOPAS-nBio extension repository, for documentation and license see: https://topas-nbio.readthedocs.io/

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