TOPAS-nBio v2.0

This is the new official full TOPAS-nBio release v2.0 (Oct. 2022)!

TOPAS-nBio is described here: https://topas-nbio.readthedocs.io/. This page includes a class documentation and the license.

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. Additional manuscripts describing the code can be found on the documentation website and within the examples.

We encourage contribution of user-developed extensions that fit within the TOPAS-nBio scheme.
Please continue to test the code.

If you want to add your own code of have edits to the current code, please commit them here.

General information
TOPAS-nBio runs with TOPAS 3.8 and newer versions.
Featured updates:
Geometry:
- New geometries added
- DNA has been updated
- Hi-C geometry for nucleus available
- new cell + nanoparticle + organelles provided by Marc Hahn
Scoring:
- New scoring system
- New method to score indirect damage to bases
Chemistry:
- IRT has been included
- Additional scorers for G-values were added
Biology:
- DaMaRiS has been fully integrated.

This release includes several fixes and improvements.

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

TOPAS-nBio v1.0

This is the first official full TOPAS-nBio release!

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.
Please continue to test the code.

If you want to add your own code of have edits to the current code, please commit them here.

General information

Pre-requisites:

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

TOPAS-nBio v1.0-beta.1

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• TOPAS-nBio v1.0-beta.1

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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

Pre-requisites:

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

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

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

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

Unzip the Geant4Headers.zip

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

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

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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• Note:

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This is the first beta release of TOPAS-nBio.
Users are encouraged to try out the code. Please report any issues back to the developers on the TOPAS-nBio section of the forum:
https://groups.google.com/forum/#!forum/topas-nbio-users