RBE Scorer extensions for OpenTOPAS

• David Hall. First commit 07/2017.
• Jan Schuemann. Major revision 11/2019.
• Jose Ramos-Mendez. Update to OpenTOPAS v4.0/Geant4 v11.1.3 05/2024

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Installation.

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/

Debian

Follow installation for Debian/Ubuntu procedures after and including step 8.4. Then:

$ cd $HOME/Applications/

Clone the repository:

$ git clone https://github.com/OpenTOPAS/OpenTOPAS-RBE.git

Return to the topas-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/OpenTOPAS-RBE

Build:

$ make -j8 install

MacOS

Follow installation for MacOS procedures after and including step 7.4. Then:

$ cd /Applications

Clone the repository:

$ git clone https://github.com/OpenTOPAS/OpenTOPAS-RBE.git

Return to the topas-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/OpenTOPAS-RBE

Build:

$ make -j8 install

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Implementation of the models and corresponding references can be found at:

📚 Polster, et al., "Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endopoints" doi:10.1088/0031-9155/60/13/5053

Full documentation is found at

📚 https://OpenTOPAS.readthedocs.io/en/latest

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These extension scorers require OpenTOPAS version 4.0 or later.

The directory consists of the following file types: Scorers:

. TsScoreDose* : These score quantities in the ProcessHits function like normal scorers.

RBE Scorers: These do not have a ProcessHits function and instead combine scored properties (dose, LET, etc) to RBE or biological dose, etc.

. TsV*: Base classes for the scorers

Additionally, the example directory contains an example experiment irradiation (experiment.txt) scoring each of the available RBE scorers (rbe_scorers.txt) for V79 cells (CellLineV79.txt). V79 cells are used because they are one of the most studied cells and biological parameters for all models were available.

The simulations can be run with "topas run.txt" and analyzed with the provided python script. Before running examples/run.txt make sure that the directory results/ exists in the examples/ directory, otherwise, create it with:

cd OpenTOPAS-RBE/examples/ mkdir results/

In order to change the experimental setup edit experiment.txt_.

In order to change the cell line, provide a new cell line file and change

sv:Sc/CellLines = 1 "CellLineV79"

in run.txt.

run.txt also controls the Prescribed dose used to calculate RBE and the output quantity. The output quantities available depend on the RBE model.

RBE scorers are defined in rbe_scorers.txt and can be edited there. Typically, we recommend not to run too many scorers at once as that increases memory use. In particular, the two parameters:

`ReferencedSubScorer_Dose`

and

`ReferencedSubScorer_LET`

should be set if a dose and LET scorer already exists, otherwise each RBE scorer will create scorers for all properties it needs, potentially resulting in multiple parallel dose scorers.