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0001
0002 ================================================================================================
0003 Geant4 - an Object-Oriented Toolkit for Simulation in HEP
0004 ================================================================================================
0005
0006 dsbandrepair
0007 ---------
0008
0009 **A Geant4-DNA application for simulating early DNA damage**
0010
0011 # AUTHORS
0012 L. T. Anh, Y. Perrot, C. Villagrasa, S. Meylan, H. N. Tran
0013
0014 contact: yann.perrot@irsn.fr or le.tuan.anh@vinatom.gov.vn
0015
0016 # REFERENCE
0017
0018 Please cite:
0019 Anh et al., Physica Medica 124 (2024) 103422, https://doi.org/10.1016/j.ejmp.2024.103422
0020
0021 # Introduction
0022
0023 “dsbandrepair” is a Geant4-DNA simulation chain for evaluating the early radiation-induced DNA damage.
0024 The first development of the simulation chain was carried out by Meylan et al. in 2017 (Sci. Rep. 2017 7:11923)
0025 The "extended/medical/dna/dnadamage1" example is a simplified version of "dsbanrepair"
0026
0027 “dsbandrepair” supports all types of DNA geometries constructed with DNAFabric (Comput. Phys. Comm. 2016 204:159-169).
0028 Geometries for human cell nuclei (fibroblast, endothelium) and yeast were provided along with the release of “dsbandrepair”.
0029 Users can use a free version of DNAFabric (https://bitbucket.org/sylMeylan/opendnafabric/src/master/) to create customed geometries. Or they can contact Y. Perrot for specific geometries.
0030 The geometric models are constructed from 10 voxels to form a continuous chromatin fiber for each chromosme including heterochromatin (VoxelStraight, VoxelRight,...) and euchromatin (VoxelStraight2, VoxelRight2,...) distribution (Med. Phys. 2019 46:1501-1511).
0031
0032 Physical stage and chemical stage allow the calculation of direct and indirect Strand Breaks in the whole nucleus.
0033
0034 Furthermore, repair models were added in the analysis part:
0035
0036 - The Two Lesion Kinetic model developed by Stewart (Radiat. Res. 2001 156:365-378) provides a method to link DSBs (subdivided into simple and complex DSBs) with cell death. It suggests that DSB repair depends on the severity of the lesion. It includes non-saturable first and second order repair processes. DNA fragments associated with DSBs can interact with each other in paors and form lethal or non-lethal chromosomal aberrations.
0037
0038 - The Local Effect Model IV from Tommasino et al (Radiat. Res. 2013 180:524-538) was included to calculate the fraction of un-rejoined DSBs.
0039 It is based on the spatial distribution of DSBs by looking at the number of DSBs present in 2 Mbp chromatin loops.
0040 DSBs in the loops are consideres as "isolated DSB" or "cluster of DSBs". the fraction of unrepaired DSBs is calculated by a two-phase exponential decay.
0041
0042 - The Belov's model (J. Theo. Biol. 2015 366:115-130) for double-strand breaks repair is provided but has not been compared to experimental data.
0043
0044
0045 # How to build and run
0046
0047 To build dsbandrepair, in the terminal, use:
0048 * shell$ mkdir build
0049 * shell$ cd build
0050 * shell$ cmake /path-to/dsbandrepair
0051 (Or if users don't want to download geometry files while compiling the dsbandrepair, use: cmake -DDOWNLOAD_GEOMETRY=FALSE /path-to/dsbandrepair )
0052 * shell$ make (or 'make -jN' with N = 1,2,3 .... )
0053
0054 And to run:
0055 * shell$ ./dsbandrepair dsbandrepair.in
0056
0057 where dsbandrepair.in is a macrofile. User can change it to his/her own macrofile.
0058
0059 Note that: dsbandrepair was designed in a modular way that offers users to run physical stage chemcal stage independently. By default, dsbandrepair runs in physical stage mode. To run chemical stage, use :
0060 * shell$ rm -rf chem_ouput
0061 * shell$ ./dsbandrepair chem.in chem
0062
0063 where chem.in is a macrofile. User can change it to his/her own macrofile.
0064
0065 ## Running with mpi library
0066
0067 To improve the simulation in term of computational time, user can run dsbandrepair with mpi library.
0068
0069 MPI interface: Thanks to the work of K. Murakami and A. Dotti (DOI: https://doi.org/10.1109/NSSMIC.2015.7581867), an MPI interface was introduced into Geant4 and it’s now used in this work (see "/examples/extended/parallel/MPI"). User has to follow this example to install g4mpi library.
0070
0071 To compile the "dsbandrepair" with g4mpi:
0072 * shell$ mkdir build
0073 * shell$ cd build
0074 * shell$ cmake -DUSE_MPI=TRUE -DG4mpi_DIR=<g4mpi-path>/lib[64]/G4mpi-V.m.n /path-to/dsbandrepair
0075 * shell$ make (or 'make -jN' with N = 1,2,3 .... )
0076 And to run:
0077 * shell$ mpiexec -np $nranks ./dsbandrepair dsbandrepair.in
0078
0079 where $nranks is the number of mpi processes you want to run.
0080
0081 Or ro run chemical stage:
0082
0083 * shell$ rm -rf chem_ouput
0084 * shell$ mpiexec -np $nranks ./dsbandrepair chem.in chem
0085
0086 # Analyzing results
0087 To run "analysis" module, in the "build" directory, build this module with the commands:
0088 * shell$ mkdir analysis
0089 * cd analysis
0090 * cmake /path/to/analysis
0091 * make
0092 * cd ../
0093
0094 At this point, user can launch the analysis module:
0095 * shell$ ./analysis/runAna
0096 or
0097 * shell$ ./analysis/runAna macrofile
0098
0099 where the macro file allows user to interact with the code.
0100 Example: ./analysis/runAna analysis.in
0101
0102 ## Outputs
0103 By default, the output of "Analysis" module will be written in 4 different text files:
0104 * SB results: this text file contains all SB results, such as total SB, direct and indirect SBs, SSB and DSB.
0105 * SDD format: All damages are written in SDD format (Radiat. Res. 2019 191:11). File name starts with "SDD_"
0106 * TLK result: File name starts with "TLK_". This file contains results from TLK model.
0107 * LEM-IV result: File name starts with "LEMIV_". This file contains results from LEMIV model.
0108
0109 # Maro files:
0110 Some macro files are provided along with this code, user can change them based on their own needs.
0111
0112 * macro files for physical stage:
0113 * dsbansrepair.in : This macro is for a light geometry for testing the code
0114 * fibroblast.in: This macro is for fibroblast cell nucleus.
0115 * endophys.in: This macro is for endothelium cell nucleus.
0116 * yeastphys.in: This macro is for yeast cell nucleus.
0117 * macro files for chem stage:
0118 * chem.in
0119 * macro files for analysis module:
0120 * analysis.in: allows user to set parameter for scoring, classifying damages and setting repair models parameters.
0121
0122 # An alternative example for DNA damage calculation can be found in examples/extended/medical/dna/moleculardna
0123
0124 # Acknowledgments
0125 The transition from the initial simulation chain of Meylan et al. to a version adapted for a Geant4 example benefited from funds from the BioRad3 project financed by the ESA (grant DAR 4000132935/21/NL/CRS)
