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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 carmen.villagrasa@irsn.fr
0015
0016 # Introduction
0017
0018 “dsbandrepair” is a Geant4-DNA simulation chain for evaluating the early radiation-induced DNA damage.
0019 The first development of the simulation chain was carried out by Meylan et al. in 2017 (Sci. Rep. 2017 7:11923)
0020 The "extended/medical/dna/dnadamage1" example is a simplified version of "dsbanrepair"
0021
0022 “dsbandrepair” supports all types of DNA geometries constructed with DNAFabric (Comput. Phys. Comm. 2016 204:159-169).
0023 Geometries for human cell nuclei (fibroblast, endothelium) and yeast were provided along with the release of “dsbandrepair”.
0024 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.
0025 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).
0026
0027 Physical stage and chemical stage allow the calculation of direct and indirect Strand Breaks in the whole nucleus.
0028
0029 Furthermore, the Two Lesion Kinetic model (Radiat. Res. 2001 156:365-378) and the Local Effect Model IV (Radiat. Res. 2013 180:524-538) were also included to allow users calculate the survival fraction and un-rejoined DSBs.
0030 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.
0031
0032
0033 # How to build and run
0034
0035 To build dsbandrepair, in the terminal, use:
0036 * shell$ mkdir build
0037 * shell$ cd build
0038 * shell$ cmake /path-to/dsbandrepair
0039 (Or if users don't want to download geometry files while compiling the dsbandrepair, use: cmake -DDOWNLOAD_GEOMETRY=FALSE /path-to/dsbandrepair )
0040 * shell$ make (or 'make -jN' with N = 1,2,3 .... )
0041
0042 And to run:
0043 * shell$ ./dsbandrepair dsbandrepair.in
0044
0045 where dsbandrepair.in is a macrofile. User can change it to his/her own macrofile.
0046
0047 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 :
0048 * shell$ rm -rf chem_ouput
0049 * shell$ ./dsbandrepair chem.in chem
0050
0051 where chem.in is a macrofile. User can change it to his/her own macrofile.
0052
0053 ## Running with mpi library
0054
0055 To improve the simulation in term of computational time, user can run dsbandrepair with mpi library.
0056
0057 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.
0058
0059 To compile the "dsbandrepair" with g4mpi:
0060 * shell$ mkdir build
0061 * shell$ cd build
0062 * shell$ cmake -DUSE_MPI=TRUE -DG4mpi_DIR=<g4mpi-path>/lib[64]/G4mpi-V.m.n /path-to/dsbandrepair
0063 * shell$ make (or 'make -jN' with N = 1,2,3 .... )
0064 And to run:
0065 * shell$ mpiexec -np $nranks ./dsbandrepair dsbandrepair.in
0066
0067 where $nranks is the number of mpi processes you want to run.
0068
0069 Or ro run chemical stage:
0070
0071 * shell$ rm -rf chem_ouput
0072 * shell$ mpiexec -np $nranks ./dsbandrepair chem.in chem
0073
0074 # Analyzing results
0075 To run "analysis" module, in the "build" directory, build this module with the commands:
0076 * shell$ mkdir analysis
0077 * cd analysis
0078 * cmake /path/to/analysis
0079 * make
0080 * cd ../
0081
0082 At this point, user can launch the analysis module:
0083 * shell$ ./analysis/runAna
0084 or
0085 * shell$ ./analysis/runAna macrofile
0086
0087 where the macro file allows user to interact with the code.
0088 Example: ./analysis/runAna analysis.in
0089
0090 ## Outputs
0091 By default, the output of "Analysis" module will be written in 4 different text files:
0092 * SB results: this text file contains all SB results, such as total SB, direct and indirect SBs, SSB and DSB.
0093 * SDD format: All damages are written in SDD format (Radiat. Res. 2019 191:11). File name starts with "SDD_"
0094 * TLK result: File name starts with "TLK_". This file contains results from TLK model.
0095 * LEM-IV result: File name starts with "LEMIV_". This file contains results from LEMIV model.
0096
0097 # Maro files:
0098 Some macro files are provided along with this code, user can change them based on their own needs.
0099
0100 * macro files for physical stage:
0101 * dsbansrepair.in : This macro is for a light geometry for testing the code
0102 * fibroblast.in: This macro is for fibroblast cell nucleus.
0103 * endophys.in: This macro is for endothelium cell nucleus.
0104 * yeastphys.in: This macro is for yeast cell nucleus.
0105 * macro files for chem stage:
0106 * chem.in
0107 * macro files for analysis module:
0108 * analysis.in: allows user to set parameter for scoring, classifying damages and setting repair models parameters.
0109
0110 # An alternative example for DNA damage calculation can be found in examples/extended/medical/dna/moleculardna
0111
0112 # Acknowledgments
0113 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)
