cathytangjing / simulation-of-dna-damage-using-improved-dbscan Goto Github PK

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          Simulation of DNA damage using improved DBSCAN
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Jing Tang(a) and Qinfeng Xiao(b)
(a) Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data,
North University of China.

(b) School of Computer and Information Technology,
Beijing Jiaotong University

This is a new example and it may contain bugs. If you find a bug, please contact:
 [email protected] and [email protected]

---->0. INTRODUCTION.

This work presents an improved version of the algorithm “Density-Based Spatial
Clustering of Applications with Noise” (DBSCAN) using a KD-Tree approach to find
neighbors of each point for calculating clustered DNA damage.

This example is based on the work described in ()
and Comput Meth Prog Bio.101(2011) 265-267

Any report or published results obtained using the Geant4-DNA software shall
cite the following Geant4-DNA collaboration publications:
Phys. Med. 31 (2015) 861-874
Med. Phys. 37 (2010) 4692-4708

 1 - GEOMETRY DEFINITION

    The world volume is a simple box which represents a 'pseudo infinite'
    homogeneous medium.

    The target volume is an ellipsoid of half-axes of 9.85, 7.1 and 2.5 µm
    which represents a fibroblast cell nucleus.

    Two parameters define the geometry :
    - the material of the volume -- for Geant4-DNA it has to be water.
    - the full size of the volume.

    The default geometry is constructed in DetectorConstruction class.

 2 - PHYSICS LIST

    PhysicsList is Geant4 modular physics list using G4EmDNAPhysics &
    G4EmDNAChemistry constructors.

 3 - ACTION INITALIZATION

    The class ActionInitialization instantiates and registers
    to Geant4 kernel all user action classes.

    While in sequential mode the action classes are instantiated just once,
    via invoking the method:
    ActionInitialization::Build()
    in multi-threading mode the same method is invoked for each thread worker
    and so all user action classes are defined thread-local.

    A run action class is instantiated both thread-local
    and global that's why its instance is created also in the method:
    ActionInitialization::BuildForMaster()
    which is invoked only in multi-threading mode.

 4 - AN EVENT: THE PRIMARY GENERATOR

    The primary particle emission position is randomly and homogeneously
    distributed on the surface of the ellipsoidal nucleus. The type of the
    particle and its energy are set in the  PrimaryGeneratorAction class,
    and can be changed via the G4 build-in commands of G4ParticleGun class.
    The chemistry module is triggered in the StackingAction class when all
    physical tracks have been processed.

 5 - STACKING ACTION

     StackingAction::NewStage is called when a stack of tracks has been processed
     (for more details, look at the Geant4 documentation).
     A verification on whether physical tracks remain to be processed is done.
     If no tracks remain to be processed, the chemical module is then triggered.

 6 - VISUALISATION

    The visualization manager is set via the G4VisExecutive class
    in the main() function in chem5.cc.
    The initialisation of the drawing is done via a set of /vis/ commands
    in the macro vis.mac. To activate the visualization mode run:
     ./clustering -gui

 7 - OUTPUT
    The output results containing for each event:
    - the yield of single strand break
    - the yield of complex single strand break
    - the yield of double strand break
    - the yield of double strand break plus
    - the yield of double strand break plus plus
    - the ratio of single strand break and double strand break
    - the cluster size distribution
    - the energy deposit in the Target
    - the absorbed dose in the Target