Welcome to the documentation of the Standard for DNA Damage (SDD) data format!

Note

The manuscrtipt detailing the SDD standard that should be cited when using or referring to the SDD can be found at:

Schuemann, J., McNamara, A. L., Warmenhoven, J. W., Henthorn, N. T., Kirkby, K. J., Merchant, M. J., et al. (2019). A New Standard DNA Damage (SDD) Data Format. Radiation Research, 191(1), 76. http://doi.org/10.1667/rr15209.1

Getting Started

Introduction to SDD

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A standard way of describing DNA damage!

The Standard for DNA Damage (SDD)

The SDD is an international collaborative effort to standardise the reporting of DNA damage from computational simulations. The file format consists of both a header, detailing the parameters of the simulation, and a data section, detailing the DNA damage (see Figure 1). The format has been designed to encompass the broad range of DNA damage simulations carried out by research groups in the field. The format can be used minimally, with many fields being optional, or, as we would recommend, fully with as many fields filled in as the simulation can account for. Whilst at the point of the SDD paper publication a large proportion of simulation parameters and damage recordings have been accounted for if further requirements of the standard become apparent the format is expandable to accommodate. In order to keep the format intact and to avoid ambiguity, if you would like to submit a change to the format you can do so via the Contribute to the SDD page.

For all manuals that use the SDD, we would appreciate referencing the definition paper: “A New Standard DNA Damage (SDD) Data Format”, J. Schuemann et al., Radiation Research, (in print).

The tables and figures on this website are reproduced (with permission) from the above paper.

_images/Figure1.png

Motivation

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Creating SDD files

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The SDD file

The SDD header

Field by field summary of header
Field Value Notes Type
1 SDD version Version number of SDD definition String (e.g. SDDv1.0)
2 Software Program name, version and access link if any String (Free text)
3 Author Corresponding author, date, references String (Free text)
4 Simulation details Description of details of simulation settings and parameters String (Free text)
5 Source Description of source properties String (Free text)
6 Source Type Monoenergetic, distribution, phase space, GCR, … Int
7 Incident particles Definition of primary incident irradiation particle(s) in PDG code format Int(s)
8 Mean Particle Energy Mean incident energy for each particle in MeV Float(s)
9 Energy Distribution Fully energy distribution specification String(s) + Floats
10 Particle fraction Fraction of fluence of each particle in field Float(s)
11 Dose or fluence Define dose of fluence in each exposure, or note that the simulation was for a single track Int + Float (+ Float)
12 Dose Rate Dose rate of irradiation field Float
13 Irradiation Target Description of simulated cell of target (DNA) region and microenviroment String (Free text)
14 Volumes Shape parameter plus X,Y,Z extents (µm) 2x (Int + 6 Float)
15 Chromosome sizes Number and base pair size of chromosomes Int + (Int) Floats
16 DNA Density Density of base pairs in volume (MBP/µm^3) Float
17 Cell Cycle Phase Cell cycle phase index and progression Int + Float
18 DNA structure Additional field to define DNA structure 2 Ints
19 In vitro / in vivo Experimental condition Int
20 Proliferation status Proliferative or quiescent and status details Int + String (Free text)
21 Microenviroment Temperature (°C) and molar O_2 concentration 2 Float
22 Damage definition Define how types of damage were determined 1 Float + 1 Int + 1 Bool + 2 Float
23 Time Time point at which damages were recorded Float
24 Damage and primary count Number of distant damage lesions scored & primaries simulated 2 Int
25 Data Entries Number of fields included in the data section 14 Bool
26 Additional Information Field of additional information that may be relevant String (Free text)
27 ***EndOfHeader*** Empty field to mark end of header.  

The SDD data section

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Parsing SDD files

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Description of parsing SDD files with python

Placeholder for adding code blocks

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import sdd_parser
fp = filepath.sdd
ds = sdd_parser(fp)
print(ds)

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Example SDD files

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These examples for structural purposes only.

Proton 0.975 MeV 1 Gy - Minimal

Minimal SDD File

Proton 0.975 MeV 1 Gy - Full

Full SDD File

Citation and References

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Please use the SDD main paper when referencing the SDD:

Schuemann, J., McNamara, A. L., Warmenhoven, J. W., Henthorn, N. T., Kirkby, K. J., Merchant, M. J., et al. (2019). A New Standard DNA Damage (SDD) Data Format. Radiation Research, 191(1), 76. http://doi.org/10.1667/rr15209.1

The following papers used the SDD standard:

If you have referenced the SDD paper and used the standard, please let us know and we will add your paper here.

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The SDD Collaboration

Members of the SDD Collaboration

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Founding members for the SDD
Member Primary Institution
  1. Schuemann
 Massachusetts General Hospital & Harvard Medical School (USA)
A.L. McNamara Massachusetts General Hospital & Harvard Medical School (USA)
J.W. Warmenhoven The University of Manchester (UK)
N.T. Henthorn The University of Manchester (UK)
  1. Kirkby
 The University of Manchester (UK)
M.J. Merchant The University of Manchester (UK)
  1. Ingram
 The University of Manchester (UK)
  1. Paganetti
 Massachusetts General Hospital & Harvard Medical School (USA)
KD. Held Massachusetts General Hospital & Harvard Medical School (USA)
  1. Ramos-Mendez
 University of California San Francisco (USA)
  1. Faddegon
 University of California San Francisco (USA)
  1. Perl
 SLAC National Accelerator Laboratory (USA)
D.T. Goodhead Medical Research Council (UK)
  1. Plante
 KBRwyle (USA)
  1. Rabus
 Physikalisch-Technische Bundesanstalt (GER)
  1. Nettelbeck
 Physikalisch-Technische Bundesanstalt (GER)
  1. Friedland
 European Radiation Dosimetry Group e.V. (GER)
  1. Kundrát
 German Research Center for Environmental Health (GER)
  1. Ottolenghi
 University of Pavia (I)
  1. Baiocco
 University of Pavia (I)
  1. Barbieri
 University of Pavia (I)
  1. Dingfelder
 East Carolina University (USA)
  1. Incerti
 CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (FR)
  1. Villagrasa
 Institut de Radioprotection et Sûreté Nucléaire (FR)
  1. Bueno
 Institut de Radioprotection et Sûreté Nucléaire (FR)
M.A. Berna State University of Campinas (Brazil)
  1. Guatelli
 University of Wollongong (AUS)
  1. Sakata
 University of Wollongong (AUS)
J.M.C. Brown Delft University of Technology (NL)
  1. Francis
 Saint Joseph University (Lebanon)
  1. Kyriakou
 University of Ioannina Medical School (GR)
  1. Lampe
 CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (FR)
  1. Ballarini
 University of Pavia (I)
M.P. Carante University of Pavia (I)
  1. Davídková
 Nuclear Physics Institute of the CAS (Czech Republic)
  1. Štěpán
 Nuclear Physics Institute of the CAS (Czech Republic)
  1. Jia
 University of Texas Southwestern Medical Center (USA)
F.A. Cucinotta University of Nevada Las Vegas (USA)
  1. Schulte
 Loma Linda University (USA)
R.D. Stewart University of Washington (USA)
D.J. Carlson Yale University School of Medicine (USA)
  1. Galer
 National Physical Laboratory (UK)
  1. Kuncic
 University of Sydney (AUS)
  1. Lacombe
 University Paris-Saclay (FR)
  1. Milligan
  
S.H. Cho The University of Texas MD Anderson Cancer Center (USA)
  1. Sawakuchi
 The University of Texas MD Anderson Cancer Center (USA)
  1. Inaniwa
 National Institute of Radiological Sciences (JPN)
  1. Sato
 Japan Atomic Energy Agency (JPN)
  1. Li
 German Research Center for Environmental Health (GER)
A.V. Solov’yov MBN Research Center (GER)
  1. Surdutovich
 Oakland University (USA)
  1. Durante
 GSI Helmholtzzentrum fuer Schwerionenforschung (GER)
  1. Prise
 Queens University Belfast (UK)
S.J. McMahon Queens University Belfast (UK)

Mission Statement

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Join the SDD User List

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Contribute to the SDD

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To Re-phrase: The SDD data format anticipates that with increasing use cases, numbering schemes will need to be expanded to define additional details or options in some fields. In order to keep the numbering scheme unique and continue to allow users to share their SDD files without ambiguity, we recommend that requests for new numbering schemes are submitted to the SDD collaboration (represented by the authors of this manuscript, headed by the groups at Massachusetts General Hospital / Harvard Medical School, University of Manchester and Queen’s University Belfast). Each new specification for fields in the header or data block will be assigned a specified number and documentation about all fields will be provided and updated.

… Include template email: …

Indices and tables

Note

This website will continue to be updated. We anticipate an option to actively contribute to the efforts to update the standard to include new features as necessary. If you are interested in contributing, please join the SDD user list (see link on the left).