This readme.txt file was generated on 2019-08-20 by Bijram 

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GENERAL INFORMATION
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Title of Dataset:

    Matlab code supporting: Simulations corroborate telegraph model predictions for the extension distributions of nanochannel confined DNA

Author Information (Name, Institution, Address, Email)

    Bhandari, Aditya Bikram
    Dorfman, Kevin D. (dorfman@umn.edu)


Funding information:
    Sponsorship: NIH R01-HG006851

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SHARING/ACCESS INFORMATION
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License:

    CC0 1.0 Universal

Recommended citation for the data:

Suggested Citation

    Bhandari, Aditya Bikram; Dorfman, Kevin D.. (2019). Simulations corroborate telegraph model predictions for the extension distributions of nanochannel confined DNA. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/ZVCG-0M25. 

Referenced by

    Bhandari, A. B., & Dorfman, K. D. (2019). Simulations corroborate telegraph model predictions for the extension distributions of nanochannel confined DNA. Biomicrofluidics, 13(4), 044110. https://doi.org/10.1063/1.5109566 

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DATA & FILE OVERVIEW
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analysis_codes
│   ├── ad_statistic_calc.m
│   ├── analysis_1.m
│   ├── cramervonmises_statistic_calc.m
│   ├── plot_distribution.m
│   └── rmse_calc.m
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├── figures
│   ├── fig(n).eps corresponds to Figure n in https://doi.org/10.1063/1.5109566
│   ├── SI/fig(n).eps corresponds to the probability distribution functions for case n in the Supplementary Material for https://doi.org/10.1063/1.5109566
│   ├── SIfig(n)c.eps corresponds to the cumulative distribution functions for case n in the Supplementary Material for https://doi.org/10.1063/1.5109566    
│   ├── distribution.opj is the Origin file for making the figures
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├── processed_data
│   ├── asymptotic: 
|   |       *data processed in the form of histogram points as well as individual values*
│   ├── error
│   │       *data processed in the form of histogram points as well as individual values*
│   ├── non_asymptotic
|   |       *data processed in the form of histogram points as well as individual values*
|   |
│   └── results.xlsx
|           *results spreadsheet with final results*
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├── raw_data
│   ├── asymptotic
│   │       *raw data files from simulations of extensions and weights*
|   |
│   ├── data_key.xlsx
|   |       *excel file to match the file numbers to the parameters*
|   |
│   └── error
|          *raw data files from simulations of extensions and weights*
|  
└── readme.txt



Analysis Code Usage

    1) analysis_1.m is used to create the x_values, x_hist and y_hist files in the processed_data folder from the raw simulation data in raw_data
    2) plot_distribution.m is used to create the x_theory and y_theory files in the processed_data folder for the same parameters used in the simulations
    3) ad_statistic.m, cramervonmises_statistic.m and rmse_calc.m are used to get the results for the statistical tests in Figure 7 of https://doi.org/10.1063/1.5109566

Analysis Code Dependencies

    The code was run on MATLAB_R2017a
    Plots were made using Origin (figures/distribution.opj file)



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FILE-SPECIFIC INFORMATION 
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- figures/distribution.opj is the Origin file containing the data points and plots for all of the figures reported
- raw_data/*/*/spans(n).0.dat contains the chain extensions for the simulations by the n-th node
- raw_data/*/*/weights(n).0.dat contains the weights corresponding to the above spans for the simulations by the n-th node
- raw_data/*/*/lp0 contains information about the input parameters for the simulations
- processed_data/*/x_values*.txt contains the individual values of extension from the simulations accounting for the weights
- processed_data/*/x_hist*.txt contains the x bins for the simulated distributions
- processed_data/*/y_hist*.txt contains the frequencies for the simulated distributions
- processed_data/*/x_theory*.txt contains the x bins for the theoretical distributions
- processed_data/*/y_theory*.txt contains the frequencies for the theoretical distributions