This readme.txt file was generated on 20190820 by Bijram

GENERAL INFORMATION

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 R01HG006851

SHARING/ACCESS INFORMATION

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/ZVCG0M25.
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

DATA & FILE OVERVIEW

analysis_codes
│ ├── ad_statistic_calc.m
│ ├── analysis_1.m
│ ├── cramervonmises_statistic_calc.m
│ ├── plot_distribution.m
│ └── rmse_calc.m

├── 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


├── 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*

├── 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)

FILESPECIFIC INFORMATION

 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 nth node
 raw_data/*/*/weights(n).0.dat contains the weights corresponding to the above spans for the simulations by the nth 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