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Software used for "Spot-On: robust model-based analysis of single-particle tracking experiments"

Anders Sejr Hansen; Maxime Woringer; Jonathan B Grimm; Luke D Lavis; Robert Tjian; Xavier Darzacq


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.835171", 
  "author": [
    {
      "family": "Anders Sejr Hansen"
    }, 
    {
      "family": "Maxime Woringer"
    }, 
    {
      "family": "Jonathan B Grimm"
    }, 
    {
      "family": "Luke D Lavis"
    }, 
    {
      "family": "Robert Tjian"
    }, 
    {
      "family": "Xavier Darzacq"
    }
  ], 
  "issued": {
    "date-parts": [
      [
        2017, 
        7, 
        26
      ]
    ]
  }, 
  "abstract": "<p><strong>Introduction</strong></p>\n\n<p>This deposit contains the softwares used in the paper: \"Spot-On: robust model-based analysis of single-particle tracking experiments\". These scripts should enable a user to reproduce the full simulations and analyses performed in the paper. Some of the softwares are hosted elsewhere, and we only reference to them in this description.</p>\n\n<p><strong>In this folder</strong></p>\n\n<ul>\n\t<li><em>170718_simSPT_simulations.zip</em> : contains the code to generate the confined motion simulation, including a comprehensive README detailing all the parameters used for the simulation. A more updated version of the software to perform simulations (called <em>simSPT</em>) is available on Gitlab: https://gitlab.com/tjian-darzacq-lab/simSPT and the exact version used for the simulations is version 1.0: https://gitlab.com/tjian-darzacq-lab/simSPT/tags/v1.0</li>\n\t<li><em>MSDi_code.zip</em> : contains the code to analyze the simulated trajectories using a procedure derived from single-trajectory MSD fitting. This code derives from <em>MSDanalyzer</em> (https://tinevez.github.io/msdanalyzer/), where a fitting of the distribution of the histogram of the fitted coefficients has been added.</li>\n\t<li><em>vbSPT_comparison.zip</em> : contains the code to analyze the simulated trajectories using the <em>vbSPT</em> software (http://vbspt.sourceforge.net/). Additional scripts take care of the generation of a set of instruction files that automate the analysis of the simulated dataset, and come with a comprehensive README file.</li>\n</ul>\n\n<p><strong>Online repositories</strong></p>\n\n<p>Some tools we used are not included in this folder, because they have their own, well-maintained online repositories. This is the case for <em>Spot-On</em> (all Matlab, web and Python versions) and <em>simSPT</em>, that can be accessed through the following links:</p>\n\n<ul>\n\t<li>https://gitlab.com/tjian-darzacq-lab/Spot-On</li>\n\t<li>https://gitlab.com/tjian-darzacq-lab/spot-on-matlab</li>\n\t<li>https://gitlab.com/tjian-darzacq-lab/Spot-On-cli</li>\n</ul>\n\n<p><strong>About the LICENSE</strong></p>\n\n<p>All the code uploaded below is Open-Source, but might have a different license than the CC-BY specified by Zenodo. This is because Zenodo does not seem to allow to specify licenses such as the GNU/GPL.</p>", 
  "title": "Software used for \"Spot-On: robust model-based analysis of single-particle tracking experiments\"", 
  "type": "article", 
  "id": "835171"
}
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