Anders Sejr Hansen
Maxime Woringer
Jonathan B Grimm
Luke D Lavis
Robert Tjian
Xavier Darzacq
2017-07-26
<p><strong>Introduction</strong></p>
<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>
<p><strong>In this folder</strong></p>
<ul>
<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>
<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>
<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>
</ul>
<p><strong>Online repositories</strong></p>
<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>
<ul>
<li>https://gitlab.com/tjian-darzacq-lab/Spot-On</li>
<li>https://gitlab.com/tjian-darzacq-lab/spot-on-matlab</li>
<li>https://gitlab.com/tjian-darzacq-lab/Spot-On-cli</li>
</ul>
<p><strong>About the LICENSE</strong></p>
<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>
https://doi.org/10.5281/zenodo.835171
oai:zenodo.org:835171
Zenodo
https://doi.org/10.5281/zenodo.835541
https://doi.org/10.5281/zenodo.834787
https://doi.org/10.5281/zenodo.835170
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Software used for "Spot-On: robust model-based analysis of single-particle tracking experiments"
info:eu-repo/semantics/other