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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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  <identifier identifierType="DOI">10.5281/zenodo.835171</identifier>
  <creators>
    <creator>
      <creatorName>Anders Sejr Hansen</creatorName>
      <affiliation>Howard Hughes Medical Institute, Berkeley, CA 94720, USA  and Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Maxime Woringer</creatorName>
      <affiliation>Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA and Unité Imagerie et Modélisation, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France and Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, 75252 Paris cedex 05, France and Centre National de la Recherche Scientifique (CNRS), UMR 3691, Paris, France and Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), USR 3756, Institut Pasteur et CNRS, Paris, France</affiliation>
    </creator>
    <creator>
      <creatorName>Jonathan B Grimm</creatorName>
      <affiliation>Janelia Research Campus, Howard Hughes Medical Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Luke D Lavis</creatorName>
      <affiliation>Janelia Research Campus, Howard Hughes Medical Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Robert Tjian</creatorName>
      <affiliation>Howard Hughes Medical Institute, Berkeley, CA 94720, USA  and Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Xavier Darzacq</creatorName>
      <affiliation>Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Software used for "Spot-On: robust model-based analysis of single-particle tracking experiments"</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2017</publicationYear>
  <dates>
    <date dateType="Issued">2017-07-26</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/835171</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="Compiles">10.5281/zenodo.835541</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="Compiles">10.5281/zenodo.834787</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.835170</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Introduction&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;In this folder&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&lt;em&gt;170718_simSPT_simulations.zip&lt;/em&gt; : 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 &lt;em&gt;simSPT&lt;/em&gt;) 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&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MSDi_code.zip&lt;/em&gt; : contains the code to analyze the simulated trajectories using a procedure derived from single-trajectory MSD fitting. This code derives from &lt;em&gt;MSDanalyzer&lt;/em&gt; (https://tinevez.github.io/msdanalyzer/), where a fitting of the distribution of the histogram of the fitted coefficients has been added.&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;vbSPT_comparison.zip&lt;/em&gt; : contains the code to analyze the simulated trajectories using the &lt;em&gt;vbSPT&lt;/em&gt; 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.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;Online repositories&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Some tools we used are not included in this folder, because they have their own, well-maintained online repositories. This is the case for &lt;em&gt;Spot-On&lt;/em&gt; (all Matlab, web and Python versions) and &lt;em&gt;simSPT&lt;/em&gt;, that can be accessed through the following links:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;https://gitlab.com/tjian-darzacq-lab/Spot-On&lt;/li&gt;
	&lt;li&gt;https://gitlab.com/tjian-darzacq-lab/spot-on-matlab&lt;/li&gt;
	&lt;li&gt;https://gitlab.com/tjian-darzacq-lab/Spot-On-cli&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;About the LICENSE&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;</description>
  </descriptions>
</resource>
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