DOI: 10.5061/dryad.69p8cz958
title: Mathematical model results for: Dynamic fibronectin assembly and remodeling by leader neural crest cells prevents jamming in collective cell migration

description: Collective cell migration plays an essential role in vertebrate
 development, yet the extent to which dynamically changing
 microenvironments influence this phenomenon remains unclear. Observations
 of the distribution of the extracellular matrix (ECM) component
 fibronectin during the migration of loosely connected neural crest cells
 (NCCs) lead us to hypothesize that NCC remodeling of an initially punctate
 ECM creates a scaffold for trailing cells, enabling them to form robust
 and coherent stream patterns. We evaluate this idea in a theoretical
 setting by developing an agent-based model that incorporates reciprocal
 interactions between NCCs and their ECM. ECM remodeling, haptotaxis,
 contact guidance, and cell-cell repulsion are sufficient for cells to
 establish streams in silico, however additional mechanisms, such as
 chemotaxis, are required to consistently guide cells along the correct
 target corridor. Further investigations of the model imply that contact
 guidance and differential cell-cell repulsion between leader and follower
 cells are key contributors to robust collective cell migration by
 preventing stream breakage. Global sensitivity analysis and simulated
 underexpression/overexpression experiments suggest that long-distance
 migration without jamming is most likely to occur when leading cells
 specialize in creating ECM fibers, and trailing cells specialize in
 responding to environmental cues by upregulating mechanisms such as
 contact guidance. This dataset contains summary statistics, movies,
 parameter values, and photos obtained from individual realizations of the
 mathematical model.
description: Data was generated by running multiple simulations of the
 agent-based model described in the article. The model was implemented in
 C++, using the PhysiCell library (http://physicell.org).
 Post-processing of the data (e.g., creation of animations and photos of
 individual simulations) was accomplished by using PhysiCell-supplied
 Python scripts, as well as user-created Matlab scripts. The corresponding
 code can be found at the following Github repository: XXXXXX. 
   Statistical analysis of the data was
 also performed in Matlab, using codes that were inspired by older
 implementations originally developed by Marino et al. (http://malthus.micro.med.umich.edu/lab/usadata/).   Violin plots were generated using open-source code available at the following Github repository: https://github.com/bastibe/Violinplot-Matlab.
description: Tar.gz files need to be decompressed in order to view specific
 files.    Matlab is required
 to view any MAT and FIG files. An open source alternative to Matlab is
 Octave (https://octave.org). CSV
 files spreadsheets can be opened by Microsoft Excel or by open source
 alternatives such as Google Sheets, LibreOffice, Numbers (for Apple
 products only), etc. DOC/DOCX files may be viewed in Microsoft word or in
 LibreOffice. Any PDF viewer such as Adobe Acrobat Reader, or Preview for
 Mac, can be used to view any PDF/PNG files.
   SVG files can be opened in any web
 browser (Chrome, Safari, Firefox, etc.). 
   MP4 files can be viewed by any video
 player software, such as Quicktime Player (https://support.apple.com/downloads/quicktime).   Code in XML files can be opened by most programming applications. These can include Microsoft Visual Studio or open-source alternatives such as Atom (https://atom.io).