notch-delta-coupling

Source code for "Coupling dynamics of 2D Notch-Delta signalling", by Francisco Berkemeier and Karen M. Page

https://github.com/fberkemeier/notch-delta-coupling

Science Score: 54.0%

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Keywords

cell-biology cell-signalling drosophila-melanogaster epithelial-tissue filopodia linear-stability-analysis notch-delta notch-signaling

Last synced: 6 months ago · JSON representation ·

Repository

Source code for "Coupling dynamics of 2D Notch-Delta signalling", by Francisco Berkemeier and Karen M. Page

Basic Info

Host: GitHub
Owner: fberkemeier
License: mit
Language: Mathematica
Default Branch: main
Homepage:
Size: 62.7 MB

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Topics

cell-biology cell-signalling drosophila-melanogaster epithelial-tissue filopodia linear-stability-analysis notch-delta notch-signaling

Created about 3 years ago · Last pushed 12 months ago

Metadata Files

Readme License Citation

Notch-Delta signalling in a 2D epithelium

This code was partially developed to support the simulations presented in the paper Coupling dynamics of 2D Notch-Delta signalling, by Francisco Berkemeier¹ and Karen M. Page². For any questions regarding the code, please contact fp409@cam.ac.uk. All rights reserved.

Interactive Epithelium (IEp, version 1.0.0) aims to provide a practical tool for testing parameter robustness while simulating the dynamics of the Notch-Delta signalling pathway in an epithelium.

In order to correctly reproduce the simulations presented in the preprint, we suggest using Interactive Epithelium (IEp) in parallel with the 'MainCode.nb' notebook, since some of the plots are only achievable after data storage from simulations in IEp. When needed, a message in light blue will prompt the user to run a specific model in IEp, which needs to be loaded first. In order to load models in IEp, simply load the text files in \InteractiveEpithelium\Models corresponding to the different figures ('Model[Figure_label].txt').

For accurate performance, we recommend running each code section in the order that they are presented in 'MainCode.nb'. Figures that did not require any computation are not shown here. Note that some results are averaged over multiple simulations.

To run IEp open the notebook 'iEpithelium v1.0.0.nb' with Mathematica and scroll down to the 'iEpithelium' cell (in green). Evaluate this cell (Shift+Enter) and the remaining cells will be evaluated (click 'Yes' on the popup window). IEp was developed in Mathematica 13.0.1, so it is recommended that the same version is used.

¹Department of Pathology, University of Cambridge, UK. Contact: fp409@cam.ac.uk
²Department of Mathematics and IPLS, University College London, UK. Contact: karen.page@ucl.ac.uk

Owner

Name: Francisco Berkemeier
Login: fberkemeier
Kind: user
Location: Cambridge
Company: University of Cambridge

Website: www.franciscoberkemeier.com
Twitter: fpberkemeier
Repositories: 1
Profile: https://github.com/fberkemeier

Postdoctoral Researcher @ University of Cambridge, currently working in the Department of Pathology on DNA replication modelling

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Interactive Epithelium
message: >-
  A Mathematica tool for hybrid Notch-Delta
  epithelial signalling and mechanical simulations
type: software
authors:
  - given-names: Francisco
    family-names: Berkemeier
    email: fp409@cam.ac.uk
    affiliation: >-
      Department of Pathology, University of
      Cambridge
    orcid: 'https://orcid.org/0000-0001-9850-3666'
repository-code: >-
  https://github.com/fberkemeier/Notch-Delta-Coupling.git
abstract: >-
  We introduce a new Mathematica-based software that
  enables modelling and simulations of hybrid
  intercellular signalling and mechanical properties
  of two-dimensional epithelial tissues. The code
  combines different mathematical models and
  simulation techniques to accurately reproduce the
  dynamics of these tissues in a variety of contexts.
  This approach allows for a more comprehensive
  understanding of the complex interactions between
  cells and the signalling pathways that drive tissue
  differentiation. Overall, the development of this
  software represents a significant advance in the
  field of tissue modelling and simulation, and it
  has the potential to greatly facilitate the study
  of epithelial tissue behaviour, for
  Mathematica-driven researchers.
keywords:
  - Notch
  - Notch-delta signalling
  - Mathematica
  - Protrusions
  - Long-range signalling
  - Pattern formation
  - Drosophila melanogaster
license: CC-BY-NC-4.0
version: 1.0.0
date-released: '2022-12-27'

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