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Open Source Science

https://github.com/ashleefv/surgicalmenopausebone

https://github.com/ashleefv/surgicalmenopausebone

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: ashleefv
  • License: bsd-3-clause
  • Language: MATLAB
  • Default Branch: master
  • Size: 1.17 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 2
Created 10 months ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

SurgicalMenopauseBone

DOI

Analysis scripts for paper "Mathematical Modeling of Bone Remodeling in Surgical Menopause"

Authors

Primary code editors: Anna C. Nelson(1), Edwina Yeo(2), Ashlee N. Ford Versypt (3) - (1) Department of Mathematics & Statistics, University of New Mexico, Albuquerque, NM, USA - (2) Department of Mathematics, University College London, London, United Kingdom - (3) Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA

Full author list: A. C. Nelson, E. F. Yeo, Y. Zhang, C. V. Cook, S. Fischer-Holzhausen, L. Keeler Bruce, P. Dutta, S. Gholami, B. J. Smith, and A. N. Ford Versypt

Overview

To run all analysis and create all figures evaluate main.m. This repositiory contains an ODE based model which simulates the dynamics of bone cells in the BMU and predits BMD density over time.

Data import files

  • Spine_data.m: contains surgical and natural menopause data from humans studies of spinal BMD
  • readinparameters.m reads model parameters2 and sets plotting parameters
  • params.txt: read in by readinparameters.m

Functions

  • getinitialcondition.m: solves model at steady state and returns normalisation values for each cells species
  • solve_model.m: solves model returning cell species and BMD percentage over time.
  • activation.m & repression.m are hill functions
  • estrogen.m returns either relative natural or surgical estrogen concs over time.
  • oderhs.m is the ODE function passed to solvemodel.m
  • RHSofequations.m generates the RHS of the equations to pass to oderhs and getinitial_condition

Analysis scripts

  • Refit-bone-params.m: re-estimates bone parameters using wide natural menopause dataset
  • Fitnewparams.m: estimates parameters for new effects using surgical menopause datasets.
  • main.m: runs all analysis and creates figures.

Plotting scripts:

  • Figure1.m and Figure3.m generate paper figures.

Owner

  • Name: Ashlee Ford Versypt
  • Login: ashleefv
  • Kind: user
  • Location: Buffalo, NY
  • Company: University at Buffalo, The State University of New York

GitHub Events

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  • Fork event: 1
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Last Year
  • Member event: 2
  • Push event: 10
  • Fork event: 1
  • Create event: 2