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virtualcolon

Spatiotemporal modelling of metabolic interactions in a computational colonic environment

https://github.com/maringos/virtualcolon

Science Score: 57.0%

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Repository

Spatiotemporal modelling of metabolic interactions in a computational colonic environment

Basic Info
  • Host: GitHub
  • Owner: maringos
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 51.8 KB
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Metadata Files
Readme License Citation

README.md

Virtual Colon

Spatiotemporal modelling of metabolic interactions in a computational colonic environment

This repository contains the source and input files needed to run the Virtual Colon.

  • The Mono-colonalisation.R file simulates mono-colonisation experiments with context-specific colonic cells and bacterial ones.

  • The SIHUMIx.R file simulates context-specific colonic cells with the SIHUMIx minimal model microbiome.

It requires the following software / R packages: 1. R 2. sybil 3. BacArena 4. cplexAPI

The gplkAPI would theoritically suffice instead of cplexAPI. However, it is not tested and may lead to significant increase of computational time.

Example of usage

You can try our code with the example datasets. To this end, you have to choose the required models from the file simulations_sequence.RDS by selecting the respective row.

For instance, please use the command Rscript SIHUMIx.R $nodes in the command line, where $nodes is the number of the selected row in simulations_sequence.RDS.

References and acknowlegments

This research was supported in part through high-performance computing resources available at the Kiel University Computing Centre. See our manuscript for a full list of other work cited.

  1. Eugen Bauer, Johannes Zimmermann, et al., BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities, doi:10.1371/journal.pcbi.1005544
  2. R Core Team. R: A Language and Environment for Statistical Computing [Internet]. Vienna, Austria: R Foundation for Statistical Computing; Available from: https://www.R-project.org/
  3. Gelius-Dietrich G, Desouki AA, et al., sybil – Efficient constraint-based modelling in R. BMC Syst Biol. 2013 Dec;7(1):125.
  4. Becker N., Kunath J., et al., Human intestinal microbiota: Characterization of a simplified and stable gnotobiotic rat model. Gut Microbes 2, 25–33 (2011).
  5. Geva-Zatorsky N., Sefik E., et al.,Mining the Human Gut Microbiota for Immunomodulatory Organism, Cell. 2017 Feb 23;168(5):928-943.e11

Citation

Georgios Marinos, Johannes Zimmermann, Jan Taubenheim, and Christoph Kaleta, Virtual Colon: Spatiotemporal modelling of metabolic interactions in a computational colonic environment, 2024, www.doi.org/10.1101/2024.06.11.598488

*shared first authorship with an interchangeable order

GNU General Public License version 3.0 (GPLv3) is applied to all copyrightable parts of this software.

Contact details: https://www.iem.uni-kiel.de/de/medizinische-systembiologie/medizinische-systembiologie

Owner

  • Name: Georgios Marinos
  • Login: maringos
  • Kind: user
  • Location: Kiel, Germany
  • Company: UKSH - Kiel University

Postdoctoral researcher in the field of Systems Biology

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Marinos"
  given-names: "Georgios"
  orcid: "https://orcid.org/0000-0002-6443-7696"
- family-names: "Zimmermann"
  given-names: "Johannes"
  orcid: "https://orcid.org/0000-0002-5041-1954"
- family-names: "Taubenheim"
  given-names: "Jan"
  orcid: "https://orcid.org/0000-0001-7283-1768"
- family-names: "Kaleta"
  given-names: "Christoph"
  orcid: "https://orcid.org/0000-0001-8004-9514"
title: "Virtual Colon: Spatiotemporal modelling of metabolic interactions in a computational colonic environment"
doi: 10.1101/2024.06.11.598488 
url: "https://github.com/maringos/VirtualColon/"

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