Use cases

Note

Feel free to suggest links to Jupyter notebooks made with the CoLoMoTo Docker distribution (supplementary information of papers, tutorials, etc.).

See also

See also our Zenodo Community - and please submit your colomoto-related zenodo record there!

• Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial. The tutorial specifically focuses on the analysis of a previously published model of the regulatory network controlling mammalian cell proliferation by Sizek et al, 2019.
  

• UpPMaBoSS notebook for the cell fate model. This Jupyter notebook implements all the analyses presented in the UpPMaBoSS: a tool for dynamic cell population modeling manuscript by Stoll et al.
  

• Immune fate and Treg to Th17 reprogramming
  

• Executable paper showing combination of GINsim, bioLQM, MaBoSS, and Pint
  

• A reproducibility study using colomoto-docker. This Jupyter notebook reproduces the results from Gupta et al. (2018) using the different tools provided by the colomoto-docker and performs dynamical simulation and analysis of an extended version of the published model.