murefi

This package provides useful data structures and mapping objects for mu​lti-re​plicate fi​tting, mainly of ordinary differential euqation (ODE) models. To see implementation examples & excercises, you can go to notebooks/.

Installation

murefi is released on PyPI:

pip install murefi

Documentation

Read the package documentation here.

Usage and Citing

murefi is licensed under the GNU Affero General Public License v3.0.

When using murefi in your work, please cite the Helleckes & Osthege et al. (2022) paper and the corresponding software version.

Note that the paper is a shared first co-authorship, which can be indicated by ¹ in the bibliography.

@article{calibr8Paper,
  doi       = {10.1371/journal.pcbi.1009223},
  author    = {Helleckes$^1$, Laura Marie and
               Osthege$^1$, Michael and
               Wiechert, Wolfgang and
               {von Lieres}, Eric and
               Oldiges, Marco},
  journal   = {PLOS Computational Biology},
  publisher = {Public Library of Science},
  title     = {Bayesian and calibration, process modeling and uncertainty quantification in biotechnology},
  year      = {2022},
  month     = {03},
  volume    = {18},
  url       = {https://doi.org/10.1371/journal.pcbi.1009223},
  pages     = {1-46},
  number    = {3}
}
@software{murefi,
  author       = {Michael Osthege and
                  Laura Helleckes},
  title        = {JuBiotech/murefi: v5.1.0},
  month        = feb,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v5.1.0},
  doi          = {10.5281/zenodo.6006488},
  url          = {https://doi.org/10.5281/zenodo.6006488}
}

Head over to Zenodo to generate a BibTeX citation for the latest release.