This package provides useful data structures and mapping objects for multi-replicate fitting, mainly of ordinary differential euqation (ODE) models. To see implementation examples & excercises, you can go to notebooks/.
murefi is released on PyPI:
pip install murefi
Read the package documentation here.
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.