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CADET-Core 5.0

CADET-Core 5.0: High-Performance Solver for Advanced Biotechnology Process Modeling - Published in JOSS (2025)

https://github.com/cadet/cadet-core

Science Score: 100.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 19 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    7 of 19 committers (36.8%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

cadet chromatography chromatography-analysis general-rate-model simulator

Scientific Fields

Mathematics Computer Science - 40% confidence
Last synced: 4 months ago · JSON representation ·

Repository

The heart of CADET. A modular, fast, and accurate modeling and simulation framework for biotechnology processes.

Basic Info
  • Host: GitHub
  • Owner: cadet
  • License: gpl-3.0
  • Language: C++
  • Default Branch: master
  • Homepage:
  • Size: 64 MB
Statistics
  • Stars: 76
  • Watchers: 13
  • Forks: 36
  • Open Issues: 130
  • Releases: 25
Topics
cadet chromatography chromatography-analysis general-rate-model simulator
Created almost 12 years ago · Last pushed 4 months ago
Metadata Files
Readme Contributing License Code of conduct Citation Security Authors Zenodo Cla

README.rst 

CADET-Core
==========

.. image:: https://img.shields.io/github/release/cadet/cadet-core.svg
   :target: https://github.com/cadet/cadet-core/releases

.. image:: https://github.com/cadet/cadet-core/actions/workflows/ci.yml/badge.svg?branch=master
   :target: https://github.com/cadet/cadet-core/actions/workflows/ci.yml?query=branch%3Amaster

.. image:: https://joss.theoj.org/papers/282a9ec56a0680e51ed4f1fa8fda3650/status.svg
   :target: https://joss.theoj.org/papers/282a9ec56a0680e51ed4f1fa8fda3650

.. image:: https://anaconda.org/conda-forge/cadet/badges/downloads.svg
   :target: https://anaconda.org/conda-forge/cadet

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8179015.svg
   :target: https://doi.org/10.5281/zenodo.8179015

.. image:: https://img.shields.io/badge/JuRSE_Code_Pick-Oct_2024-blue.svg
   :target: https://www.fz-juelich.de/en/rse/community-initiatives/jurse-code-of-the-month/october-2024

- **Website (including documentation):** https://cadet.github.io
- **Forum:** https://forum.cadet-web.de
- **Source:** https://github.com/cadet/cadet-core
- **Bug reports:** https://github.com/cadet/cadet-core/issues
- **Demo:** https://www.cadet-web.de 
- **Newsletter:** https://cadet-web.de/newsletter/

Installation
------------
CADET-Core can be installed via conda from the ``conda-forge`` channel.

``conda install -c conda-forge cadet``

This requires a working `conda installation `_.

`Additional information `_ and a `tutorial `_ are available to guide you through the installation and the first steps of using CADET.

Citing
------------
The development of CADET-Core has been a collaborative effort, with multiple dedicated individuals contributing their expertise to create a powerful and versatile open-source software tool.
Countless hours of hard work have been invested to provide the scientific community with a valuable resource.
As an open-source project, CADET-Core relies on the support and recognition from users and researchers to thrive.
Therefore, we kindly ask that any publications or projects leveraging the capabilities of CADET-Core acknowledge its creators and their contributions by citing an adequate selection of our publications.

**General:**

- Leweke, S.; Breuer, J.; Schmölder, J.; Jäpel, R.; Lanzrath, H.; Rao, J.; Hassan, J.; Zhang, W.; Berger, A.; Heymann, W.; von Lieres, E.: `CADET-Core 5.0: High-Performance Solver for Advanced Biotechnology Process Modeling `_, Journal of Open Source Software **10** (2025), 7881.

- Leweke, S.; von Lieres, E.: `Chromatography Analysis and Design Toolkit (CADET) `_, Computers and Chemical Engineering **113** (2018), 274–294.

- von Lieres, E.; Andersson, J.: `A fast and accurate solver for the general rate model of column liquid chromatography `_, Computers and Chemical Engineering **34,8** (2010), 1180–1191.

**Major extensions:**

- Breuer, J. M.; Leweke, S.; Schmölder, J.; Gassner, G.; von Lieres, E.: `Spatial discontinuous Galerkin spectral element method for a family of chromatography models in CADET `_, Computers and Chemical Engineering **177** (2023), 108340.

- Zhang, W.; Przybycien T., Breuer J. M. , Leweke S. , von Lieres E.: `Solving crystallization/precipitation population balance models in CADET, part II: Size-based Smoluchowski coagulation and fragmentation equations in batch and continuous modes `_, Computers and Chemical Engineering **192** (2025), 108860.

- Zhang, W.; Przybycien T., Schmölder J. , Leweke S. , von Lieres E.: `Solving crystallization/precipitation population balance models in CADET, part I: Nucleation growth and growth rate dispersion in batch and continuous modes on nonuniform grids `_, Computers and Chemical Engineering **183** (2024), 108612.

- Püttmann, A.; Schnittert, S.; Naumann, U.; von Lieres, E.: `Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography `_, Computers and Chemical Engineering **56** (2013), 46–57.

Additionally, to ensure reproducibility of your work, we recommend citing the zenodo doi corresponding to the specific CADET-Core release that you used.

For a comprehensive list and guidance on citing CADET-Core publications, please refer to the publications section of the `documentation `_.

Ongoing Development
-------------------

We do our best to provide you with a stable API. However, CADET-Core is actively developed and breaking changes can sometimes be unavoidable. For non-developers, it is recommended to upgrade from release to release instead of always working with the most recent commit.

Bugs
----

Please report any bugs that you find `here `_. Or, even better, fork the repository on `GitHub `_ and create a pull request (PR) with the fix. 

Donations
---------

`Donations `_ for helping to host, maintain, and further develop the CADET-Core project are highly appreciated.


Copyright and License Notice
----------------------------

Copyright (C) 2008-present: The CADET-Core Authors (see `AUTHORS.md `_).

This program is free software: you can redistribute it and/or modify it under the terms of the
GNU General Public License as published by the Free Software Foundation, either version 3 of
the License, or (at your option) any later version (see `LICENSE.txt `_).

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program, see below.
If not, see .

Except as contained in this notice, the name of a copyright holder shall not be used in advertising
or otherwise to promote the sale, use, or other dealings in this Software without prior written
authorization of the copyright holder.


Acknowledgments
---------------

Please refer to the `list of contributors `_ who helped building and funding this project.

Owner

  • Name: CADET
  • Login: cadet
  • Kind: organization
  • Email: cadet@fz-juelich.de

JOSS Publication

CADET-Core 5.0: High-Performance Solver for Advanced Biotechnology Process Modeling
Published
July 03, 2025
DOI
Volume 10, Issue 111, Page 7881
Authors
Samuel Leweke ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany
Jan Breuer ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany
Johannes Schmölder ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany
Ronald Jäpel ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany
Hannah Lanzrath ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany, RWTH Aachen University, Computational Systems Biotechnology, Aachen, 52074, Germany
Jayghosh Rao ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany
Jazib Hassan ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany
Wendi Zhang ORCID
Rensselaer Polytechnic Institute, Department of Chemical and Biological Engineering, Troy, 12180, New York, United States of America
Antonia Berger ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany, RWTH Aachen University, Computational Systems Biotechnology, Aachen, 52074, Germany
William Heymann ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany
Eric von Lieres ORCID
Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany, RWTH Aachen University, Computational Systems Biotechnology, Aachen, 52074, Germany
Editor
Jed Brown ORCID
Tags
Modeling Simulation Chromatography Biotechnology CADET
View PDF Review Thread Software Archive

Citation (CITATION.bib) 

% As an open-source project, CADET relies on the support and recognition from users and researchers to thrive.
% Therefore, we kindly ask that any publications or projects leveraging the capabilities of CADET acknowledge its creators and their contributions by citing an adequate selection of our publications.

% General:

@article{Leweke2025,
doi = {10.21105/joss.07881},
url = {https://doi.org/10.21105/joss.07881},
year = {2025},
publisher = {The Open Journal},
volume = {10},
number = {111},
pages = {7881},
author = {Samuel Leweke and Jan Breuer and Johannes Schmölder and Ronald Jäpel and Hannah Lanzrath and Jayghosh Rao and Jazib Hassan and Wendi Zhang and Antonia Berger and William Heymann and Eric von Lieres},
title = {CADET-Core 5.0: High-Performance Solver for Advanced Biotechnology Process Modeling},
journal = {Journal of Open Source Software}
}

@article{Leweke2018CADET,
title = {Chromatography Analysis and Design Toolkit (CADET)},
year = {2018},
author = {Leweke, Samuel and von Lieres, Eric},
doi = {10.1016/j.compchemeng.2018.02.025},
journal = {Computers & Chemical Engineering},
volume = {113},
pages = {274-294},
issn = {0098-1354},
keywords = {Column liquid chromatography, General rate model, Modeling and simulation platform, Model calibration, Process analysis and design, Statistical analysis, Experimental design},
abstract = {CADET is an open source modeling and simulation framework for column liquid chromatography. The software is freely distributed to both academia and industry under the GPL license (http://github.com/modsim/cadet). CADET is based on a core simulator that is written in object oriented C++ and applies modern mathematical algorithms for efficiently solving a variety of customary chromatography models. This simulation engine is interfaced to a suite of MATLAB tools for setting up and executing the most common scientific workflows, e.g., model calibration, process design, robustness analysis, statistical analysis, and experimental design. The model library and numerical methods are continuously extended and improved. For instance, binding models with multiple bound states, pH and/or temperature dependence of binding parameters, surface diffusion, and arbitrary spacing of the radial discretization have been recently added. Moreover, numerical accuracy and computational speed of the code are comprehensively benchmarked using high precision reference solutions and realistic model problems. Versatility of the CADET modeling platform is demonstrated with several examples that are also published as open source code and can be freely adapted to specific use cases. In one of several case studies, sequential and simultaneous optimization of elution gradient shape and cut times are compared for a three component separation. This process is designed to achieve Pareto optimal purity and yield of the central fraction. Moreover, the robustness of these designs with respect to typical process variations is systematically studied. The last case study illustrates the optimal design of experiments for estimating model parameters with maximal accuracy.}
}

@article{VonLieres2010a,
title = {{A fast and accurate solver for the general rate model of column liquid chromatography}},
year = {2010},
author = {von Lieres, Eric and Andersson, Joel},
doi = {10.1016/j.compchemeng.2010.03.008},
journal = {Computers {\&} Chemical Engineering},
issn = {00981354},
month = aug,
number = {8},
pages = {1180--1191},
volume = {34},
}

% DG discretization of transport models:

@article{Breuer2023,
title = {Spatial discontinuous Galerkin spectral element method for a family of chromatography models in CADET},
year = {2023},
author = {Jan Michael Breuer and Samuel Leweke and Johannes Schmölder and Gregor Gassner and Eric {von Lieres}},
doi = {10.1016/j.compchemeng.2023.108340},
journal = {Computers \& Chemical Engineering},
volume = {177},
pages = {108340},
issn = {0098-1354},
}

% Crystallization:

@article{Zhang2025,
title = {Solving crystallization/precipitation population balance models in CADET, Part II: Size-based Smoluchowski coagulation and fragmentation equations in batch and continuous modes},
year = {2025},
author = {Wendi Zhang and Todd Przybycien and Jan Michael Breuer and Eric {von Lieres}},
doi = {https://doi.org/10.1016/j.compchemeng.2024.108860},
journal = {Computers & Chemical Engineering},
volume = {192},
pages = {108860},
issn = {0098-1354}
}

@article{Zhang2024,
title = {Solving crystallization/precipitation population balance models in CADET, part I: Nucleation growth and growth rate dispersion in batch and continuous modes on nonuniform grids},
year = {2024},
author = {Zhang, Wendi and Przybycien, Todd and Schmölder, Johannes and Leweke, Samuel and von Lieres, Eric},
doi = {10.1016/j.compchemeng.2024.108612},
journal = {Computers \& Chemical Engineering},
pages = {108612},
publisher = {Elsevier},
}

% Parameter sensitivities and Algorithmic Differentiation

@article{Puttmann2013,
title = {{Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography}},
year = {2013},
author = {Püttmann, Andreas and Schnittert, Sebastian and Naumann, Uwe and von Lieres, Eric},
doi = {10.1016/j.compchemeng.2013.04.021},
journal = {Computers {\&} Chemical Engineering},
issn = {00981354},
month = sep,
pages = {46--57},
volume = {56},
}

@article{Puttmann2016,
title = {{Utilizing algorithmic differentiation to efficiently compute chromatograms and parameter sensitivities}},
year = {2016},
author = {Püttmann, Andreas and Schnittert, Sebastian and Leweke, Samuel and von Lieres, Eric},
doi = {10.1016/j.ces.2015.08.050},
journal = {Chemical Engineering Science},
issn = {00092509},
month = jan,
volume = {139},
pages = {152--162},
}

GitHub Events

Total
  • Create event: 79
  • Commit comment event: 1
  • Release event: 5
  • Issues event: 92
  • Watch event: 22
  • Delete event: 72
  • Issue comment event: 178
  • Push event: 774
  • Pull request review comment event: 80
  • Pull request review event: 126
  • Pull request event: 165
  • Fork event: 10
Last Year
  • Create event: 79
  • Commit comment event: 1
  • Release event: 5
  • Issues event: 92
  • Watch event: 22
  • Delete event: 73
  • Issue comment event: 178
  • Push event: 774
  • Pull request review comment event: 80
  • Pull request review event: 126
  • Pull request event: 166
  • Fork event: 10

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 867
  • Total Committers: 19
  • Avg Commits per committer: 45.632
  • Development Distribution Score (DDS): 0.336
Past Year
  • Commits: 173
  • Committers: 11
  • Avg Commits per committer: 15.727
  • Development Distribution Score (DDS): 0.399
Top Committers
Name Email Commits
Samuel Leweke s****e@f****e 576
Jan Breuer j****r@g****e 113
Johannes Schmölder j****r@f****e 54
Samuel Leweke s****e@b****m 27
Ronald Jäpel r****l@g****m 24
Eric von Lieres e****s@f****e 15
Lanzrath, Hannah h****h@f****e 14
Jayghosh Rao j****r@g****m 11
Jazib Hassan 6****h 7
Antonia Berger 1****r 5
Flynn Zhang z****3@g****m 5
r.jaepel r****l@f****e 3
Geoffrey Oxberry g****y@g****m 3
William Heymann i****n@g****m 3
franzperdido f****o 2
ronald.jaepel r****l@i****e 2
Florian Hülsmann fh@c****e 1
Jonathan Rocher j****r@k****m 1
Salah Azzouzi s****i@f****e 1
Committer Domains (Top 20 + Academic)
fz-juelich.de: 6 kbibiopharma.com: 1 cbix.de: 1 ime.fraunhofer.de: 1 bayer.com: 1 gmx.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 127
  • Total pull requests: 212
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 15
  • Total pull request authors: 16
  • Average comments per issue: 0.52
  • Average comments per pull request: 1.27
  • Merged pull requests: 148
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 73
  • Pull requests: 157
  • Average time to close issues: 29 days
  • Average time to close pull requests: 8 days
  • Issue authors: 11
  • Pull request authors: 13
  • Average comments per issue: 0.27
  • Average comments per pull request: 0.96
  • Merged pull requests: 112
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jbreue16 (41)
  • schmoelder (22)
  • AntoniaBerger (17)
  • sleweke (15)
  • ronald-jaepel (11)
  • hannahlanzrath (9)
  • goxberry (3)
  • spdavern (2)
  • avasyanin (1)
  • freeware-superman (1)
  • vwkoppejan (1)
  • bdice (1)
  • Yuvraj2710 (1)
  • MoritzImendoerffer (1)
  • Immudzen (1)
Pull Request Authors
  • jbreue16 (101)
  • ronald-jaepel (24)
  • AntoniaBerger (24)
  • schmoelder (17)
  • hannahlanzrath (12)
  • goxberry (6)
  • WFlynnZ (6)
  • sleweke (5)
  • sleweke-bayer (4)
  • cbix (4)
  • lieres (3)
  • daklauss (2)
  • Daniel-H2 (1)
  • freeware-superman (1)
  • Kats1247 (1)
Top Labels
Issue Labels
enhancement (17) feature request (16) bug (16) maintenance (16) dev-call (13) documentation (12) interface (9) test (9) numerics (7) reaction model (5) meta-issue (5) good first issue (5) binding model (3) unit operation model (3) system model (1) help wanted (1) duplicate (1)
Pull Request Labels
maintenance (54) documentation (53) test (23) bug (22) feature request (16) enhancement (13) interface (12) unit operation model (12) reaction model (11) dev-call (10) binding model (9) numerics (6) good first issue (2) duplicate (1)

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
conda-forge.org: cadet

CADET-Core is an open-source software platform offering powerful tools for comprehensive modeling and simulation of biotechnology processes, powered by state-of-the-art numerical algorithms. CADET-Core supports unit operations such as chromatography, filtration, and crystallization, along with auxiliary components such as hold tanks, tubes, valves, and detectors. These elements can be interconnected to form complex networks, supporting closed-loop feedback and flexible structures.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 24.4%
Forks count: 38.0%
Average: 39.7%
Stargazers count: 44.7%
Dependent packages count: 51.6%
Last synced: 4 months ago

Dependencies

doc/requirements.txt pypi
  • Sphinx *
  • sphinx-sitemap *
  • sphinx_multiversion *
  • sphinxcontrib-bibtex *