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bioreactordesign

Bio Reactor Design (BiRD): a toolbox to simulate and analyze different designs of bioreactors in OpenFOAM

https://github.com/nrel/bioreactordesign

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org
  • ○
    Committers with academic emails
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary

Keywords

bioreactor inverse-modelling meshing openfoam postprocessing
Last synced: 6 months ago · JSON representation

Repository

Bio Reactor Design (BiRD): a toolbox to simulate and analyze different designs of bioreactors in OpenFOAM

Basic Info
Statistics
  • Stars: 27
  • Watchers: 8
  • Forks: 13
  • Open Issues: 10
  • Releases: 2
Topics
bioreactor inverse-modelling meshing openfoam postprocessing
Created almost 3 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

Bio Reactor Design (BiRD) bird-CI bird-pyversion bird-pypi

Quick start

  1. Follow the steps to install the python package (see Installation of python package for developers or Installation of python package for users below)
  2. Follow the steps to install the BiRD OpenFOAM solver (see Installation of BiRD OpenFOAM solver (for developers and users) below)
  3. Check that you can run any of the tutorial cases, for ex:

bash cd tutorial_cases/bubble_column_20L bash run.sh

Installation of python package for developers

bash conda create --name bird python=3.10 conda activate bird git clone https://github.com/NREL/BioReactorDesign.git cd BioReactorDesign pip install -e .

Installation of python package for users

bash conda create --name bird python=3.10 conda activate bird pip install nrel-bird=={version}

We highly recommend that you specify the version explicitly as the library is still rapidly changing.

Installation of BiRD OpenFOAM solver (for developers and users)

  1. Activate your OpenFOAM-9 environment (source <OpenFOAM-9 installation directory>/etc/<your-shell>rc)
  2. cd OFsolvers/birdmultiphaseEulerFoam/
  3. Compile ./Allwmake

Documentation

See the nrel.github.io/BioReactorDesign.

References

Software record SWR 24-35

To cite BiRD, please use these articles on CO2 interphase mass transfer (open access link ) on aerobic bioreactors and on butanediol synthesis

``` @article{hassanaly2025bayesian, title={Bayesian calibration of bubble size dynamics applied to CO2 gas fermenters}, author={Hassanaly, Malik and Parra-Alvarez, John M and Rahimi, Mohammad J and Municchi, Federico and Sitaraman, Hariswaran}, journal={Chemical Engineering Research and Design}, volume={215}, pages={312--328}, year={2025}, publisher={Elsevier} }

@article{rahimi2018computational, title={Computational fluid dynamics study of full-scale aerobic bioreactors: Evaluation of gas--liquid mass transfer, oxygen uptake, and dynamic oxygen distribution}, author={Rahimi, Mohammad J and Sitaraman, Hariswaran and Humbird, David and Stickel, Jonathan J}, journal={Chemical Engineering Research and Design}, volume={139}, pages={283--295}, year={2018}, publisher={Elsevier} }

@article{sitaraman2023reacting, title={A reacting multiphase computational flow model for 2, 3-butanediol synthesis in industrial-scale bioreactors}, author={Sitaraman, Hariswaran and Lischeske, James and Lu, Yimin and Stickel, Jonathan}, journal={Chemical Engineering Research and Design}, volume={197}, pages={38--52}, year={2023}, publisher={Elsevier} } ```

Acknowledgments

This work was authored by the National Renewable Energy Laboratory (NREL), operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. This work was supported by funding from DOE Bioenergy Technologies Office (BETO) CO2RUe consortium. The research was performed using computational resources sponsored by the Department of Energy's Office of Energy Efficiency and Renewable Energy and located at the National Renewable Energy Laboratory. The views expressed in the article do not necessarily represent the views of the DOE or the U.S. Government. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S. Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this work, or allow others to do so, for U.S. Government purposes.

Owner

  • Name: National Renewable Energy Laboratory
  • Login: NREL
  • Kind: organization
  • Location: Golden, CO

GitHub Events

Total
  • Create event: 49
  • Release event: 2
  • Issues event: 24
  • Watch event: 16
  • Delete event: 42
  • Member event: 3
  • Issue comment event: 27
  • Push event: 260
  • Pull request review comment event: 8
  • Pull request review event: 21
  • Pull request event: 100
  • Fork event: 8
Last Year
  • Create event: 49
  • Release event: 2
  • Issues event: 24
  • Watch event: 16
  • Delete event: 42
  • Member event: 3
  • Issue comment event: 27
  • Push event: 260
  • Pull request review comment event: 8
  • Pull request review event: 21
  • Pull request event: 100
  • Fork event: 8

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 655
  • Total Committers: 11
  • Avg Commits per committer: 59.545
  • Development Distribution Score (DDS): 0.053
Past Year
  • Commits: 320
  • Committers: 5
  • Avg Commits per committer: 64.0
  • Development Distribution Score (DDS): 0.078
Top Committers
Name Email Commits
Malik m****y@g****m 620
fmuni f****i@g****m 17
Rahimi m****i@n****v 4
Hariswaran Sitaraman h****m@k****v 2
Malik Hassanaly m****a@e****v 2
Malik Hassanaly m****a@k****v 2
Mohammad Rahimi m****i@k****v 2
hsitaram h****n@g****m 2
jainprana P****n@n****v 2
Malik Hassanaly m****a@e****v 1
Malik Hassanaly m****a@e****v 1
Committer Domains (Top 20 + Academic)
kl3.head.cm.kestrel.hpc.nrel.gov: 2 nrel.gov: 2 el3.ib0.cm.hpc.nrel.gov: 1 el2.ib0.cm.hpc.nrel.gov: 1 kd5.head.cm.kestrel.hpc.nrel.gov: 1 el1.ib0.cm.hpc.nrel.gov: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 32
  • Total pull requests: 156
  • Average time to close issues: 4 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 6
  • Total pull request authors: 5
  • Average comments per issue: 0.63
  • Average comments per pull request: 0.17
  • Merged pull requests: 123
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 15
  • Pull requests: 116
  • Average time to close issues: 11 days
  • Average time to close pull requests: 3 days
  • Issue authors: 5
  • Pull request authors: 5
  • Average comments per issue: 0.8
  • Average comments per pull request: 0.19
  • Merged pull requests: 84
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • malihass (26)
  • fmuni (2)
  • sustainapower (1)
  • MoritzImendoerffer (1)
  • djinnome (1)
  • asela326 (1)
Pull Request Authors
  • malihass (145)
  • mjrahimi (4)
  • fmuni (3)
  • sabinala (2)
  • jainprana (2)
Top Labels
Issue Labels
good first issue (2) documentation (1)
Pull Request Labels
good first issue (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 381 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 27
  • Total maintainers: 1
pypi.org: nrel-bird

Bio Reactor Design (BiRD): a toolbox to simulate and analyze different designs of bioreactors in OpenFOAM

  • Versions: 27
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 381 Last month
Rankings
Dependent packages count: 9.8%
Average: 37.3%
Dependent repos count: 64.7%
Maintainers (1)
malihass
Last synced: 6 months ago

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
requirements.txt pypi
  • black *
  • imageio *
  • isort *
  • matplotlib ==3.2.2
  • numpy *
  • numpy-stl *
  • scipy *