Bioverse

Bioverse is a Python package for simulating the results of a statistical survey of the properties of nearby terrestrial exoplanets via direct imaging or transit spectroscopy. An in-depth outline of the underlying statistical framework and examples of how it can be applied to astrophysics mission concepts is given in Bixel & Apai (2021). Readers are strongly encouraged to review this paper before proceeding. This documentation covers the Python implementation of Bioverse, but does not review many of its underlying statistical assumptions.

The Overview section describes the code’s structure and primary classes and should be reviewed first. Following that, the Examples section offers step-by-step examples for producing some of the results published in the paper, as well as ways to modify and expand upon the code. Most of these examples are also available as interactive Jupyter notebooks in the Notebooks directory of the GitHub repository.

Installation

The recommended way to install the latest stable version of Bioverse is via pip:

pip install bioverse

Alternatively, Bioverse can be cloned from its GitHub repository:

git clone https://www.github.com/danielapai/bioverse/
cd bioverse
pip install .

Dependencies

Bioverse is compatible with Python 3.7+. It has the following dependencies, all of which can be installed using pip:

  • astroquery

  • dynesty

  • emcee

  • matplotlib

  • numpy

  • scipy

  • tqdm (optional: provides a progress bar for long processes)

  • pandas (optional: used for data visualization)

  • PyQt5 (optional: enables configuration GUI)

Feedback & Development

Bioverse is open source and in active development. We welcome all feedback, bug reports, or feature requests. Feel free to open a pull request if you’d like to contribute! If you think you found a bug, please raise an issue.

References & Acknowledgements

Papers making use of Bioverse should cite Bixel & Apai (2021), Hardegree-Ullman et al. (2023), and Schlecker et al. (2024).

@ARTICLE{2021AJ....161..228B,
  author = {{Bixel}, Alex and {Apai}, D{\'a}niel},
  title = "{Bioverse: A Simulation Framework to Assess the Statistical Power of Future Biosignature Surveys}",
  journal = {\aj},
  keywords = {Astrobiology, Exoplanets, Exoplanet atmospheres, Astrostatistics, Open source software, 74, 498, 487, 1882, 1866, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},
  year = 2021,
  month = may,
  volume = {161},
  number = {5},
  eid = {228},
  pages = {228},
  doi = {10.3847/1538-3881/abe042},
archivePrefix = {arXiv},
  eprint = {2101.10393},
  primaryClass = {astro-ph.EP},
  adsurl = {https://ui.adsabs.harvard.edu/abs/2021AJ....161..228B},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{2023AJ....165..267H,
  author = {{Hardegree-Ullman}, Kevin K. and {Apai}, D{\'a}niel and {Bergsten}, Galen J. and {Pascucci}, Ilaria and {L{\'o}pez-Morales}, Mercedes},
  title = "{Bioverse: A Comprehensive Assessment of the Capabilities of Extremely Large Telescopes to Probe Earth-like O$_{2}$ Levels in Nearby Transiting Habitable-zone Exoplanets}",
  journal = {\aj},
  keywords = {Fundamental parameters of stars, Exoplanet systems, Exoplanets, Exoplanet atmospheres, Biosignatures, 555, 484, 498, 487, 2018, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics},
  year = 2023,
  month = jun,
  volume = {165},
  number = {6},
  eid = {267},
  pages = {267},
  doi = {10.3847/1538-3881/acd1ec},
archivePrefix = {arXiv},
  eprint = {2304.12490},
  primaryClass = {astro-ph.EP},
  adsurl = {https://ui.adsabs.harvard.edu/abs/2023AJ....165..267H},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{2024PSJ.....5....3S,
  author = {{Schlecker}, Martin and {Apai}, D{\'a}niel and {Lichtenberg}, Tim and {Bergsten}, Galen and {Salvador}, Arnaud and {Hardegree-Ullman}, Kevin K.},
  title = "{Bioverse: The Habitable Zone Inner Edge Discontinuity as an Imprint of Runaway Greenhouse Climates on Exoplanet Demographics}",
  journal = {\psj},
  keywords = {Habitable zone, Habitable planets, Astrobiology, Extrasolar rocky planets, Planetary climates, Exoplanet atmospheres, Astronomical simulations, Exoplanets, Transit photometry, Radial velocity, Bayesian statistics, Parametric hypothesis tests, 696, 695, 74, 511, 2184, 487, 1857, 498, 1709, 1332, 1900, 1904, Astrophysics - Earth and Planetary Astrophysics},
  year = 2024,
  month = jan,
  volume = {5},
  number = {1},
  eid = {3},
  pages = {3},
  doi = {10.3847/PSJ/acf57f},
  archivePrefix = {arXiv},
  eprint = {2309.04518},
  primaryClass = {astro-ph.EP},
  adsurl = {https://ui.adsabs.harvard.edu/abs/2024PSJ.....5....3S},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

If you make use of the integrated hypothesis testing and parameter fitting, you should also include references to the emcee and dynesty packages.

Bioverse was developed with support from the following grants and collaborations:

  • Alien Earths and Earths in Other Solar Systems

  • NASA Earth and Space Science Fellowship Program (grant No. 80NSSC17K0470)

  • NASA’s Nexus for Exoplanet System Science (NExSS)