Cesium a public database containing approximately 2000 oscillating networks with between three and nine species created using a customized evolution algorithm, an optimization process based on the iterative improvement of candidate models. The source code for the algorithm that generated these evolved models can be found here: https://github.com/sys-bio/evolution. Also within this database are approximately 8000 randomly generated models with between one and ten species. All models are written in Antimony, a chemical network modeling language.
More information about Antimony:
- Antimony reference: https://tellurium.readthedocs.io/en/latest/antimony.html
- Github repo: https://github.com/sys-bio/antimony
Our paper on chemical network oscillator generation: an be found here:
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997760/
Lillian T. Tatka, Wesley Luk, Timothy C. Elston, Joseph L. Hellerstein, Herbert M. Sauro, Cesium: A public database of evolved oscillatory reaction networks, Biosystems, Vol 224, 2023, 104836, ISSN 0303-2647, https://doi.org/10.1016/j.biosystems.2023.104836.
Current website, under construction: https://sys-bio.github.io/cesium/
The former website can be found at https://cesiumdb.herokuapp.com/
- Original Repository is here: https://github.com/WesleyyL/cesium
- Current website and model database design based directly on the work and GitHub repository of Matthew Epshtein: https://github.com/epshteinmatthew/OscillatorDatabase
- Project was supervised by Dr. Herbert Sauro at the University of Washington, Bioengineering Department.