Flint - a simulator for biological and physiological models

Flint is a simulator for biological and physiological models written in CellML, PHML, and/or SBML. Originally developed as part of an in silico platform of Physiome, now it aims to provide an open, language-agnostic resource for reproducible simulation studies. While existing simultion tools, e.g. COPASI and OpenCOR, are great for simulation of models in a specific language, you may find Flint useful if searching a unified solution.

Flint has the following features:

• It can numerically solve ordinary or stochastic differential equations derived from models.
• It runs on Windows, macOS, Linux, etc.
• It provides fully-featured graphical user interface with simplified command-line interface.
• It is open source under the MIT license.

You can read NEWS about Flint 2.4 released at 2020-09-29.

• Flint 2.4: The User Guide (or its HTML version)
• Tutorial videos on YouTube
• PhysioDesigner's tutorial videos on YouTube: contain some examples running simulation with Flint.
• ISD format specification

Flint's source repository is in GitHub. Patches and/or suggestions are welcome.

Please feel free to submit an issue on Flint's GitHub Issues for bugs or feature requests that you come up with when using Flint. For any question or suggestion about Flint, send an email to the author or to the official mailing list if you prefer open, transparent communication.

Please cite the following article when referring Flint in a scientific article:

• Abe et al., (2020). Flint: a simulator for biological and physiological models in ordinary and stochastic differential equations. Journal of Open Source Software, 5(53), 2331, https://doi.org/10.21105/joss.02331

• Uchida, S., Asai, Y., Kariya, Y. et al. Integrative and theoretical research on the architecture of a biological system and its disorder. J Physiol Sci 69, 433–451 (2019). https://doi.org/10.1007/s12576-019-00667-8
• Asai Y, Abe T, Li L, Oka H, Nomura T and Kitano H (2015) Databases for multilevel biophysiology research available at Physiome.jp. Front. Physiol. 6:251. doi: 10.3389/fphys.2015.00251
• T. Okuyama et al., "Accelerating ODE-Based Simulation of General and Heterogeneous Biophysical Models Using a GPU," in IEEE Transactions on Parallel and Distributed Systems, vol. 25, no. 8, pp. 1966-1975, Aug. 2014, doi: 10.1109/TPDS.2013.198.
• Y. Asai et al., "Multilevel Modeling of Physiological Systems and Simulation Platform: PhysioDesigner, Flint and Flint K3 Service," 2012 IEEE/IPSJ 12th International Symposium on Applications and the Internet, Izmir, 2012, pp. 215-219. doi: 10.1109/SAINT.2012.40

• PhysioDesigner project