Tissue Forge Documentation
Tissue Forge is an interactive, particle-based physics, chemistry and biology modeling and simulation environment. Tissue Forge provides the ability to create, simulate and explore models, simulations and virtual experiments of soft condensed matter physics at multiple scales using a simple, intuitive interface. Tissue Forge is designed with an emphasis on problems in complex subcellular, cellular and tissue biophysics. Tissue Forge enables interactive work with simulations on heterogeneous computing architectures, where models and simulations can be built and interacted with in real-time during execution of a simulation, and computations can be selectively offloaded onto available GPUs on-the-fly.
Tissue Forge is a native compiled C++ shared library that’s designed to be used for model and simulation specification in compiled C++ code. Tissue Forge includes extensive C, C++ and Python APIs and additional support for interactive model and simulation specification in an IPython console and a Jupyter Notebook. Tissue Forge currently supports installations on 64-bit Windows, Linux and MacOS systems.
Quick Summary
This documentation provides information on a number of topics related to Tissue Forge. If you’re looking for something specific, refer to the following,
To get Tissue Forge, refer to Getting Tissue Forge.
To get started with Tissue Forge, refer to Quickstart.
To learn about the physics and philosophy of Tissue Forge, refer to Introduction.
For walkthroughs, examples and other discussions, refer to Notes.
For application-specific models and tools, refer to Models.
To dive into the code, refer to Tissue Forge API Reference.
Note
Tissue Forge supports modeling and simulation in multiple programming languages. While many variables, classes and methods are named and behave the same across all supported languages, inevitably there are some differences. Most examples in this documentation demonstrate usage in Python, and specific cases where Tissue Forge behaves differently in a particular language are explicitly addressed. In general, assume that a documented example or code snippet in one language is the same in another unless stated otherwise. For specific details about Tissue Forge in a particular language, refer to Tissue Forge API Reference.
Funding
Tissue Forge is funded with generous support by NIBIB U24 EB028887.
Citing
To use Tissue Forge in research, please cite the following:
Sego et al. (2023). “Tissue Forge: Interactive biological and biophysics simulation environment.” PLoS Computational Biology, 19(10), e1010768.
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