Concluding Remarks

Building computational models of biochemical processes is usually a demanding task, especially for experimental biologists without modeling experience. This chapter aims to provide a guide on how one can quickly build and simulate spatially resolved biochemical models with the Spatiocyte software. We started with the basic theory of the Spatiocyte method and continued with the installation and simulation procedures. The various modules available to Spatiocyte users were also explained with accompanying model examples.

We plan to continuously develop and improve the Spatiocyte software and user experience. The contents of this guide will also therefore, evolve with the addition of new features and enhancements. The latest version of this guide will be available along with the Spatiocyte source code, which at the time of writing, is hosted at GitHub. The Spatiocyte website, also contains the latest information about the Spatiocyte method and software.

In future, we would like to introduce the ability of subunits to polymerize on the membrane and in the cytoplasm. A polymerization strategy using the HCP lattice was proposed recently (Arjunan, 2009). Diffusion of compartments, and molecules with different shapes and sizes are also in the future development plan. Parallel implementation of the Spatiocyte method to run on multi-core architectures and graphics processing units is also being considered. We are also currently working on introducing compartments with complex surface geometries. Spatiocyte users are encouraged to submit feature requests and bug reports, while independent developers can submit their own algorithm modules, code improvements and bug fixes.


The author thanks Goh Su Hua for creating the cluster model in the parameter tuning example.


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