- The STEPS validation package can be downloaded via (http://steps.sourceforge.net/STEPS/download/validation_package.zip). This package compares analytical solutions of typical mesoscopic spatial/well-mixed reaction-diffusion models with STEPS simulation results. Model information as well as validation metrics can be found in each Python simulation script. For a more detailed description of the analytical system and equivalent STEPS model see: http://www.biomedcentral.com/content/supplementary/1752-0509-6-36-s4.pdf. Please check the README file within the package for detailed instructions.
- The models used to validate NeuroRD version2.0 is available here. Most of these models were used in modeling/software publications and compared to the deterministic solutions. The spatial gene oscillator has not yet been published. Additional publications using these models are listed in the ValidationSetNeuroRDv2.doc included in the zip file.
- The models used to validate NeuroRD version3.0 is available on github. This package compares the new asynchronous tau leaping with either the analytical solution (for simple models) or the exact stochastic simulation results.
- The models used to demonstrate pyURDME are available on github, and include the minD oscillator. For a nice discussion about the scope of the software see: and a benchmark comparing URDME, STEPS and MesoRD using either 2D diffusion or the 3D minD oscillator is available in the supplement