STEPS

STochastic Engine for Pathway Simulation

To Reference STEPS:

Hepburn I, Chen W, Wils S and De Schutter E (2012) STEPS: Efficient simulation of stochastic reaction-diffusion models in realistic morphologies. BMC Systems Biology, 6:36. Article

To Reference the Parallel Distributed Mesh Implementation:

Chen W, Carel T, Awile O, Cantarutti N, Castiglioni G, Cattabiani A, Del Marmol B, Hepburn I, King JG, Kotsalos C, Kumbhar P, Lallouette J, Melchior S, Schürmann F and De Schutter E (2022) STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale. Front. Neuroinform. 16:883742. doi: 10.3389/fninf.2022.883742 Article

To Reference the Parallelization Implementation:

Chen W and De Schutter E (2017). Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers. Front. Neuroinform. 11:13. doi: 10.3389/fninf.2017.00013. Article

Hepburn I, Chen W and De Schutter E (2016) Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations. The Journal of Chemical Physics, 145, 054118. Article

Technical Reports:

Hepburn I, Anwar H and De Schutter E, Technical report: Hybrid simulations in STEPS (2013). Article

User Manual:

STEPS online user manual and API references can be accessed from Here.