STEPS

STochastic Engine for Pathway Simulation

Articles about STEPS Development:

  • Hepburn I, Lallouette J, Chen W, Gallimore AR, Nagasawa-Soeda S, De Schutter E (2024) Vesicle and reaction-diffusion hybrid modeling with STEPS. Commun Biol 7, 573. doi: doi.org/10.1038/s42003-024-06276-5 (STEPS 5.0, Vesicle simulations) Article

  • 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 (STEPS 4.0, Parallel distributed mesh solver) Article, Simulation Scripts

  • 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. (Parallelization) Article, Simulation Scripts

  • 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. (Parallelization) Article, Simulation Scripts

  • Chen W and De Schutter E (2014) Python-based geometry preparation and simulation visualization toolkit for STEPS. Frontiers in Neuroinformatics 8:37. (Utilities, Visualization) Article, Simulation Scripts

  • Hepburn I, Cannon R and De Schutter E (2013) Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS. Frontiers in Computational Neuroscience 7:129. (Electric field simulation) Article, Simulation Scripts

  • 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. (Software infrastructure, Reaction-diffusion simulation) Article

  • Wils S and De Schutter E (2009) STEPS: Modeling and simulating complex reaction-diffusion systems with Python. Frontiers in Neuroinformatics 3:15. (Software infrastructure, Reaction-diffusion simulation) Article

Published modelling studies that use STEPS:

  • Santos JPG, Pajo K, Trpevski D, Stepaniuk A, Eriksson O, Nair AG, Keller D, Hellgren Kotaleski J and Kramer A (2022) A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. Neuroinform 20, 241–259 https://doi.org/10.1007/s12021-021-09546-3

  • Denizot A, Arizono M, Nägerl UV, Berry H, De Schutter E (2022) Control of Ca2+ signals by astrocyte nanoscale morphology at tripartite synapses. Glia. 2022 Dec;70(12):2378-2391. doi: 10.1002/glia.24258. Epub 2022 Sep 13. PMID: 36097958; PMCID: PMC9825906. Article

  • Stillman NR, Balaz I, Tsompanas MA, Kovacevic M, Azimi S, Lafond S, Adamatzky A and Hauert S (2021) Evolutionary computational platform for the automatic discovery of nanocarriers for cancer treatment. npj Computational Materials 7, 150. Article

  • Stillman N R and Hauert S (2021) How Spatiality Impacts In Silico Experiments of Nanoparticle-Cell Interactions. 2021 IEEE 21st International Conference on Nanotechnology (NANO), Montreal, QC, Canada, pp. 279-282, doi: 10.1109/NANO51122.2021.9514334.

  • Denizot A, Arizono M, Nägerl UV, Soula H, Berry H (2019) Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity. PLOS Computational Biology 15(8): e1006795. Article, Simulation Scripts

  • Zamora Chimal CG and De Schutter E (2018) Ca2+ Requirements for Long-Term Depression Are Frequency Sensitive in Purkinje Cells. Frontiers in molecular neuroscience, 11, 438. doi:10.3389/fnmol.2018.00438 Article, Simulation Scripts

  • Hepburn I, Jain A, Gangal H, Yamamoto Y, Tanaka-Yamamoto K and De Schutter E (2017) A Model of Induction of Cerebellar Long-Term Depression Including RKIP Inactivation of Raf and MEK. Front. Mol. Neurosci. 10:19. doi: 10.3389/fnmol.2017.00019 Article, Simulation Scripts

  • Schelker M, Mair CM, Jolmes F, Welke RW, Klipp E, et al. (2016) Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency. PLoS Comput Biol 12(10): e1005075. doi: 10.1371/journal.pcbi.1005075

  • Mohapatra, N., Tønnesen, J., Vlachos, A., Kuner, T., Deller, T., Nägerl, U.V., Santamaria, F. and Jedlicka, P., 2016. Spines slow down dendritic chloride diffusion and affect short-term ionic plasticity of GABAergic inhibition. Scientific Reports, 6, p.23196.

  • Matolcsi, M. and Giordano, N., 2015. A Novel Explanation for Observed CaMKII Dynamics in Dendritic Spines with Added EGTA or BAPTA. Biophysical journal, 108(4), pp.975-985.

  • Anwar H, Roome CJ, Nedelescu H, Chen W, Kuhn B and De Schutter E (2014) Dendritic diameters affect the spatial variability of intracellular calcium dynamics in computer models. Frontiers in Cellular Neuroscience. 2014;8:168. doi:10.3389/fncel.2014.00168

  • Anwar H, Hepburn I, Nedelescu H, Chen W and De Schutter E (2013) Stochastic calcium mechanisms cause dendritic calcium spike variability. J Neurosci 33(40):15848-67.

  • Hepburn I, Cannon R and De Schutter E (2013) Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS. Front. Comput. Neurosci. 7:129. doi: 10.3389/fncom.2013.00129.

  • Hituri K and Linne ML (2013) Comparison of models for IP3 receptor kinetics using stochastic simulations. PLoS One 8(4):e59618

  • 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.

  • Antunes G and De Schutter E (2012) A Stochastic Signaling Network Mediates the Probabilistic Induction of Cerebellar Long-Term Depression. The Journal of Neuroscience 32(27): 9288-9300

  • Tewari SG (2011) Stochastic Simulation of a Dimer Sodium Pump. Journal of Biological Systems 19(4):551

  • Wils S and De Schutter E (2009) STEPS: Modeling and simulating complex reaction-diffusion systems with Python. Frontiers in Neuroinformatics 3: 15