De Schutter E. (2014). The dangers of plug-and-play simulation using shared models. Neuroinformatics. 12 [PubMed]

Gewaltig MO, Cannon R. (2014). Current practice in software development for computational neuroscience and how to improve it. PLoS computational biology. 10 [PubMed]

Gleeson P et al. (2010). NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS computational biology. 6 [PubMed]

Hituri K, Linne ML. (2013). Comparison of models for IP3 receptor kinetics using stochastic simulations. PloS one. 8 [PubMed]

• IP3R model comparison (Hituri and Linne 2013) [Model]

Manninen T, Havela R, Linne M-L. (2017). Reproducibility and comparability of computational models for astrocyte calcium excitability Front. Neuroinform..

• Ca2+ oscillations in single astrocytes (Lavrentovich and Hemkin 2008) (python) (Manninen et al 2017) [Model]
• Glutamate-evoked Ca2+ oscillations in single astrocytes (De Pitta et al. 2009) (Manninen et al 2017) [Model]
• Spontaneous calcium oscillations in single astrocytes (Riera et al. 2011) (Manninen et al 2017) [Model]
• Glutamate-evoked Ca2+ oscillations in single astrocytes (Modified from Dupont et al. 2011) [Model]
• Reproducibility and comparability of models for astrocyte Ca2+ excitability (Manninen et al 2017) [Model]

McDougal RA, Hines ML, Lytton WW. (2013). Reaction-diffusion in the NEURON simulator. Frontiers in neuroinformatics. 7 [PubMed]

• Reaction-diffusion in the NEURON simulator (McDougal et al 2013) [Model]

Newton AJH, McDougal RA, Hines ML, Lytton WW. (2018). Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics. Frontiers in neuroinformatics. 12 [PubMed]

• Using NEURON for reaction-diffusion modeling of extracellular dynamics (Newton et al 2018) [Model]

Neymotin SA, Chadderdon GL, Kerr CC, Francis JT, Lytton WW. (2013). Reinforcement learning of two-joint virtual arm reaching in a computer model of sensorimotor cortex. Neural computation. 25 [PubMed]

• Sensorimotor cortex reinforcement learning of 2-joint virtual arm reaching (Neymotin et al. 2013) [Model]

Neymotin SA et al. (2015). Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model. Neural computation. 27 [PubMed]

• Neuronal dendrite calcium wave model (Neymotin et al, 2015) [Model]