Translating network models to parallel hardware in NEURON (Hines and Carnevale 2008)

Bush PC, Prince DA, Miller KD. (1999). Increased pyramidal excitability and NMDA conductance can explain posttraumatic epileptogenesis without disinhibition: a model. Journal of neurophysiology. 82 [PubMed]

• Cortical network model of posttraumatic epileptogenesis (Bush et al 1999) [Model]

Davison AP, Feng J, Brown D. (2003). Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model. Journal of neurophysiology. 90 [PubMed]

• Olfactory Bulb Network (Davison et al 2003) [Model]

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML. (2006). Parallel network simulations with NEURON. Journal of computational neuroscience. 21 [PubMed]

• Parallel network simulations with NEURON (Migliore et al 2006) [Model]

Santhakumar V, Aradi I, Soltesz I. (2005). Role of mossy fiber sprouting and mossy cell loss in hyperexcitability: a network model of the dentate gyrus incorporating cell types and axonal topography. Journal of neurophysiology. 93 [PubMed]

• Dentate gyrus network model (Santhakumar et al 2005) [Model]
• Dentate gyrus (Morgan et al. 2007, 2008, Santhakumar et al. 2005, Dyhrfjeld-Johnsen et al. 2007) [Model]

García-Grajales JA, Rucabado G, García-Dopico A, Peña JM, Jérusalem A. (2015). Neurite, a finite difference large scale parallel program for the simulation of electrical signal propagation in neurites under mechanical loading. PloS one. 10 [PubMed]

• Neurite: electrophysiological-mechanical coupling simulation framework (Garcia-Grajales et al 2015) [Model]

Hines ML, Davison AP, Muller E. (2009). NEURON and Python. Frontiers in neuroinformatics. 3 [PubMed]

• NEURON + Python (Hines et al. 2009) [Model]

Hines ML, Eichner H, Schürmann F. (2008). Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors. Journal of computational neuroscience. 25 [PubMed]

• Cell splitting in neural networks extends strong scaling (Hines et al. 2008) [Model]

Kumaravelu K, Oza CS, Behrend CE, Grill WM. (2018). Model-based deconstruction of cortical evoked potentials generated by subthalamic nucleus deep brain stimulation. Journal of neurophysiology. 120 [PubMed]

• Deconstruction of cortical evoked potentials generated by subthalamic DBS (Kumaravelu et al 2018) [Model]

Kumaravelu K, Sombeck J, Miller LE, Bensmaia SJ, Grill WM. (2022). Stoney vs. Histed: Quantifying the spatial effects of intracortical microstimulation Brain stimulation. 15 [PubMed]

• Stoney vs Histed: Quantifying spatial effects of intracortical microstims (Kumaravelu et al 2022) [Model]

Lytton WW et al. (2016). Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural computation. 28 [PubMed]

• Parallelizing large networks in NEURON (Lytton et al. 2016) [Model]

Masoli S, Solinas S, D'Angelo E. (2015). Action potential processing in a detailed Purkinje cell model reveals a critical role for axonal compartmentalization. Frontiers in cellular neuroscience. 9 [PubMed]

• A detailed Purkinje cell model (Masoli et al 2015) [Model]

Schneider CJ, Cuntz H, Soltesz I. (2014). Linking macroscopic with microscopic neuroanatomy using synthetic neuronal populations. PLoS computational biology. 10 [PubMed]

• Generation of granule cell dendritic morphology (Schneider et al. 2014) [Model]

Schwarzacher SW, Cuntz H, Jedlicka P, Beining M, Mongiat LA. (2017). T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells eLife.

• GC model (Beining et al 2017) [Model]
• Mature and young adult-born dentate granule cell models (T2N interface) (Beining et al. 2017) [Model]

Soltesz I, Armstrong C, Raikov I, Bezaire M, Burk K. (2016). SimTracker tool and code template to design, manage and analyze neural network model simulations in parallel NEURON bioRxiv.

• Hippocampal CA1 NN with spontaneous theta, gamma: full scale & network clamp (Bezaire et al 2016) [Model]

Sterratt DC, Graham B, Gillies A, Willshaw D. (2011). Principles of Computational Modelling in Neuroscience, Cambridge University Press.

• Principles of Computational Modelling in Neuroscience (Book) (Sterratt et al. 2011) [Model]

Tikidji-Hamburyan RA, El-Ghazawi TA, Narayana V, Bozkus Z. (2017). Software for Brain Network Simulations: A Comparative Study Front. Neuroinform..

• Brain networks simulators - a comparative study (Tikidji-Hamburyan et al 2017) [Model]

Tsai D et al. (2012). Responses of retinal ganglion cells to extracellular electrical stimulation, from single cell to population: model-based analysis. PloS one. 7 [PubMed]

• Retinal ganglion cells responses and activity (Tsai et al 2012, Guo et al 2016) [Model]