Andrews SS, Addy NJ, Brent R, Arkin AP (2010) Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput Biol 6:e1000705 [Journal] [PubMed]

Blackwell KT (2005) A new era in computational neuroscience. Neuroinformatics 3:163-6 [Journal] [PubMed]

Bower JM, Beeman D (1998) The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System

Brandi M, Brocke E, Talukdar HA, Hanke M, Bhalla US, Kotaleski JH (2011) Connecting MOOSE and NeuroRD through MUSIC: towards a communication framework for multi-scale modeling BMC Neurosci. 12(Suppl 1):77

Brown SA, Moraru II, Schaff JC, Loew LM (2011) Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling. J Comput Neurosci 31:385-400 [Journal] [PubMed]

•	A simplified cerebellar Purkinje neuron (the PPR model) (Brown et al. 2011) [Model]

Cannon RC, Gewaltig MO, Gleeson P, Bhalla US, Cornelis H, Hines ML, Howell FW, Muller E, Stiles JR, Wils S, De Schutter E (2007) Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics 5:127-38 [Journal] [PubMed]

Cannon RC, Hasselmo ME, Koene RA (2003) From biophysics to behavior: Catacomb2 and the design of biologically-plausible models for spatial navigation. Neuroinformatics 1:3-42 [Journal] [PubMed]

•	Biologically-plausible models for spatial navigation (Cannon et al 2003) [Model]

Carnevale NT, Hines ML (2006) The NEURON Book [Journal]

Coombes S, Hinch R, Timofeeva Y (2004) Receptors, sparks and waves in a fire-diffuse-fire framework for calcium release. Prog Biophys Mol Biol 85:197-216 [Journal] [PubMed]

Cornelis H, Rodriguez AL, Coop AD, Bower JM (2012) Python as a federation tool for GENESIS 3.0. PLoS One 7:e29018 [Journal] [PubMed]

Davison AP, Hines ML, Muller E (2009) Trends in programming languages for neuroscience simulations. Front Neurosci 3:374-80 [Journal] [PubMed]

De Schutter E (2008) Why are computational neuroscience and systems biology so separate? PLoS Comput Biol 4:e1000078 [Journal] [PubMed]

Faeder JR, Blinov ML, Hlavacek WS (2009) Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol 500:113-67 [Journal] [PubMed]

Ferrante M, Blackwell KT, Migliore M, Ascoli GA (2008) Computational models of neuronal biophysics and the characterization of potential neuropharmacological targets. Curr Med Chem 15:2456-71 [PubMed]

•	Computational neuropharmacology of CA1 pyramidal neuron (Ferrante et al. 2008) [Model]

Fleidervish IA, Lasser-Ross N, Gutnick MJ, Ross WN (2010) Na+ imaging reveals little difference in action potential-evoked Na+ influx between axon and soma. Nat Neurosci 13:852-60 [Journal] [PubMed]

•	Action potential-evoked Na+ influx are similar in axon and soma (Fleidervish et al. 2010) [Model]
•	Action potential-evoked Na+ influx similar in axon and soma (Fleidervish et al. 2010) (Python) [Model]

Gardner D, Toga AW, Ascoli GA, Beatty JT, Brinkley JF, Dale AM, Fox PT, Gardner EP, George JS, Goddard N, Harris KM, Herskovits EH, Hines ML, Jacobs GA, Jacobs RE, Jones EG, Kennedy DN, Kimberg DY, Mazziotta JC, Miller PL, Mori S, Mountain DC, Reiss AL, Rosen GD, Rottenberg DA, Shepherd GM, Smalheiser NR, Smith KP, Strachan T, Van Essen DC, Williams RW, Wong ST (2003) Towards effective and rewarding data sharing. Neuroinformatics 1:289-95 [Journal] [PubMed]

Gillespie DT (1976) A General method for numerically simulating the stochastic time evolution of coupledchemical reactions J Comput Phys 22:403-434

Gillespie DT (2001) Approximate accelerated stochastic simulation of chemically reacting systems The Journal Of Chemical Physics 115:1716-1733

Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput Biol 6:e1000815 [Journal] [PubMed]

Hindmarsh AC, Brown PN, Grant KE, Lee SL, Serban R, Shumaker DE, Woodward C (2005) SUNDIALS: Suite of nonlinear and differential-algebraic equation solvers ACM Trans Math Software 31:363-396

Hines M (1984) Efficient computation of branched nerve equations. Int J Biomed Comput 15:69-76 [PubMed]

Hines ML, Carnevale NT (2000) Expanding NEURON's repertoire of mechanisms with NMODL. Neural Comput 12:995-1007 [Journal] [PubMed]

Hines ML, Davison AP, Muller E (2009) NEURON and Python. Front Neuroinform 3:1 [Journal] [PubMed]

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

Hines ML, Morse TM, Carnevale NT (2007) Model structure analysis in NEURON : toward interoperability among neural simulators. Methods Mol Biol 401:91-102 [Journal] [PubMed]

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J, SBML Forum (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524-31 [PubMed]

Jones E, Oliphant T, Peterson P, Et_al (2001) http:--www.scipy.org- SciPy: open source scientific tools for Python

Keller DX, Franks KM, Bartol TM, Sejnowski TJ (2008) Calmodulin activation by calcium transients in the postsynaptic density of dendritic spines. PLoS One 3:e2045 [Journal] [PubMed]

Kelly MT, Crary JF, Sacktor TC (2007) Regulation of protein kinase Mzeta synthesis by multiple kinases in long-term potentiation. J Neurosci 27:3439-44 [Journal] [PubMed]

Kernighan BW, Pike R (1984) The UNIX Programming Environment Hoc Manual :329-333

Kerr CC, Van Albada SJ, Neymotin SA, Chadderdon GL, Robinson PA, Lytton WW (2013) Cortical information flow in Parkinson's disease: a composite network/field model. Front Comput Neurosci 7:39 [Journal] [PubMed]

•	Composite spiking network/neural field model of Parkinsons (Kerr et al 2013) [Model]

Lisman J, Yasuda R, Raghavachari S (2012) Mechanisms of CaMKII action in long-term potentiation. Nat Rev Neurosci 13:169-82 [Journal] [PubMed]

Loew LM, Schaff JC (2001) The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol 19:401-6 [Journal] [PubMed]

Lytton WW (1997) Brain organization: from molecules to parallel processing Contemporary Behavioral Neurology, Trimble M:Cummings J, ed. pp.5

Lytton WW, Hines M (2004) Hybrid neural networks--combining abstract and realistic neural units. Conf Proc IEEE Eng Med Biol Soc 6:3996-8 [Journal] [PubMed]

Lytton WW, Hines ML (2005) Independent variable time-step integration of individual neurons for network simulations. Neural Comput 17:903-21 [Journal] [PubMed]

•	Local variable time step method (Lytton, Hines 2005) [Model]

Lytton WW, Stewart M (2006) Rule-based firing for network simulations. Neurocomputing 69:1160-1164

Peercy BE (2008) Initiation and propagation of a neuronal intracellular calcium wave. J Comput Neurosci 25:334-48 [Journal] [PubMed]

Pepke S, Kinzer-Ursem T, Mihalas S, Kennedy MB (2010) A dynamic model of interactions of Ca2+, calmodulin, and catalytic subunits of Ca2+/calmodulin-dependent protein kinase II. PLoS Comput Biol 6:e1000675 [Journal] [PubMed]

Ray S, Bhalla US (2008) PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinform 2:6 [Journal] [PubMed]

•	Moose/PyMOOSE: interoperable scripting in Python for MOOSE (Ray and Bhalla 2008) [Model]

Stiles JR, Bartol TM (2001) Monte Carlo methods for simulating realistic synaptic microphysiology using MCell Computational Neuroscience: Realistic Modelling for Experimentalists, DeSchutter E, ed. pp.87

Wils S, De Schutter E (2009) STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. Front Neuroinform 3:15 [Journal] [PubMed]

Grein S, Stepniewski M, Reiter S, Knodel MM, Queisser G (2014) 1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time. Front Neuroinform 8:68 [Journal] [PubMed]

Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schürmann F, Hines ML (2016) Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Comput 28:2063-90 [Journal] [PubMed]

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

McDougal RA, Bulanova AS, Lytton WW (2016) Reproducibility in Computational Neuroscience Models and Simulations. IEEE Trans Biomed Eng 63:2021-35 [Journal] [PubMed]

McDougal RA, Morse TM, Hines ML, Shepherd GM (2015) ModelView for ModelDB: Online Presentation of Model Structure. Neuroinformatics 13:459-70 [Journal] [PubMed]

•	ModelView: online structural analysis of computational models (McDougal et al. 2015) [Model]

Neymotin SA, Dura-Bernal S, Lakatos P, Sanger TD, Lytton WW (2016) Multitarget Multiscale Simulation for Pharmacological Treatment of Dystonia in Motor Cortex. Front Pharmacol 7:157 [Journal] [PubMed]

•	Multitarget pharmacology for Dystonia in M1 (Neymotin et al 2016) [Model]

Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW (2016) Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex. Neuroscience 316:344-66 [Journal] [PubMed]

•	Ca+/HCN channel-dependent persistent activity in multiscale model of neocortex (Neymotin et al 2016) [Model]

Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW (2015) Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model. Neural Comput 27:898-924 [Journal] [PubMed]

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

Solbrå A, Bergersen AW, van den Brink J, Malthe-Sørenssen A, Einevoll GT, Halnes G (2018) A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons. PLoS Comput Biol 14:e1006510 [Journal] [PubMed]

•	Modelling large scale electrodiffusion near morphologically detailed neurons (Solbra et al 2018) [Model]