Citation Relationships

Legends: Link to a Model Reference cited by multiple papers


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

References and models cited by this paper

References and models that cite this paper

Allen Institute (2015) Documentation Allen Cell Types Database [Journal]
   Allen Institute: Htr3a-Cre VISp layer 2/3 472352327 [Model]
   Allen Institute: Rorb-IRES2-Cre-D VISp layer 5 471087975 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 2/3 472306616 [Model]
   Allen Institute: Scnn1a-Tg2-Cre VISp layer 5 472306460 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 4 329322394 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 2/3 473862496 [Model]
   Allen Institute: Rbp4-Cre VISp layer 6a 473871592 [Model]
   Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472300877 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 6a 472301074 [Model]
   Allen Institute: Sst-IRES-Cre VISp layer 5 472299363 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 5 472912177 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 4 472442377 [Model]
   Allen Institute: Gad2-IRES-Cre VISp layer 5 472447460 [Model]
   Allen Institute: Rbp4-Cre VISp layer 5 472424854 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 5 473465774 [Model]
   Allen Institute: Sst-IRES-Cre VISp layer 4 472304539 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 5 472349114 [Model]
   Allen Institute: Sst-IRES-Cre VISp layer 2/3 472304676 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 5 473862421 [Model]
   Allen Institute: Rorb-IRES2-Cre-D VISp layer 4 473863510 [Model]
   Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 473871773 [Model]
   Allen Institute: Rorb-IRES2-Cre-D VISp layer 2/3 472299294 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 4 473863035 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 4 473871429 [Model]
   Allen Institute: Rorb-IRES2-Cre-D VISp layer 2/3 472434498 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 6a 471081668 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 5 471085845 [Model]
   Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 329321704 [Model]
   Allen Institute: Sst-IRES-Cre VISp layer 6a 472440759 [Model]
   Allen Institute: Sst-IRES-Cre VISp layer 5 472450023 [Model]
   Allen Institute: Sst-IRES-Cre VISp layer 5 473835796 [Model]
   Allen Institute: Pvalb-IRES-Cre VISp layer 6a 473860269 [Model]
   Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 473863578 [Model]
   Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 473862845 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 4 472915634 [Model]
   Allen Institute: Sst-IRES-Cre VISp layer 2/3 471086533 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 4 472306544 [Model]
   Allen Institute: Rorb-IRES2-Cre-D VISp layer 5 473561660 [Model]
   Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 472455509 [Model]
   Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 473465456 [Model]
   Allen Institute: Gad2-IRES-Cre VISp layer 5 473561729 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 4 473834758 [Model]
   Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 473872986 [Model]
   Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 472363762 [Model]
   Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472912107 [Model]
   Allen Institute: Htr3a-Cre VISp layer 2/3 472421285 [Model]
   Allen Institute: Ntsr1-Cre VISp layer 4 472430904 [Model]
   Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472427533 [Model]
   Allen Institute: Nr5a1-Cre VISp layer 4 472451419 [Model]
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]
Antolík J, Davison AP (2013) Integrated workflows for spiking neuronal network simulations. Front Neuroinform 7:34 [Journal] [PubMed]
Ascoli GA (2006) The ups and downs of neuroscience shares. Neuroinformatics 4:213-6 [Journal] [PubMed]
Ascoli GA (2015) Sharing Neuron Data: Carrots, Sticks, and Digital Records. PLoS Biol 13:e1002275 [Journal] [PubMed]
Ascoli GA, Donohue DE, Halavi M (2007) NeuroMorpho.Org: a central resource for neuronal morphologies. J Neurosci 27:9247-51 [Journal] [PubMed]
Ausbrooks R, Buswell S, Dalmas S, Devitt S, Diaz A, Et_al (2001) Mathematical Markup Language (MathML) Version 2.0. W3C Recommendation.
Baddeley A (1992) Working memory. Science 255:556-9 [PubMed]
Baxter DA, Byrne JH (2007) Simulator for neural networks and action potentials. Methods Mol Biol 401:127-54 [Journal] [PubMed]
Bednar JA (2008) Understanding Neural Maps with Topographica Brains, Minds Media 3:bmm1402
Bednar JA (2009) Topographica: Building and Analyzing Map-Level Simulations from Python, C/C++, MATLAB, NEST, or NEURON Components. Front Neuroinform 3:8 [Journal] [PubMed]
Beeman D (2013) History of neural simulation software 20 Years of Computational Neuroscience :33-71
Ben-Shalom R, Liberman G, Korngreen A (2013) Accelerating compartmental modeling on a graphical processing unit. Front Neuroinform 7:4 [Journal] [PubMed]
Bergmann FT, Sauro HM (2008) Comparing simulation results of SBML capable simulators. Bioinformatics 24:1963-5 [Journal] [PubMed]
Bezaire MJ, Soltesz I (2013) Quantitative assessment of CA1 local circuits: knowledge base for interneuron-pyramidal cell connectivity. Hippocampus 23:751-85 [Journal] [PubMed]
Bhalla US (2002) Use of Kinetikit and GENESIS for modeling signaling pathways. Methods Enzymol 345:3-23 [PubMed]
Bower JM, Beeman D (1995) The Book of GENESIS: Exploring Realistic Neural Models with the GEneral NEural SImulation System. [Journal]
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
Bray T, Paoli J, Sperberg-McQueen CM (1998) Extensible Markup Language (XML) 1.0 http:--www.w3.org-TR-REC-xml W3C Recommendation.
Britten RD (2015) Encyclopedia of Computational Neuroscience :1182-1186
Britten RD, Christie GR, Little C, Miller AK, Bradley C, Wu A, Yu T, Hunter P, Nielsen P (2013) FieldML, a proposed open standard for the Physiome project for mathematical model representation. Med Biol Eng Comput 51:1191-207 [Journal] [PubMed]
Brown (2012) Spatial organization and diffusion in neuronal signaling Computational Systems Neurobiology. :133-161
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, Gleeson P, Crook S, Ganapathy G, Marin B, Piasini E, Silver RA (2014) LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Front Neuroinform 8:79 [Journal] [PubMed]
Cannon RC, O'Donnell C, Nolan MF (2010) Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS Comput Biol [Journal] [PubMed]
   Stochastic ion channels and neuronal morphology (Cannon et al. 2010) [Model]
Cannon RC, Turner DA, Pyapali GK, Wheal HV (1998) An on-line archive of reconstructed hippocampal neurons. J Neurosci Methods 84:49-54 [PubMed]
Carnevale NT,et al (2014) The neuroscience gateway portal: high performance computing made easy, BMC Neuroscience 15(1):P101
Casadevall A, Fang FC (2010) Reproducible science. Infect Immun 78:4972-5 [Journal] [PubMed]
Castelvecchi D (2015) The biggest mystery in mathematics: Shinichi Mochizuki and the impenetrable proof. Nature 526:178-81 [Journal] [PubMed]
Christie GR, Nielsen PM, Blackett SA, Bradley CP, Hunter PJ (2009) FieldML: concepts and implementation. Philos Trans A Math Phys Eng Sci 367:1869-84 [Journal] [PubMed]
Clewley R (2012) Hybrid models and biological model reduction with PyDSTool. PLoS Comput Biol 8:e1002628 [Journal] [PubMed]
Cooper J, Vik JO, Waltemath D (2015) A call for virtual experiments: accelerating the scientific process. Prog Biophys Mol Biol 117:99-106 [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]
Crook S,et al (2013) Learning from the past: approaches for reproducibility in computational neuroscience 20 Years of Computational Neuroscience :73-102
Cuellar AA, Et_al (2003) An overview of CellML 1.1, a biological model description language Simulation 79:740-747
Davison A (2012) Automated capture of experiment context for easier reproducibility in computational research Computing In Science And Engineering 14:48-56
Davison AP (2012) Collaborative modelling: The future of computational neuroscience? Network: Computation in Neural Systems 23(4):157-166
Davison AP, Brüderle D, Eppler J, Kremkow J, Muller E, Pecevski D, Perrinet L, Yger P (2008) PyNN: A Common Interface for Neuronal Network Simulators. Front Neuroinform 2:11 [Journal] [PubMed]
Davison AP, Hines ML, Muller E (2009) Trends in programming languages for neuroscience simulations. Front Neurosci 3:374-80 [Journal] [PubMed]
Davison AP,Mattioni M,Samarkanov D,Sumatra TB (2014) Sumatra: A toolkit for reproducible research Implementing reproducible, research, Stodden V:Leisch F, ed. pp.57
De Kemps M,Baier V (2007) Multiple interacting instantiations of neuronal dynamics (MIIND): a library for rapid prototyping of models in cognitive neuroscience, Neural Networks IJCNN International Joint Conference, Aug :2829-2834
De Schutter E (2014) The dangers of plug-and-play simulation using shared models. Neuroinformatics 12:227-8 [Journal] [PubMed]
Dematté L (2012) Smoldyn on graphics processing units: massively parallel Brownian dynamics simulations. IEEE/ACM Trans Comput Biol Bioinform 9:655-67 [Journal] [PubMed]
Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Kotaleski JH, Ekeberg O (2010) Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics 8:43-60 [Journal] [PubMed]
Drummond C (2009) Replicability is not Reproducibility: Nor is it Good Science Proc. of the Evaluation Methods for Machine Learning Workshop at the 26th ICML, Montreal, Canada
Dudani N,Ray S,George S,Bhalla US (2009) Multiscale modeling and interoperability in MOOSE BMC Neuroscience 10(1):p54
Eppler JM, Helias M, Muller E, Diesmann M, Gewaltig MO (2008) PyNEST: A Convenient Interface to the NEST Simulator. Front Neuroinform 2:12 [Journal] [PubMed]
Ermentrout GB (2002) Simulating, Analyzing, and Animating Dynamical System: A Guide to XPPAUT for Researchers and Students Society for Industrial and Applied Mathematics (SIAM)
Fenton AA, Lytton WW, Barry JM, Lenck-Santini PP, Zinyuk LE, Kubík S, Bures J, Poucet B, Muller RU, Olypher AV (2010) Attention-like modulation of hippocampus place cell discharge. J Neurosci 30:4613-25 [Journal] [PubMed]
Ferguson AR, Nielson JL, Cragin MH, Bandrowski AE, Martone ME (2014) Big data from small data: data-sharing in the 'long tail' of neuroscience. Nat Neurosci 17:1442-7 [Journal] [PubMed]
Folk M, Cheng A, Mcgrath RE (1999) HDF5: A new file format and I-O library for scientific data management Astronom-ical data analysis software and systems VIII proceedings, Mehringer DM:Plante RL:Roberts DA, ed.
Gerkin RC,Omar C (2014) Collaboratively testing the validity of neuroscientific models Frontiers in Neuroinformatics
Gladkov DV,et al (2011) Accelerating the Smoldyn spatial stochastic biochemical reaction network simulator using GPUs Proceedings of the 19th High Performance C. Symposia. Society for Computer Simulation International :151-158
Glaser JR, Glaser EM (1990) Neuron imaging with Neurolucida--a PC-based system for image combining microscopy. Comput Med Imaging Graph 14:307-17 [PubMed]
Gleeson (2007) Using NeuroML and neuroConstruct to build neuronal network models for multiple simulators BMC Neuroscience 8(2):P1
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]
Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219-35 [Journal] [PubMed]
Gleeson PPIASINIE,Crook S,Cannon R,Steuber V,Jaeger D,Et AL (2012) The Open Source Brain Initiative: enabling collaborative modelling in computational neuroscience Twenty First Annual Computational Neuroscience Meeting: CNS*2012
Goddard N, Hood N (1997) Parallel GENESIS for large scale modeling Computational Neuroscience, Trends In Research, Bower JM, ed. pp.911
Goddard NH, Hucka M, Howell F, Cornelis H, Shankar K, Beeman D (2001) Towards NeuroML: model description methods for collaborative modelling in neuroscience. Philos Trans R Soc Lond B Biol Sci 356:1209-28 [Journal] [PubMed]
Goodman D, Brette R (2008) Brian: a simulator for spiking neural networks in python. Front Neuroinform 2:5 [Journal] [PubMed]
Goodman DF,et al (2014) Brian 2: neural simulations on a variety of computational hardware BMC Neuroscience 15(1):P199
Gorgolewski KJ, Margulies DS, Milham MP (2013) Making data sharing count: a publication-based solution. Front Neurosci 7:9 [Journal] [PubMed]
Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Müller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME (2008) Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF). Neuroinformatics 6:205-17 [Journal] [PubMed]
Halavi M, Hamilton KA, Parekh R, Ascoli GA (2012) Digital reconstructions of neuronal morphology: three decades of research trends. Front Neurosci 6:49 [Journal] [PubMed]
Halchenko YO, Hanke M (2012) Open is Not Enough. Let's Take the Next Step: An Integrated, Community-Driven Computing Platform for Neuroscience. Front Neuroinform 6:22 [Journal] [PubMed]
Hamilton DJ, Shepherd GM, Martone ME, Ascoli GA (2012) An ontological approach to describing neurons and their relationships. Front Neuroinform 6:15 [Journal] [PubMed]
Hedley WJ,et al (2001) A short introduction to CellML Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, 359(1738):1073-1089
Henderson RL (1995) ob scheduling under the portable batch system Job scheduling strategies for parallel processing :279-294
Hernjak N, Slepchenko BM, Fernald K, Fink CC, Fortin D, Moraru II, Watras J, Loew LM (2005) Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells. Biophys J 89:3790-806 [Journal] [PubMed]
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 [PubMed]
Hines ML, Markram H, Schürmann F (2008) Fully implicit parallel simulation of single neurons. J Comput Neurosci 25:439-48 [Journal] [PubMed]
   Fully Implicit Parallel Simulation of Single Neurons (Hines et al. 2008) [Model]
Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM (2004) ModelDB: A Database to Support Computational Neuroscience. J Comput Neurosci 17:7-11 [Journal] [PubMed]
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, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N (2015) Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. Front Bioeng Biotechnol 3:19 [Journal] [PubMed]
Jin X,et al (2010) Modeling spiking neural networks on SpiNNaker Computing in Science & Engineering 12:91-97
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V (2015) BioModels: Content, Features, Functionality, and Use. CPT Pharmacometrics Syst Pharmacol 4:e3 [Journal] [PubMed]
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]
Khan MM,et al (2008) SpiNNaker: mapping neural networks onto a massively-parallel chip multiprocessor, Neural Networks EEE World Congress on Computational Intelligence). IEEE International Joint Conference :2849-2856
King JG, Hines M, Hill S, Goodman PH, Markram H, Schürmann F (2009) A Component-Based Extension Framework for Large-Scale Parallel Simulations in NEURON. Front Neuroinform 3:10 [Journal] [PubMed]
Kohn MC,Hines ML,Kootsey JM,Feezor MD (1994) A block organized model builder Mathematical and Computer Modelling 19(6):75-97
Lapicque L (1907) Recherches quantitatives sur lexcitation electrique des nerfs traitee comme une polarisation J Physiol Pathol Gen 9:620-635 [Journal]
Larson SD, Martone ME (2013) NeuroLex.org: an online framework for neuroscience knowledge. Front Neuroinform 7:18 [Journal] [PubMed]
Le Franc Y,et al (2012) Computational Neuroscience Ontology: a new tool to provide semantic meaning to your models BMC Neuroscience 13(1):P149
Lee S, Zhou ZJ (2006) The synaptic mechanism of direction selectivity in distal processes of starburst amacrine cells. Neuron 51:787-99 [Journal] [PubMed]
Lloyd CM, Halstead MD, Nielsen PF (2004) CellML: its future, present and past. Prog Biophys Mol Biol 85:433-50 [Journal] [PubMed]
Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF (2008) The CellML Model Repository. Bioinformatics 24:2122-3 [Journal] [PubMed]
Loew LM, Schaff JC (2001) The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol 19:401-6 [Journal] [PubMed]
Marenco L, Ascoli GA, Martone ME, Shepherd GM, Miller PL (2008) The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers. Neuroinformatics 6:219-27 [Journal] [PubMed]
Markram H, Muller E, Ramaswamy S, Reimann MW, Abdellah M, Sanchez CA, Ailamaki A, Alonso-Nanclares L, Antille N, Arsever S, Kahou GA, Berger TK, Bilgili A, Buncic N, Chalimourda A, Chindemi G, Courcol JD, Delalondre F, Delattre V, Druckmann S, Dumusc R, Dynes J, Eilemann S, Gal E, Gevaert ME, Ghobril JP, Gidon A, Graham JW, Gupta A, Haenel V, Hay E, Heinis T, Hernando JB, Hines M, Kanari L, Keller D, Kenyon J, Khazen G, Kim Y, King JG, Kisvarday Z, Kumbhar P, Lasserre S, Le Bé JV, Magalhães BR, Merchán-Pérez A, Meystre J, Morrice BR, Muller J, Muñoz-Céspedes A, Muralidhar S, Muthurasa K, Nachbaur D, Newton TH, Nolte M, Ovcharenko A, Palacios J, Pastor L, Perin R, Ranjan R, Riachi I, Rodríguez JR, Riquelme JL, Rössert C, Sfyrakis K, Shi Y, Shillcock JC, Silberberg G, Silva R, Tauheed F, Telefont M, Toledo-Rodriguez M, Tränkler T, Van Geit W, Díaz JV, Walker R, Wang Y, Zaninetta SM (2015) Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163:456-92 [Journal] [PubMed]
   The neocortical microcircuit collaboration portal (Markram et al. 2015) [Model]
Mattioni M, Le Novère N (2013) Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum. PLoS One 8:e66811 [Journal] [PubMed]
   Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013) [Model]
Mead C (1990) Neuromorphic electronic systems Proc IEEE 78:1629-1636
Migliore M, Cavarretta F, Hines ML, Shepherd GM (2014) Distributed organization of a brain microcircuit analyzed by three-dimensional modeling: the olfactory bulb. Front Comput Neurosci 8:50 [Journal] [PubMed]
   3D model of the olfactory bulb (Migliore et al. 2014) [Model]
Migliore M, Morse TM, Davison AP, Marenco L, Shepherd GM, Hines ML (2003) ModelDB: making models publicly accessible to support computational neuroscience. Neuroinformatics 1:135-9 [Journal] [PubMed]
Miller AK, Marsh J, Reeve A, Garny A, Britten R, Halstead M, Cooper J, Nickerson DP, Nielsen PF (2010) An overview of the CellML API and its implementation. BMC Bioinformatics 11:178 [Journal] [PubMed]
Mukherjee S,et al (2005) The soft error problem: An architectural perspective High-Performance Computer Architecture HPCA- 11. 11th International Symposium on. IEEE :243-247
Myatt DR, Hadlington T, Ascoli GA, Nasuto SJ (2012) Neuromantic - from semi-manual to semi-automatic reconstruction of neuron morphology. Front Neuroinform 6:4 [Journal] [PubMed]
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]
Nordlie E, Gewaltig MO, Plesser HE (2009) Towards reproducible descriptions of neuronal network models. PLoS Comput Biol 5:e1000456 [Journal] [PubMed]
Oliveira RF, Terrin A, Di Benedetto G, Cannon RC, Koh W, Kim M, Zaccolo M, Blackwell KT (2010) The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations. PLoS One 5:e11725 [Journal] [PubMed]
Olivier BG, Snoep JL (2004) Web-based kinetic modelling using JWS Online. Bioinformatics 20:2143-4 [Journal] [PubMed]
Pecevski D, Natschlager T, Schuch K (2009) PCSIM: A Parallel Simulation Environment for Neural Circuits Fully Integrated with Python. Front Neuroinformatics 3:11-74 [PubMed]
Peercy BE (2008) Initiation and propagation of a neuronal intracellular calcium wave. J Comput Neurosci 25:334-48 [Journal] [PubMed]
Peng H, Hawrylycz M, Roskams J, Hill S, Spruston N, Meijering E, Ascoli GA (2015) BigNeuron: Large-Scale 3D Neuron Reconstruction from Optical Microscopy Images. Neuron 87:252-6 [Journal] [PubMed]
Plesser H,et al (2015) NEST: the neural simulation tool Encyclopedia of Computational Neuroscience, Jaeger D:Jung R, ed. pp.1849
Poldrack RA, Poline JB (2015) The publication and reproducibility challenges of shared data. Trends Cogn Sci 19:59-61 [Journal] [PubMed]
Popper () Conjectures and refutations; the growth of scientific knowledge
Raikov I, De Schutter E (2012) The promise and shortcomings of XML as an interchange format for computational models of biology. Neuroinformatics 10:1-3 [Journal] [PubMed]
Raikov I,Cannon R,Clewley R,Cornelis H,Davison A,De Schutter E,et al. (2011) NineML: The network interchange for neuroscience modeling language BMC Neuroscience 12:1-2
Ray S,Deshpande R,Dudani N,Bhalla US (2008) A general biological simulator: the multiscale object oriented simulation environment, MOOSE BMC Neuroscience 9(1):p93
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]
Ray S, Chintaluri C, Bhalla US, Wójcik DK (2016) NSDF: Neuroscience Simulation Data Format. Neuroinformatics 14:147-67 [Journal] [PubMed]
Schulz M, Uhlendorf J, Klipp E, Liebermeister W (2006) SBMLmerge, a system for combining biochemical network models. Genome Inform 17:62-71 [PubMed]
Sejnowski TJ, Koch C, Churchland PS (1988) Computational neuroscience. Science 241:1299-306 [PubMed]
Shepherd GM, Brayton RK (1979) Computer simulation of a dendrodendritic synaptic circuit for self- and lateral-inhibition in the olfactory bulb. Brain Res 175:377-82 [PubMed]
   Dendro-dendritic synaptic circuit (Shepherd Brayton 1979) [Model]
Silver R, Boahen K, Grillner S, Kopell N, Olsen KL (2007) Neurotech for neuroscience: unifying concepts, organizing principles, and emerging tools. J Neurosci 27:11807-19 [Journal] [PubMed]
Sivagnanam S,Majumdar A, Yoshimoto K, Astakhov V, Bandrowski A, Martone ME, Carnevale NT (2013) Introducing the Neuroscience Gateway 2013 IWSG, volume 993 of CEUR Workshop Proceedings, CEUR-WS.org, [Journal]
Smith LP, Butterworth E, Bassingthwaighte JB, Sauro HM (2014) SBML and CellML translation in antimony and JSim. Bioinformatics 30:903-7 [Journal] [PubMed]
Stevens JL, Elver M, Bednar JA (2013) An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook. Front Neuroinform 7:44 [Journal] [PubMed]
Stewart TC, Tripp B, Eliasmith C (2009) Python scripting in the nengo simulator. Front Neuroinform 3:7 [Journal] [PubMed]
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
Stimberg M, Goodman DF, Benichoux V, Brette R (2014) Equation-oriented specification of neural models for simulations. Front Neuroinform 8:6 [Journal] [PubMed]
Szigeti B, Gleeson P, Vella M, Khayrulin S, Palyanov A, Hokanson J, Currie M, Cantarelli M, Idili G, Larson S (2014) OpenWorm: an open-science approach to modeling Caenorhabditis elegans. Front Comput Neurosci 8:137 [Journal] [PubMed]
Taichman DB, Backus J, Baethge C, Bauchner H, de Leeuw PW, Drazen JM, Fletcher J, Frizelle FA, Groves T, Haileamlak A, James A, Laine C, Peiperl L, Pinborg A, Sahni P, Wu S (2016) Sharing Clinical Trial Data: A Proposal From the International Committee of Medical Journal Editors. Ann Intern Med 164:505-6 [Journal] [PubMed]
Teeters JL, Harris KD, Millman KJ, Olshausen BA, Sommer FT (2008) Data sharing for computational neuroscience. Neuroinformatics 6:47-55 [Journal] [PubMed]
Toni N, Teng EM, Bushong EA, Aimone JB, Zhao C, Consiglio A, van Praag H, Martone ME, Ellisman MH, Gage FH (2007) Synapse formation on neurons born in the adult hippocampus. Nat Neurosci 10:727-34 [Journal] [PubMed]
Tripathy SJ, Savitskaya J, Burton SD, Urban NN, Gerkin RC (2014) NeuroElectro: a window to the world's neuron electrophysiology data. Front Neuroinform 8:40 [Journal] [PubMed]
Uhrmacher AM (2012) Seven pitfalls in modeling and simulation research, Proceedings of the Winter Simulation Conference. Winter Simulation Conference :318
Usui S (2003) Visiome: neuroinformatics research in vision project. Neural Netw 16:1293-300 [Journal] [PubMed]
Van Rossum G,Drake FL () Python reference manual
Vella M, Cannon RC, Crook S, Davison AP, Ganapathy G, Robinson HP, Silver RA, Gleeson P (2014) libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience. Front Neuroinform 8:38 [Journal] [PubMed]
Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N (2011) Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC Syst Biol 5:198 [Journal] [PubMed]
Waltemath D, Henkel R, Hälke R, Scharm M, Wolkenhauer O (2013) Improving the reuse of computational models through version control. Bioinformatics 29:742-8 [Journal] [PubMed]
Wearne SL, Rodriguez A, Ehlenberger DB, Rocher AB, Henderson SC, Hof PR (2005) New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience 136:661-80 [Journal] [PubMed]
Weeks WT,et al (1973) Algorithms for ASTAP–a network-analysis program Circuit Theory, IEEE Transactions 20(6):628-634
Wheeler DW, White CM, Rees CL, Komendantov AO, Hamilton DJ, Ascoli GA (2015) Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus. Elife [Journal] [PubMed]
Williams R (2015) Can't Get No Reproduction: Leading Researchers Discuss the Problem of Irreproducible Results. Circ Res 117:667-70 [Journal] [PubMed]
Wils S, De Schutter E (2009) STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. Front Neuroinform 3:15 [Journal] [PubMed]
Yamazaki T, Ikeno H, Okumura Y, Satoh S, Kamiyama Y, Hirata Y, Inagaki K, Ishihara A, Kannon T, Usui S (2011) Simulation Platform: a cloud-based online simulation environment. Neural Netw 24:693-8 [Journal] [PubMed]
Yavuz E, Turner J, Nowotny T (2016) GeNN: a code generation framework for accelerated brain simulations. Sci Rep 6:18854 [Journal] [PubMed]
Yoo AB,et al (2003) Slurm: Simple linux utility for resource management ob Scheduling Strategies for Parallel Processing :44-60
Ziv I, Baxter DA, Byrne JH (1994) Simulator for neural networks and action potentials: description and application. J Neurophysiol 71:294-308 [Journal] [PubMed]
Bezaire M, Raikov I, Burk K, Armstrong C, Soltesz I (2016) SimTracker tool and code template to design, manage and analyze neural network model simulations in parallel NEURON bioRxiv [Journal]
   Hippocampal CA1 NN with spontaneous theta, gamma: full scale & network clamp (Bezaire et al 2016) [Model]
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]
(163 refs)