Ajay SM, Bhalla US. (2004). A role for ERKII in synaptic pattern selectivity on the time-scale of minutes. The European journal of neuroscience. 20 [PubMed]
Ascher D, Martelli A, Ravenscroft AM. (2005). Python Cookbook.
Bazhenov M, Howell F, Goddard N, Rogister P, Seznowski T. (2002). Scaling a slow-wave sleep cortical network model using NEOSIM. Neurocomputing. 44-46
Beazley DM. (1996). SWIG: an easy to use tool for integrating scripting languages with C and C++ Proceedings of the 4th Annual USENIX Tcl-Tk Workshop, Monterey, CA..
Beeman D, Howell F, Gleeson P, Crook S. (2005). XML for model specification in neuroscience. Special Issue on Realistic Neuro Modeling - Wam-Bamm '05 Tutorials. 1
Bhalla US. (1998). Advanced XODUS techniques. The Book of GENESIS:Exploring Realistic Neural Models with the General Neural Simulation System.
Bhalla US, Iyengar R. (1999). Emergent properties of networks of biological signaling pathways. Science (New York, N.Y.). 283 [PubMed]
Bhalla US, Ram PT, Iyengar R. (2002). MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science (New York, N.Y.). 297 [PubMed]
Bower JM, Beeman D. (1998). The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System.
Bower JM, Beeman D. (2004). Simulator-independent representation of ionic conductance models with ChannelDB. Neurocomputing.
Bunow B, Segev I, Fleshman JW. (1985). Modeling the electrical behavior of anatomically complex neurons using a network analysis program: excitable membrane. Biological cybernetics. 53 [PubMed]
Cannon RC et al. (2007). Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics. 5 [PubMed]
Crook S, Gleeson P, Howell F, Svitak J, Silver RA. (2007). MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification. Neuroinformatics. 5 [PubMed]
Crook SM, Qi W. (2004). Tools for neuroinformatic data exchange: an XML application for neuronal morphology data . 58C-60C
De Schutter E, Cornelis H. (2003). NeuroSpaces: New approaches in neuronal modeling software. Neurocomputing.
Ekeberg O, Djurfeldt M. (2008). MUSIC - multisimulation coordinator: request for comments Nature Proceedings.
Goddard NH et al. (2001). Towards NeuroML: model description methods for collaborative modelling in neuroscience. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 356 [PubMed]
Hines M. (1993). NEURON--a program for simulation of nerve equations. Neural Systems: Analysis And Modeling.
Hines M, De Schutter E, Howell F, Goddard N, Hood G. (2001). NEOSIM: Portable largescaleplug and play modelling Neurocomputing. 38-40
Hines ML, Carnevale NT. (2006). The NEURON Book.
Hucka M et al. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (Oxford, England). 19 [PubMed]
Le Novère N et al. (2005). Minimum information requested in the annotation of biochemical models (MIRIAM). Nature biotechnology. 23 [PubMed]
Maes P. (1987). Concepts and experiments in computational reflection Proceedings of the Conference on Object-Oriented Programming Systems, Languages, and Applications(OOPSLA)..
Migliore M, Cook EP, Jaffe DB, Turner DA, Johnston D. (1995). Computer simulations of morphologically reconstructed CA3 hippocampal neurons. Journal of neurophysiology. 73 [PubMed]
Segev I, Fleshman JW, Miller JP, Bunow B. (1985). Modeling the electrical behavior of anatomically complex neurons using a network analysis program: passive membrane. Biological cybernetics. 53 [PubMed]
Smith BC. (1982). Reflection and Semantics in a Procedural Language. Ph.D. thesis.
Bhalla US. (2011). Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability. Neural networks : the official journal of the International Neural Network Society. 24 [PubMed]
Bhalla US. (2017). Synaptic input sequence discrimination on behavioral timescales mediated by reaction-diffusion chemistry in dendrites. eLife. 6 [PubMed]
Chen W, De Schutter E. (2014). Python-based geometry preparation and simulation visualization toolkits for STEPS. Frontiers in neuroinformatics. 8 [PubMed]
Gilra A, Bhalla US. (2015). Bulbar microcircuit model predicts connectivity and roles of interneurons in odor coding. PloS one. 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]
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. Frontiers in neuroinformatics. 8 [PubMed]
Jȩdrzejewski-Szmek Z, Abrahao KP, Jȩdrzejewska-Szmek J, Lovinger DM, Blackwell KT. (2018). Parameter Optimization Using Covariance Matrix Adaptation-Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes. Frontiers in neuroinformatics. 12 [PubMed]
Lazar AA, Liu T, Turkcan MK, Zhou Y. (2021). Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era eLife. 10 [PubMed]
Lytton WW et al. (2016). Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural computation. 28 [PubMed]
Mattioni M, Cohen U, Le Novère N. (2012). Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. Frontiers in neuroinformatics. 6 [PubMed]
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 [PubMed]
McDougal RA, Bulanova AS, Lytton WW. (2016). Reproducibility in Computational Neuroscience Models and Simulations. IEEE transactions on bio-medical engineering. 63 [PubMed]
McDougal RA, Hines ML, Lytton WW. (2013). Reaction-diffusion in the NEURON simulator. Frontiers in neuroinformatics. 7 [PubMed]
Newton AJH, McDougal RA, Hines ML, Lytton WW. (2018). Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics. Frontiers in neuroinformatics. 12 [PubMed]
Parekh R, Ascoli GA. (2013). Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Neuron. 77 [PubMed]