Bibliography#
Marianne J Bezaire, Ivan Raikov, Kelly Burk, Dhrumil Vyas, and Ivan Soltesz. Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent ca1 circuit. eLife, 5:e18566, dec 2016. URL: https://doi.org/10.7554/eLife.18566, doi:10.7554/eLife.18566.
Inga Blundell, Romain Brette, Thomas A. Cleland, Thomas G. Close, Daniel Coca, Andrew P. Davison, Sandra Diaz-Pier, Carlos Fernandez Musoles, Padraig Gleeson, Dan F. M. Goodman, Michael Hines, Michael W. Hopkins, Pramod Kumbhar, David R. Lester, Bóris Marin, Abigail Morrison, Eric Müller, Thomas Nowotny, Alexander Peyser, Dimitri Plotnikov, Paul Richmond, Andrew Rowley, Bernhard Rumpe, Marcel Stimberg, Alan B. Stokes, Adam Tomkins, Guido Trensch, Marmaduke Woodman, and Jochen Martin Eppler. Code generation in computational neuroscience: a review of tools and techniques. Frontiers in Neuroinformatics, 12:68, 2018. doi:10.3389/fninf.2018.00068.
Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini, and R. Angus Silver. LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Frontiers in Neuroinformatics, 2014. doi:10.3389/fninf.2014.00079.
Sharon Crook, Padraig Gleeson, Fred Howell, Joseph Svitak, and R. Angus Silver. MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification. Neuroinformatics, 5(2):96–104, 5 2007. doi:10.1007/s12021-007-0003-6.
KA Ferguson, CYL Huh, B Amilhon, S Williams, and FK Skinner. Data set of CA1 pyramidal cell recordings using an intact whole hippocampus preparation, including recordings of rebound firing (V2). May 2015. URL: https://doi.org/10.5281/zenodo.17794, doi:10.5281/zenodo.17794.
D. Gardner, K. H. Knuth, M. Abato, S. M. Erde, T. White, R. DeBellis, and E. P. Gardner. Common data model for neuroscience data and data model exchange. Journal of the American Medical Informatics Association, 8(1):17–33, 1 2001. doi:10.1136/jamia.2001.0080017.
Padraig Gleeson, Matteo Cantarelli, Boris Marin, Adrian Quintana, Matt Earnshaw, Sadra Sadeh, Eugenio Piasini, Justas Birgiolas, Robert C. Cannon, N. Alex Cayco-Gajic, Sharon Crook, Andrew P. Davison, Salvador Dura-Bernal, András Ecker, Michael L. Hines, Giovanni Idili, Frederic Lanore, Stephen D. Larson, William W. Lytton, Amitava Majumdar, Robert A. McDougal, Subhashini Sivagnanam, Sergio Solinas, Rokas Stanislovas, Sacha J. van Albada, Werner van Geit, and R. Angus Silver. Open source brain: a collaborative resource for visualizing, analyzing, simulating, and developing standardized models of neurons and circuits. Neuron, 103(3):395–411, 2019. doi:10.1016/j.neuron.2019.05.019.
Padraig Gleeson, Sharon Crook, Robert C. Cannon, Michael L. Hines, Guy O. Billings, Matteo Farinella, Thomas M. Morse, Andrew P. Davison, Subhasis Ray, Upinder S. Bhalla, Simon R. Barnes, Yoana D. Dimitrova, and R. Angus Silver. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Computational Biology, 6(6):e1000815, 2010. doi:10.1371/journal.pcbi.1000815.
Padraig Gleeson, Volker Steuber, and R. Angus Silver. neuroConstruct: a tool for modeling networks of neurons in 3d space. Neuron, 54(2):219–235, 4 2007. doi:10.1016/j.neuron.2007.03.025.
Nigel H. Goddard, Michael Hucka, Fred Howell, Hugo Cornelis, Kavita Shankar, and David Beeman. Towards NeuroML: model description methods for collaborative modelling in neuroscience. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 356(1412):1209–1228, 8 2001. doi:10.1098/rstb.2001.0910.
Alan L. Hodgkin and Andrew F. Huxley. A quantitative description of membrane current and its application to conduction and excitation in nerve. The Journal of physiology, 117(4):500, 1952.
F. Howell, R. Cannon, N. Goddard, H. Bringmann, P. Rogister, and H. Cornelis. Linking computational neuroscience simulation tools—a pragmatic approach to component-based development. Neurocomputing, 52-54:289–294, 6 2003. doi:10.1016/s0925-2312(02)00781-6.
Eugene M. Izhikevich. Dynamical systems in neuroscience. MIT Press, 2007.
Edward N. Lorenz. Deterministic nonperiodic flow. Journal of Atmospheric Sciences, 20(2):130–141, 1963. doi:10.1175/1520-0469(1963)020<0130:dnf>2.0.co;2.
Astrid A. Prinz, Dirk Bucher, and Eve Marder. Similar network activity from disparate circuit parameters. Nature Neuroscience, 7(12):1345–1352, 2004. doi:10.1038/nn1352.
Weihong Qi and Sharon Crook. Tools for neuroinformatic data exchange: an XML application for neuronal morphology data. Neurocomputing, 58-60:1091–1095, 6 2004. doi:10.1016/j.neucom.2004.01.171.
Subhasis Ray, Zane N. Aldworth, and Mark A. Stopfer. Feedback inhibition and its control in an insect olfactory circuit. eLife, 9:e53281, 2020. URL: https://doi.org/10.7554/eLife.53281, doi:10.7554/eLife.53281.
Cyrille Rossant, Dan F. Goodman, Bertrand Fontaine, Jonathan Platkiewicz, Anna Magnusson, and Romain Brette. Fitting neuron models to spike trains. Frontiers in Neuroscience, 5:9, 2011. URL: https://www.frontiersin.org/article/10.3389/fnins.2011.00009, doi:10.3389/fnins.2011.00009.
Arfon M. Smith, Daniel S. Katz, Kyle E. Niemeyer, and FORCE11 Software Citation Working Group. Software citation principles. PeerJ Computer Science, 2:e86, 2016. URL: https://doi.org/10.7717/peerj-cs.86, doi:10.7717/peerj-cs.86.
Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver, and Padraig Gleeson. Libneuroml and pylems: using python to combine procedural and declarative modeling approaches in computational neuroscience. Frontiers in neuroinformatics, 8:38, 2014. doi:10.3389/fninf.2014.00038.