PyRhO: A multiscale optogenetics simulation platform (Evans et al 2016)


Evans BD, Jarvis S, Schultz SR, Nikolic K. (2016). PyRhO: A Multiscale Optogenetics Simulation Platform. Frontiers in neuroinformatics. 10 [PubMed]

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References and models cited by this paper

Adamantidis AR, Zhang F, Aravanis AM, Deisseroth K, de Lecea L. (2007). Neural substrates of awakening probed with optogenetic control of hypocretin neurons. Nature. 450 [PubMed]

Airan RD, Thompson KR, Fenno LE, Bernstein H, Deisseroth K. (2009). Temporally precise in vivo control of intracellular signalling. Nature. 458 [PubMed]

Aravanis AM et al. (2007). An optical neural interface: in vivo control of rodent motor cortex with integrated fiberoptic and optogenetic technology. Journal of neural engineering. 4 [PubMed]

Arenkiel BR et al. (2007). In vivo light-induced activation of neural circuitry in transgenic mice expressing channelrhodopsin-2. Neuron. 54 [PubMed]

Arlow RL, Foutz TJ, McIntyre CC. (2013). Theoretical principles underlying optical stimulation of myelinated axons expressing channelrhodopsin-2. Neuroscience. 248 [PubMed]

Arrenberg AB, Stainier DY, Baier H, Huisken J. (2010). Optogenetic control of cardiac function. Science (New York, N.Y.). 330 [PubMed]

Avants BW, Murphy DB, Dapello JA, Robinson JT. (2015). NeuroPG: open source software for optical pattern generation and data acquisition. Frontiers in neuroengineering. 8 [PubMed]

Ayling OG, Harrison TC, Boyd JD, Goroshkov A, Murphy TH. (2009). Automated light-based mapping of motor cortex by photoactivation of channelrhodopsin-2 transgenic mice. Nature methods. 6 [PubMed]

AzimiHashemi N et al. (2014). Synthetic retinal analogues modify the spectral and kinetic characteristics of microbial rhodopsin optogenetic tools. Nature communications. 5 [PubMed]

Bamann C, Kirsch T, Nagel G, Bamberg E. (2008). Spectral characteristics of the photocycle of channelrhodopsin-2 and its implication for channel function. Journal of molecular biology. 375 [PubMed]

Berndt A, Yizhar O, Gunaydin LA, Hegemann P, Deisseroth K. (2009). Bi-stable neural state switches. Nature neuroscience. 12 [PubMed]

Boyden ES, Zhang F, Bamberg E, Nagel G, Deisseroth K. (2005). Millisecond-timescale, genetically targeted optical control of neural activity. Nature neuroscience. 8 [PubMed]

Boyle PM, Williams JC, Ambrosi CM, Entcheva E, Trayanova NA. (2013). A comprehensive multiscale framework for simulating optogenetics in the heart. Nature communications. 4 [PubMed]

Bruegmann T, Sasse P. (2015). Optogenetic cardiac pacemakers: science or fiction? Trends in cardiovascular medicine. 25 [PubMed]

Busskamp V, Roska B. (2011). Optogenetic approaches to restoring visual function in retinitis pigmentosa. Current opinion in neurobiology. 21 [PubMed]

Chow BY et al. (2010). High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature. 463 [PubMed]

Chuong AS et al. (2014). Noninvasive optical inhibition with a red-shifted microbial rhodopsin. Nature neuroscience. 17 [PubMed]

Davison AP et al. (2008). PyNN: A Common Interface for Neuronal Network Simulators. Frontiers in neuroinformatics. 2 [PubMed]

De Schutter E et al. (2011). NineML: declarative, mathematically-explicit descriptions of spiking neuronal networks Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics.

Degenaar P et al. (2009). Optobionic vision--a new genetically enhanced light on retinal prosthesis. Journal of neural engineering. 6 [PubMed]

Eppler JM, Helias M, Muller E, Diesmann M, Gewaltig MO. (2008). PyNEST: A Convenient Interface to the NEST Simulator. Frontiers in neuroinformatics. 2 [PubMed]

Ernst OP et al. (2008). Photoactivation of channelrhodopsin. The Journal of biological chemistry. 283 [PubMed]

Et AL et al. (2008). Channelrhodopsins: Molecular Properties and Applications Washington, DC: Society for Neuroscience.

Feldbauer K et al. (2009). Channelrhodopsin-2 is a leaky proton pump. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]

Foutz TJ, Arlow RL, McIntyre CC. (2012). Theoretical principles underlying optical stimulation of a channelrhodopsin-2 positive pyramidal neuron. Journal of neurophysiology. 107 [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]

Goodman D, Brette R. (2008). Brian: a simulator for spiking neural networks in python. Frontiers in neuroinformatics. 2 [PubMed]

Goodman DF, Brette R. (2009). The brian simulator. Frontiers in neuroscience. 3 [PubMed]

Gradinaru V, Mogri M, Thompson KR, Henderson JM, Deisseroth K. (2009). Optical deconstruction of parkinsonian neural circuitry. Science (New York, N.Y.). 324 [PubMed]

Gradinaru V et al. (2007). Targeting and readout strategies for fast optical neural control in vitro and in vivo. The Journal of neuroscience : the official journal of the Society for Neuroscience. 27 [PubMed]

Gradmann D, Berndt A, Schneider F, Hegemann P. (2011). Rectification of the channelrhodopsin early conductance. Biophysical journal. 101 [PubMed]

Gradmann D, Ehlenbeck S, Hegemann P. (2002). Modeling light-induced currents in the eye of Chlamydomonas reinhardtii. The Journal of membrane biology. 189 [PubMed]

Granger BE, Pérez F. (2007). IPython: A System for Interactive Scientific Computing Computing in Science & Engineering. 9

Grossman N, Nikolic K, Toumazou C, Degenaar P. (2011). Modeling study of the light stimulation of a neuron cell with channelrhodopsin-2 mutants. IEEE transactions on bio-medical engineering. 58 [PubMed]

Grossman N et al. (2013). The spatial pattern of light determines the kinetics and modulates backpropagation of optogenetic action potentials. Journal of computational neuroscience. 34 [PubMed]

Gunaydin LA et al. (2010). Ultrafast optogenetic control. Nature neuroscience. 13 [PubMed]

Han X, Boyden ES. (2007). Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution. PloS one. 2 [PubMed]

Hegemann P, Ehlenbeck S, Gradmann D. (2005). Multiple photocycles of channelrhodopsin. Biophysical journal. 89 [PubMed]

Hegemann P, Möglich A. (2011). Channelrhodopsin engineering and exploration of new optogenetic tools. Nature methods. 8 [PubMed]

Hernandez VH et al. (2014). Optogenetic stimulation of the auditory pathway. The Journal of clinical investigation. 124 [PubMed]

Hines ML, Carnevale NT. (2000). Expanding NEURON's repertoire of mechanisms with NMODL. Neural computation. 12 [PubMed]

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

Ishizuka T, Kakuda M, Araki R, Yawo H. (2006). Kinetic evaluation of photosensitivity in genetically engineered neurons expressing green algae light-gated channels. Neuroscience research. 54 [PubMed]

Klapoetke NC et al. (2014). Independent optical excitation of distinct neural populations. Nature methods. 11 [PubMed]

Konermann S et al. (2013). Optical control of mammalian endogenous transcription and epigenetic states. Nature. 500 [PubMed]

Kuhne J et al. (2015). Early formation of the ion-conducting pore in channelrhodopsin-2. Angewandte Chemie (International ed. in English). 54 [PubMed]

Lagali PS et al. (2008). Light-activated channels targeted to ON bipolar cells restore visual function in retinal degeneration. Nature neuroscience. 11 [PubMed]

Lin JY. (2011). A user's guide to channelrhodopsin variants: features, limitations and future developments. Experimental physiology. 96 [PubMed]

Lin JY, Lin MZ, Steinbach P, Tsien RY. (2009). Characterization of engineered channelrhodopsin variants with improved properties and kinetics. Biophysical journal. 96 [PubMed]

Liu Y et al. (2015). OptogenSIM: a 3D Monte Carlo simulation platform for light delivery design in optogenetics. Biomedical optics express. 6 [PubMed]

Muller E et al. (2015). Python in neuroscience. Frontiers in neuroinformatics. 9 [PubMed]

Nagel G et al. (2003). Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proceedings of the National Academy of Sciences of the United States of America. 100 [PubMed]

Newville M, Stensitzki T, Allen DB, Ingargiola A. (2014). LMFIT: Non-Linear Least-Square Minimization and Curve-Fitting for Python Zenodo.

Nikolic K et al. (2009). Photocycles of channelrhodopsin-2. Photochemistry and photobiology. 85 [PubMed]

Nikolic K et al. (2007). A non-invasive retinal prosthesis - testing the concept. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference. 2007 [PubMed]

Petreanu L, Mao T, Sternson SM, Svoboda K. (2009). The subcellular organization of neocortical excitatory connections. Nature. 457 [PubMed]

Shoham S, Deisseroth K. (2010). Special issue on optical neural engineering: advances in optical stimulation technology. Journal of neural engineering. 7 [PubMed]

Stehfest K, Hegemann P. (2010). Evolution of the channelrhodopsin photocycle model. Chemphyschem : a European journal of chemical physics and physical chemistry. 11 [PubMed]

Topalidou M, Leblois A, Boraud T, Rougier NP. (2015). A long journey into reproducible computational neuroscience. Frontiers in computational neuroscience. 9 [PubMed]

Wang H et al. (2007). High-speed mapping of synaptic connectivity using photostimulation in Channelrhodopsin-2 transgenic mice. Proceedings of the National Academy of Sciences of the United States of America. 104 [PubMed]

Williams JC et al. (2013). Computational optogenetics: empirically-derived voltage- and light-sensitive channelrhodopsin-2 model. PLoS computational biology. 9 [PubMed]

Yizhar O, Fenno LE, Davidson TJ, Mogri M, Deisseroth K. (2011). Optogenetics in neural systems. Neuron. 71 [PubMed]

Zhang F et al. (2011). The microbial opsin family of optogenetic tools. Cell. 147 [PubMed]

Zhang F, Wang LP, Boyden ES, Deisseroth K. (2006). Channelrhodopsin-2 and optical control of excitable cells. Nature methods. 3 [PubMed]

Zhang F et al. (2007). Multimodal fast optical interrogation of neural circuitry. Nature. 446 [PubMed]

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