ArticleFrontiers in neuroinformatics2016
PyRhO: A Multiscale Optogenetics Simulation Platform.
Article in Frontiers in neuroinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Dentate gyrus interneurons modulate winner-take-all network dynamics in freely behaving mice.Neuron · 2026Article
- Theoretical analysis of low power synergistic sono-optogenetic control of calcium-dependent synaptic plasticity.Scientific reports · 2026Article
- Theoretical analysis of low-power optogenetic suppression of action potentials in human ventricular cardiomyocytes expressed with potassium-selective channelrhodopsins.Scientific reports · 2026Article
- Bridging Model and Experiment in Systems Neuroscience with Cleo: The Closed-Loop, Electrophysiology, and Optophysiology Simulation Testbed.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Chimeric reference panels for genomic imputation.Genetics · 2026Article
- Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed.bioRxiv : the preprint server for biology · 2025Article
- Theoretical analysis of low power optogenetic control of synaptic plasticity with subcellular expression of CapChR2 at postsynaptic spine.Scientific reports · 2025Article
- Theoretical analysis of low-power deep synergistic sono-optogenetic excitation of neurons by co-expressing light-sensitive and mechano-sensitive ion-channels.Communications biology · 2025Article
- Theoretical prediction of broadband ambient light optogenetic vision restoration with ChRmine and its mutants.Scientific reports · 2024Article
- Optogenetically mediated large volume suppression and synchronized excitation of human ventricular cardiomyocytes.Pflugers Archiv : European journal of physiology · 2023Article
- Optogenetic manipulation of inhibitory interneurons can be used to validate a model of spatiotemporal sequence learning.Frontiers in computational neuroscience · 2023Article
- Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate.Biophysical journal · 2021Article
- Nonlinear response characteristics of neural networks and single neurons undergoing optogenetic excitation.Network neuroscience (Cambridge, Mass.) · 2020Article
- Theoretical optimization of high-frequency optogenetic spiking of red-shifted very fast-Chrimson-expressing neurons.Neurophotonics · 2019Article
- Theoretical analysis of low-power fast optogenetic control of firing of Chronos-expressing neurons.Neurophotonics · 2018Article
- Neuronal gain modulability is determined by dendritic morphology: A computational optogenetic study.PLoS computational biology · 2018Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO. The purpose of developing PyRhO is three-fold: (i) to characterize new (and existing) opsins by automatically fitting a minimal set of experimental data to three-, four-, or six-state kinetic models, (ii) to simulate these models at the channel, neuron and network levels, and (iii) provide functional insights through model selection and virtual experiments in silico. The module is written in Python with an additional IPython/Jupyter notebook based GUI, allowing models to be fit, simulations to be run and results to be shared through simply interacting with a webpage. The seamless integration of model fitting algorithms with simulation environments (including NEURON and Brian2) for these virtual opsins will enable neuroscientists to gain a comprehensive understanding of their behavior and rapidly identify the most suitable variant for application in a particular biological system. This process may thereby guide not only experimental design and opsin choice but also alterations of the opsin genetic code in a neuro-engineering feed-back loop. In this way, we expect PyRhO will help to significantly advance optogenetics as a tool for transforming biological sciences.
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