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PyRhO: A Multiscale Optogenetics Simulation Platform.

Evans BD, Jarvis S, Schultz SR, Nikolic K - Front Neuroinform (2016)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Centre for Bio-Inspired Technology, Institute of Biomedical Engineering, Department of Electrical and Electronic Engineering, Imperial College London London, UK.

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.

No MeSH data available.


Related in: MedlinePlus

Photocurrent plots from the “recovery” protocol with fitted peak recovery function.
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Figure 4: Photocurrent plots from the “recovery” protocol with fitted peak recovery function.

Mentions: Recovery rate: {Gr0}. Two long light pulses with varying inter-pulse-interval (IPI), Voltage clamp: −70 mV. Light on (first pulse)—light off for e.g., tIPI = {0.5, 1, 2.5, 5, 10}s—light on (second pulse). The software will automatically find the peak values for each recording, align the data to the end of the first pulse and fit an appropriate exponential curve of the form . We note here that this expression is strictly speaking correct only when both O1 and O2 states are empty. Consequently a is left as a free fitting parameter and very short values for tIPI should be avoided to prevent the distortions caused by the faster transitions. An example for wild-type ChR2 is given in Figure 4, where tIPI ≳ 100 ms.


PyRhO: A Multiscale Optogenetics Simulation Platform.

Evans BD, Jarvis S, Schultz SR, Nikolic K - Front Neuroinform (2016)

Photocurrent plots from the “recovery” protocol with fitted peak recovery function.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834562&req=5

Figure 4: Photocurrent plots from the “recovery” protocol with fitted peak recovery function.
Mentions: Recovery rate: {Gr0}. Two long light pulses with varying inter-pulse-interval (IPI), Voltage clamp: −70 mV. Light on (first pulse)—light off for e.g., tIPI = {0.5, 1, 2.5, 5, 10}s—light on (second pulse). The software will automatically find the peak values for each recording, align the data to the end of the first pulse and fit an appropriate exponential curve of the form . We note here that this expression is strictly speaking correct only when both O1 and O2 states are empty. Consequently a is left as a free fitting parameter and very short values for tIPI should be avoided to prevent the distortions caused by the faster transitions. An example for wild-type ChR2 is given in Figure 4, where tIPI ≳ 100 ms.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Centre for Bio-Inspired Technology, Institute of Biomedical Engineering, Department of Electrical and Electronic Engineering, Imperial College London London, UK.

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.

No MeSH data available.


Related in: MedlinePlus