Dopaminergic and Cholinergic Modulation of Large Scale Networks in silico Using Snudda

Neuromodulation is present throughout the nervous system and serves a critical role for circuit function and dynamics. The computational investigations of neuromodulation in large scale networks require supportive software platforms. Snudda is a software for the creation and simulation of large scale networks of detailed microcircuits consisting of multicompartmental neuron models. We have developed an extension to Snudda to incorporate neuromodulation in large scale simulations. The extended Snudda framework implements neuromodulation at the level of single cells incorporated into large-scale microcircuits. We also developed Neuromodcell, a software for optimizing neuromodulation in detailed multicompartmental neuron models. The software adds parameters within the models modulating the conductances of ion channels and ionotropic receptors. Bath application of neuromodulators is simulated and models which reproduce the experimentally measured effects are selected. In Snudda, we developed an extension to accommodate large scale simulations of neuromodulation. The simulator has two modes of simulation – denoted replay and adaptive. In the replay mode, transient levels of neuromodulators can be defined as a time-varying function which modulates the receptors and ion channels within the network in a cell-type specific manner. In the adaptive mode, spiking neuromodulatory neurons are connected via integrative modulating mechanisms to ion channels and receptors. Both modes of simulating neuromodulation allow for simultaneous modulation by several neuromodulators that can interact dynamically with each other. Here, we used the Neuromodcell software to simulate dopaminergic and muscarinic modulation of neurons from the striatum. We also demonstrate how to simulate different neuromodulatory states with dopamine and acetylcholine using Snudda. All software is freely available on Github, including tutorials on Neuromodcell and Snudda-neuromodulation.

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CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

10.1101/102848 ◽

2017 ◽

Author(s):

Venkata Manem ◽

George Adam ◽

Tina Gruosso ◽

Mathieu Gigoux ◽

Nicholas Bertos ◽

...

Keyword(s):

Stromal Cells ◽

Large Scale ◽

Network Visualization ◽

Visualization Tool ◽

Biological Processes ◽

Web Based ◽

Link Type ◽

A Cell ◽

Large Scale Networks ◽

User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

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ICGenealogy: Mapping the Function of Neuronal Ion Channels in Model and Experiment

10.1101/058685 ◽

2016 ◽

Cited By ~ 2

Author(s):

William F Podlaski ◽

Alexander Seeholzer ◽

Lukas N Groschner ◽

Gero Miesenböck ◽

Rajnish Ranjan ◽

...

Keyword(s):

Ion Channels ◽

Ion Channel ◽

Large Scale ◽

Building Blocks ◽

Web Interface ◽

Neuron Models ◽

Channel Models ◽

Ion Channel Kinetics ◽

Scale Classification

SummaryIon channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretability of simulations. However, the number of published models, and the lack of standardization, make the comparison of models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and model responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling.

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SodaPop: A computational suite for simulating the dynamics of asexual populations

10.1101/189142 ◽

2017 ◽

Author(s):

Louis Gauthier ◽

Rémicia Di Franco ◽

Adrian W.R. Serohijos

Keyword(s):

Protein Evolution ◽

Large Scale ◽

Fitness Landscape ◽

Viral Evolution ◽

Supplementary Information ◽

Fitness Effects ◽

A Cell ◽

Supplementary Material ◽

Asexual Populations ◽

Large Scale Simulations

AbstractMotivationSimulating protein evolution with realistic constraints from population genetics is essential in addressing problems in molecular evolution, from understanding the forces shaping the evolutionary landscape to the clinical challenges of antibiotic resistance, viral evolution and cancer.ResultsTo address this need, we present SodaPop, a new forward-time simulator of large asexual populations aimed at studying their structure, dynamics and the distribution of fitness effects with flexible assumptions on the fitness landscape. SodaPop integrates biochemical and biophysical properties in a cell-based, object-oriented framework and provides an efficient, open-source toolkit for performing large-scale simulations of protein evolution.Availability and implementationSource code and binaries are freely available at https://github.com/louisgt/SodaPop under the GNU GPLv3 license. The software is implemented in C++ and supported on Linux, Mac OS/X and [email protected] informationSupplementary information is available on the Github project page.

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Thalamocortical Assemblies: How Ion Channels, Single Neurons and Large-Scale Networks Organize Sleep Oscillations Alain Destexhe, Terrence J. Sejnowski (Eds.), Oxford University, Oxford

Thalamus & Related Systems ◽

10.1017/s1472928802000341 ◽

2002 ◽

Vol 2 (01) ◽

pp. 87

Author(s):

RodolfoR. Llinás

Keyword(s):

Ion Channels ◽

Large Scale ◽

Single Neurons ◽

Oxford University ◽

Large Scale Networks

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Thalamocortical Assemblies: How Ion Channels, Single Neurons and Large-Scale Networks Organize Sleep OscillationsAlain Destexhe, Terrence J. Sejnowski (Eds.), Oxford University Press, Oxford

Thalamus & Related Systems ◽

10.1016/s1472-9288(02)00034-1 ◽

2002 ◽

Vol 2 (1) ◽

pp. 87-88

Author(s):

R LLINAS

Keyword(s):

Ion Channels ◽

Large Scale ◽

Single Neurons ◽

Oxford University ◽

Large Scale Networks ◽

Oxford University Press

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Mapping the function of neuronal ion channels in model and experiment

eLife ◽

10.7554/elife.22152 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 13

Author(s):

William F Podlaski ◽

Alexander Seeholzer ◽

Lukas N Groschner ◽

Gero Miesenböck ◽

Rajnish Ranjan ◽

...

Keyword(s):

Ion Channels ◽

Ion Channel ◽

Large Scale ◽

Building Blocks ◽

Web Interface ◽

Neuron Models ◽

Channel Models ◽

Ion Channel Kinetics ◽

Scale Classification

Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of simulations. However, the number of published models, and the lack of standardization, make the comparison of ion channel models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling.

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Distribution of spiking and bursting in Rulkov’s neuron model

The European Physical Journal Special Topics ◽

10.1140/epjs/s11734-021-00413-5 ◽

2022 ◽

Author(s):

Gonzalo Marcelo Ramírez-Ávila ◽

Stéphanie Depickère ◽

Imre M. Jánosi ◽

Jason A. C. Gallas

Keyword(s):

Large Scale ◽

Dynamical Response ◽

Neuron Models ◽

Linear Combinations ◽

Neuron Networks ◽

Parameter Ranges ◽

Realistic Neuron ◽

Large Scale Simulations ◽

The Brain ◽

Neuron Dynamics

AbstractLarge-scale brain simulations require the investigation of large networks of realistic neuron models, usually represented by sets of differential equations. Here we report a detailed fine-scale study of the dynamical response over extended parameter ranges of a computationally inexpensive model, the two-dimensional Rulkov map, which reproduces well the spiking and spiking-bursting activity of real biological neurons. In addition, we provide evidence of the existence of nested arithmetic progressions among periodic pulsing and bursting phases of Rulkov’s neuron. We find that specific remarkably complex nested sequences of periodic neural oscillations can be expressed as simple linear combinations of pairs of certain basal periodicities. Moreover, such nested progressions are robust and can be observed abundantly in diverse control parameter planes which are described in detail. We believe such findings to add significantly to the knowledge of Rulkov neuron dynamics and to be potentially helpful in large-scale simulations of the brain and other complex neuron networks.

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Nursing professionals’ attitudes toward use of physical restraints in Styrian nursing homes Austria

Pflege ◽

10.1024/1012-5302/a000649 ◽

2019 ◽

Vol 32 (1) ◽

pp. 57-63

Author(s):

Hannes Mayerl ◽

Tanja Trummer ◽

Erwin Stolz ◽

Éva Rásky ◽

Wolfgang Freidl

Keyword(s):

Nursing Homes ◽

Large Scale ◽

Critical Role ◽

Physical Restraint ◽

Care Practice ◽

Physical Restraints ◽

Convenience Sample ◽

Restraint Use ◽

Positive Attitudes ◽

Nursing Professionals

Abstract. Background: Given that nursing staff play a critical role in the decision regarding use of physical restraints, research has examined nursing professionals’ attitudes toward this practice. Aim: Since nursing professionals’ views on physical restraint use have not yet been examined in Austria to date, we aimed to explore nursing professionals’ attitudes concerning use of physical restraints in nursing homes of Styria (Austria). Method: Data were collected from a convenience sample of nursing professionals (N = 355) within 19 Styrian nursing homes, based on a cross-sectional study design. Attitudes toward the practice of restraint use were assessed by means of the Maastricht Attitude Questionnaire in the German version. Results: The overall results showed rather positive attitudes toward the use of physical restraints, yet the findings regarding the sub-dimensions of the questionnaire were mixed. Although nursing professionals tended to deny “good reasons” for using physical restraints, they evaluated the consequences of physical restraint use rather positive and considered restraint use as an appropriate health care practice. Nursing professionals’ views regarding the consequences of using specific physical restraints further showed that belts were considered as the most restricting and discomforting devices. Conclusions: Overall, Austrian nursing professionals seemed to hold more positive attitudes toward the use of physical restraints than counterparts in other Western European countries. Future nationwide large-scale surveys will be needed to confirm our findings.

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