scholarly journals Mapping the function of neuronal ion channels in model and experiment

eLife ◽  
2017 ◽  
Vol 6 ◽  
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.

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

2016 ◽  
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.

Large-scale classification of major depressive disorder via distributed Lasso

2017 ◽  
Author(s):  
Dajiang Zhu ◽  
Qingyang Li ◽  
Brandalyn C. Riedel ◽  
Neda Jahanshad ◽  
Derrek P. Hibar ◽  
...  
Keyword(s):  
Major Depressive Disorder ◽  
Depressive Disorder ◽  
Large Scale ◽  
Major Depressive ◽  
Scale Classification

Large-scale classification of traffic signs under real-world conditions

2012 ◽  
Author(s):  
Lykele Hazelhoff ◽  
Ivo Creusen ◽  
Dennis van de Wouw ◽  
Peter H. N. de With
Keyword(s):  
Real World ◽  
Large Scale ◽  
Traffic Signs ◽  
Scale Classification

scholarly journals Multi-Branch-CNN: classification of ion channel interacting peptides using parallel convolutional neural networks

2021 ◽  
Author(s):  
Jielu Yan ◽  
Bob Zhang ◽  
Mingliang Zhou ◽  
Hang Fai Kwok ◽  
Shirley W.I. Siu
Keyword(s):  
Neural Networks ◽  
Ion Channels ◽  
Ion Channel ◽  
Convolutional Neural Networks ◽  
Data Sets ◽  
The Novel ◽  
Sodium Potassium ◽  
Test Set ◽  
Drug Candidates

Ligand peptides that have high affinity for ion channels are critical for regulating ion flux across the plasma membrane. These peptides are now being considered as potential drug candidates for many diseases, such as cardiovascular disease and cancers. There are several studies to identify ion channel interacting peptides computationally, but, to the best of our knowledge, none of them published available tools for prediction. To provide a solution, we present Multi-branch-CNN, a parallel convolutional neural networks (CNNs) method for identifying three types of ion channel peptide binders (sodium, potassium, and calcium). Our experiment shows that the Multi-Branch-CNN method performs comparably to thirteen traditional ML algorithms (TML13) on the test sets of three ion channels. To evaluate the predictive power of our method with respect to novel sequences, as is the case in real-world applications, we created an additional test set for each ion channel, called the novel-test set, which has little or no similarities to the sequences in either the sequences of the train set or the test set. In the novel-test experiment, Multi-Branch-CNN performs significantly better than TML13, showing an improvement in accuracy of 6%, 14%, and 15% for sodium, potassium, and calcium channels, respectively. We confirmed the effectiveness of Multi-Branch-CNN by comparing it to the standard CNN method with one input branch (Single-Branch-CNN) and an ensemble method (TML13-Stack). To facilitate applications, the data sets, script files to reproduce the experiments, and the final predictive models are freely available at https://github.com/jieluyan/Multi-Branch-CNN.

A cultura como holismo: grandes divisões espaciais do mundo na pesquisa geográfica germanófona

GEOgraphia ◽  
2010 ◽  
Vol 10 (19) ◽  
pp. 7
Author(s):  
Jörg Scheffer
Keyword(s):  
Cultural Differences ◽  
Large Scale ◽  
Alternative Form ◽  
Current Debate ◽  
The World ◽  
Holistic Concept ◽  
German Speaking ◽  
Scale Classification

Resumo: As divisões do mundo pautadas por marcos culturais têm uma longa tradição na geografia germanófona. Até os dias de hoje, a cultura é conceitualizada como totalidade, o que leva conseqüentemente a que cada divisão absolutize as diferenças culturais. O artigo descreve esta problemática com base nos conceitos clássicos desde os primórdios da geografia até a geografia do presente. Também para a discussão atual pode-se constatar que a idéia de um conceito holístico de cultura ainda permanece usual e até agora não foi substituída por uma regionalização alternativa. O artigo conclui com uma sugestão de como esta regionalização alternativa poderia ser na era da globalização. Culture as holism: large-scale classification of the world in German-speaking geography Abstract: Divisions of the world using culture as the defining trait have had a long history in German geography. Until this day, culture is being conceptionalized as a whole, with the consequence that each division poses cultural differences as absolutes. This essay aims to describe the problem by using traditional concepts from the beginning of geography up to the present. Even in the current debate, as will be shown, the idea of a holistic concept of culture is still in use and has not been replaced yet by an alternative form of regionalisation. The article will conclude with a suggestion of what this would look like in the age of globalisation. Keywords: Culture, division of the world, holism, globalisation, German classics

Utilizing brain measures for large-scale classification of autism applying EPIC

2017 ◽  
Author(s):  
Marc B. Harrison ◽  
Brandalyn C. Riedel ◽  
Gautam Prasad ◽  
Neda Jahanshad ◽  
Joshua Faskowitz ◽  
...  
Keyword(s):  
Large Scale ◽  
Scale Classification

scholarly journals Exploring ion channel mechanisms : from toxin-based tools to computational methods

2016 ◽  
Author(s):  
◽  
Autoosa Salari
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Building Blocks ◽  
Proper Function ◽  
Computational Techniques ◽  
Pharmacological Agents ◽  
Cellular Excitability ◽  
Basic Functions ◽  
Five Senses ◽  
First Time

Ion channels are the building blocks of cellular excitability, controlling the most basic functions necessary for life to the most complex behaviors. The research presented here addresses questions about the mechanisms by which different ion channels function, as well as, how various toxins from venomous animals can alter ion channel behavior. This was done using a combination of molecular biology, electrophysiology, and computational techniques. The results shed light on the specific structures of a channel required for proper function, and target by pharmacological agents. Importantly, these results have significance in developing animal toxins as research tools and as future therapeutic agents for ion channel associated diseases. Lastly, we demonstrate for the first time, a system to study a protein required for high temperature avoidance in fruit flies. This opens the door to addressing detailed questions about the most poorly understood of the five senses, temperature sensation.

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