Web-based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioural Experiment Definition and Experiment Results Visualisation
Authors: Fearghal Morgan Andoni Mujika Amunarriz Frank Callaly Brian McGinley Roberto Álvarez Sánchez Axel Blau Finn Krewer
Date: 22.10.2018
Frontiers in Neuroinformatics
Abstract
The Si elegans platform targets the complete virtualization of the nematode Caenorhabditis elegans, and its environment. This paper presents a suite of unified web-based Graphical User Interfaces (GUIs) as the main user interaction point, and discusses their underlying technologies and methods. The user-friendly features of this tool suite enable users to graphically create neuron and network models, and behavioural experiments, without requiring knowledge of domain-specific computer-science tools. The framework furthermore allows the graphical visualisation of all simulation results using a worm locomotion and neural activity viewer. Models, experiment definitions and results can be exported in a machine-readable format, thereby facilitating reproducible and cross-platform execution of in silico C.elegans experiments in other simulation environments. This is made possible by a novel XML-based behavioural experiment definition encoding format, a NeuroML XML-based model generation and network configuration description language, and their associated GUIs. User survey data confirms the platform usability and functionality, and provides insights into future directions for web-based simulation GUIs of C. elegans and other living organisms. The tool suite is available online to the scientific community and its source code has been made available.
BIB_text
title = {Web-based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioural Experiment Definition and Experiment Results Visualisation},
journal = {Frontiers in Neuroinformatics},
volume = {12},
keywds = {
C. elegans, C. elegans Experiment Definition and Results Visualisation, In silico simulation, Brain-Inspired Computation, biological neural networks, Behavioural Experiment Input Encoding, neuroml, Low Entropy Model Specification (LEMS), Neuronal Activity
}
abstract = {
The Si elegans platform targets the complete virtualization of the nematode Caenorhabditis elegans, and its environment. This paper presents a suite of unified web-based Graphical User Interfaces (GUIs) as the main user interaction point, and discusses their underlying technologies and methods. The user-friendly features of this tool suite enable users to graphically create neuron and network models, and behavioural experiments, without requiring knowledge of domain-specific computer-science tools. The framework furthermore allows the graphical visualisation of all simulation results using a worm locomotion and neural activity viewer. Models, experiment definitions and results can be exported in a machine-readable format, thereby facilitating reproducible and cross-platform execution of in silico C.elegans experiments in other simulation environments. This is made possible by a novel XML-based behavioural experiment definition encoding format, a NeuroML XML-based model generation and network configuration description language, and their associated GUIs. User survey data confirms the platform usability and functionality, and provides insights into future directions for web-based simulation GUIs of C. elegans and other living organisms. The tool suite is available online to the scientific community and its source code has been made available.
}
doi = {10.3389/fninf.2018.00080},
date = {2018-10-22},
}
