10.3389/fninf.2018.00080.s003
Gorka Epelde
Gorka
Epelde
Fearghal Morgan
Fearghal
Morgan
Andoni Mujika
Andoni
Mujika
Frank Callaly
Frank
Callaly
Peter Leškovský
Peter
Leškovský
Brian McGinley
Brian
McGinley
Roberto Álvarez
Roberto
Álvarez
Axel Blau
Axel
Blau
Finn Krewer
Finn
Krewer
Data_Sheet_3_Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization.PDF
Frontiers
2018
C. elegans experiment definition and results visualization
in silico simulation
brain-inspired computation
biological neural networks
behavioral experiment input encoding
NeuroML
low entropy model specification (LEMS)
neuronal activity visualization
2018-11-13 05:09:33
Dataset
https://frontiersin.figshare.com/articles/dataset/Data_Sheet_3_Web-Based_Interfaces_for_Virtual_C_elegans_Neuron_Model_Definition_Network_Configuration_Behavioral_Experiment_Definition_and_Experiment_Results_Visualization_PDF/7331924
<p>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 behavioral experiments, without requiring knowledge of domain-specific computer-science tools. The framework furthermore allows the graphical visualization 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 behavioral 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.</p>