The Si elegans project • Studying C. elegans behaviour in a virtual environment
Authors: Andoni Mujika Amunarriz Roberto Álvarez Sánchez Axel Blau, Lorenzo Ferrara Alexey Petrushin Martin McGinnity Pedro Machado John Wade Alicia Costalago Meruelo Kofi Appiah Fearghal Morgan, Aedan Coffey Finn Kr
Date: 01.06.2016
Abstract
Since the pioneering work of Niebur and Erdős (1991), who replicated C. elegans locomotion in software for the first time, several virtual simulations of the worm have been published (e.g. Bryden and Cohen 2008, Szigeti et al. 2014). The Si elegans project aims at extending these to the simulation of an anatomically accurate model of the nematode in a virtual environment with realistic sensory input from multiple external stimuli.
The Si elegans platform will provide a publicly available online toolset where behavioural studies with C. elegans can be executed in a completely virtual, yet physically faithful simulated laboratory environment. It uses a 3D biomechanical model for the virtual embodiment of the nematode based on the currently accepted anatomy of the worm. It considers the cuticle, the body wall muscles and the neurons as described in the WormAtlas (Altun and Hall, 2016). External stimuli including mechano-, thermo-, chemo-, photo- and electro-sensation can be defined by the user. Proprioception models are provided as well. The stimuli, as registered by the sensilla organs of the nematode, are propagated as concrete biophysical representations to the respective neurons for further processing downstream. Each of the 302 neurons is represented by a neuron-specific response model being executed on dedicated hardware based on field-programmable gate arrays (FPGAs). Neurons communicate through an electro-optical hardware connectome.
We will present on the Si elegans system architecture and on how the platform can be configured for a specific experiment with user-defined stimuli and neural processing models. We will demonstrate how the platform may help the C. elegans community and neurocomputational scientists in testing hypotheses on neural function and how it will allow to reverse-engineer the principles underlying C. elegans behaviour. The platform will be officially launched for public access in June 2016. For further information, please visit www.si-elegans.eu.
BIB_text
title = {The Si elegans project • Studying C. elegans behaviour in a virtual environment},
pages = {40-40},
keywds = {
C. Elegans, virtual simulation
}
abstract = {
Since the pioneering work of Niebur and Erdős (1991), who replicated C. elegans locomotion in software for the first time, several virtual simulations of the worm have been published (e.g. Bryden and Cohen 2008, Szigeti et al. 2014). The Si elegans project aims at extending these to the simulation of an anatomically accurate model of the nematode in a virtual environment with realistic sensory input from multiple external stimuli.
The Si elegans platform will provide a publicly available online toolset where behavioural studies with C. elegans can be executed in a completely virtual, yet physically faithful simulated laboratory environment. It uses a 3D biomechanical model for the virtual embodiment of the nematode based on the currently accepted anatomy of the worm. It considers the cuticle, the body wall muscles and the neurons as described in the WormAtlas (Altun and Hall, 2016). External stimuli including mechano-, thermo-, chemo-, photo- and electro-sensation can be defined by the user. Proprioception models are provided as well. The stimuli, as registered by the sensilla organs of the nematode, are propagated as concrete biophysical representations to the respective neurons for further processing downstream. Each of the 302 neurons is represented by a neuron-specific response model being executed on dedicated hardware based on field-programmable gate arrays (FPGAs). Neurons communicate through an electro-optical hardware connectome.
We will present on the Si elegans system architecture and on how the platform can be configured for a specific experiment with user-defined stimuli and neural processing models. We will demonstrate how the platform may help the C. elegans community and neurocomputational scientists in testing hypotheses on neural function and how it will allow to reverse-engineer the principles underlying C. elegans behaviour. The platform will be officially launched for public access in June 2016. For further information, please visit www.si-elegans.eu.
}
date = {2016-06-01},
year = {2016},
}
