Modeling Behavioral Experiment Interaction and Environmental Stimuli for a Synthetic C. elegans

  title={Modeling Behavioral Experiment Interaction and Environmental Stimuli for a Synthetic C. elegans},
  author={Andoni Mujika and Peter Leskovsk{\'y} and Roberto {\'A}lvarez and Miguel A. Otaduy and Gorka Epelde},
  journal={Frontiers in Neuroinformatics},
This paper focusses on the simulation of the neural network of the Caenorhabditis elegans living organism, and more specifically in the modeling of the stimuli applied within behavioral experiments and the stimuli that is generated in the interaction of the C. elegans with the environment. To the best of our knowledge, all efforts regarding stimuli modeling for the C. elegansare focused on a single type of stimulus, which is usually tested with a limited subnetwork of the C. elegansneural… 
Unsupervised learning of control signals and their encodings in Caenorhabditis elegans whole-brain recordings
A method to build a global, low-dimensional model of the dynamics, whereby an underlying global linear dynamical system is actuated by temporally sparse control signals which can be predicted both from neurons previously implicated in behavioural transitions but also additional neurons previously unassociated with these behaviours.
Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization
A suite of unified web-based Graphical User Interfaces (GUIs) as the main user interaction point, and discusses their underlying technologies and methods to facilitate reproducible and cross-platform execution of in silico C. elegans experiments in other simulation environments.
The Virtual Patch Clamp: Imputing C. elegans Membrane Potentials from Calcium Imaging
We develop a stochastic whole-brain and body simulator of the nematode roundworm Caenorhabditis elegans (C. elegans) and show that it is sufficiently regularizing to allow imputation of latent


A Physically-based Simulation of a Caenorhabditis elegans
The main contribution of the work is the utilization of biphasic springs in the structure that represents the worm in the virtual environment and a Finite Element Method based internal force field to simulate the internal pressure of the body.
A model of chemotaxis and associative learning in C. elegans
A biophysical model of the ASEL and ASER neurons is constructed that captures the time course of the ASE responses in response to up- and down-steps in NaCl concentration and shows that there is a separation into upward and downward drives mediated by the left and right ASE neurons.
A dynamic body model of the nematode C. elegans with a touch-response circuit
A virtual C. elegans based on the actual nematode to analyze motor control which uses neuronal circuits and muscles and the effectiveness of the model is discussed through simulation results.
Gait Modulation in C. elegans: An Integrated Neuromechanical Model
A model of C. elegans forward locomotion is presented that includes a neuromuscular control system that relies on a sensory feedback mechanism to generate undulations and is integrated with a physical model of the body and environment and reproduces the entire swim-crawl transition with no modulatory mechanism.
The Si elegans Project - The Challenges and Prospects of Emulating Caenorhabditis elegans
The overall concepts are presented with special focus on the virtual embodiment of the nematode with a closed-feedback loop, which will result in motor commands at neuromuscular junctions at the hardware-software interface to actuate virtual muscles of the virtual nematodes.
C. elegans behavioural response germane to Hardware modelling
This paper focuses on consideration of some specific behaviours of the worm for modelling in the hardware based Si elegans system, to establish specific neurons responsible for the worm behaviours.
Neural control of Caenorhabditis elegans forward locomotion: the role of sensory feedback
A simple yet biologically-grounded model for the neural control of Caenorhabditis elegans forward locomotion finds that a minimal circuit of AVB interneurons and B-class motoneurons is sufficient to generate and sustain fictiveforward locomotion patterns that are robust to significant environmental perturbations.
Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation
A Caenorhabditis elegans (C. elegans) nematode behavioral experiment input encoding is proposed, which is a step forward towards the reproducibility and comparability of in silico simulations of the nematodes with real-world experiments.
Integration of mechanosensory stimuli in Caenorhabditis elegans
  • S. R. Wicks, C. Rankin
  • Biology, Psychology
    The Journal of neuroscience : the official journal of the Society for Neuroscience
  • 1995
The effects of ablating some neurons outside the touch circuit suggest roles for two of these cells in the integration of the tap withdrawal response, and no role for the LUA interneurons could be identified.