c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans

@article{Gleeson2018c302AM,
  title={c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans},
  author={Padraig Gleeson and David Lung and Radu Grosu and Ramin M. Hasani and Stephen David Larson},
  journal={Philosophical Transactions of the Royal Society B: Biological Sciences},
  year={2018},
  volume={373}
}
  • P. Gleeson, David Lung, S. Larson
  • Published 10 September 2018
  • Biology
  • Philosophical Transactions of the Royal Society B: Biological Sciences
The OpenWorm project has the ambitious goal of producing a highly detailed in silico model of the nematode Caenorhabditis elegans. A crucial part of this work will be a model of the nervous system encompassing all known cell types and connections. The appropriate level of biophysical detail required in the neuronal model to reproduce observed high-level behaviours in the worm has yet to be determined. For this reason, we have developed a framework, c302, that allows different instances of… 

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References

SHOWING 1-10 OF 56 REFERENCES
OpenWorm: an open-science approach to modeling Caenorhabditis elegans
TLDR
The rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.
Network control principles predict neuron function in the Caenorhabditis elegans connectome
TLDR
It is predicted that control of the muscles or motor neurons requires 12 neuronal classes, which include neuronal groups previously implicated in locomotion by laser ablation, as well as one previously uncharacterized neuron, PDB, which is validated experimentally.
Three-dimensional simulation of the Caenorhabditis elegans body and muscle cells in liquid and gel environments for behavioural analysis
TLDR
A three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure is created with a particle system–based simulation engine known as Sibernetic, which implements the smoothed particle–hydrodynamics algorithm.
Neurobiology of Caenorhabditis elegans Locomotion: Where Do We Stand?
TLDR
The nematode Caenorhabditis elegans is used for detailed studies of genetic and physiological locomotion mechanisms, and locomotion behavior, the parts constituting the locomotion system, and the relevant neuronal connectivity are described.
Structural Properties of the Caenorhabditis elegans Neuronal Network
TLDR
The wiring diagram reported here can help in understanding the mechanistic basis of behavior by generating predictions about future experiments involving genetic perturbations, laser ablations, or monitoring propagation of neuronal activity in response to stimulation.
Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light
TLDR
A two-photon technique for brain-wide calcium imaging in Caenorhabditis elegans, using wide-field temporal focusing (WF-TeFo) and a nuclear-localized, genetically encoded calcium indicator, NLS-GCaMP5K, that permits unambiguous discrimination of individual neurons within the densely packed head ganglia of C. elegans.
The Multilayer Connectome of Caenorhabditis elegans
TLDR
The C. elegans connectome can be mapped as a multiplex network with synaptic, gap junction, and neuromodulator layers representing alternative modes of interaction between neurons, providing a new topological plan for understanding how aminergic and peptidergic modulation of behaviour is achieved by specific motifs and loci of integration between hard-wired synaptic or junctional circuits.
A Computational Model Based on Multi-Regional Calcium Imaging Represents the Spatio-Temporal Dynamics in a Caenorhabditis elegans Sensory Neuron
TLDR
A novel three-unit Ordinary Differential Equation (ODE) model based on the neuronal responses derived from a Caenorhabditis elegans salt-sensing neuron is described, which can adequately reproduce and predict the temporal responses of each part of the neuron to various types of NaCl concentration changes.
Towards a virtual C. elegans: A framework for simulation and visualization of the neuromuscular system in a 3D physical environment
TLDR
A detailed demonstration of a virtual C. elegans aimed at integrating data in the form of a 3D dynamic model operating in a simulated physical environment and demonstrates successful forward and backward locomotion when sending sinusoidal patterns of neuronal activity to groups of motor neurons.
...
1
2
3
4
5
...