Si elegans: a computational model of C. elegans muscle response to light

It has long been the goal of computational neuroscientists to understand animal nervous systems, but their vast complexity has made it very difficult to fully understand even basic functions such as movement. The C. elegans nematode offers the opportunity to study a fully described connectome and link neural network to behaviour. In this paper a model of the responses of the body wall muscle in C. elegans to a random light stimulus is presented. An algorithm has been developed that tracks synapses in the nematode nervous system from the stimulus in the phototaxis sensory neurons to the muscles cells. A linear second order model was used to calculate the isometric force in each of the C. elegans body wall muscle cells. The isometric force calculated resembles that of previous investigations in muscle modelling

Emulation of chemical stimulus triggered head movement in the C. elegans nematode

For a considerable time, it has been the goal of computational neuroscientists to understand biological nervous systems. However, the vast complexity of such systems has made it very difficult to fully understand even basic functions such as movement. Because of its small neuron count, the C. elegans nematode offers the opportunity to study a fully described connectome and attempt to link neural network activity to behaviour. In this paper a simulation of the neural network in C. elegans that responds to chemical stimulus is presented and a consequent realistic head movement demonstrated. An evolutionary algorithm (EA) has been utilised to search for estimates of the values of the synaptic conductances and also to determine whether each synapse is excitatory or inhibitory in nature. The chemotaxis neural network was designed and implemented, using the parameterization obtained with the EA, on the Si elegans platform a state-of-the-art hardware emulation platform specially designed to emulate the C. elegans nematode

Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization

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