The Si elegans Project – The Challenges and Prospects of Emulating Caenorhabditis elegans

Blau, Axel; Callaly, Frank; Cawley, Seamus; Coffey, Aedan; Mauro, Alessandro De; Epelde, Gorka; Ferrara, Lorenzo; Krewer, Finn; Liberale, Carlo; Machado, Pedro; Maclair, Gregory; McGinnity, T.M.; Morgan, Frank; Mujika, Andoni; Petrushin, Alessandro; Robin, Gautier; Wade, John

doi:10.1007/978-3-319-09435-9_54

Cited by 8 publications

(8 citation statements)

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“…Stimuli models that have been defined in previous sections have been implemented for the Si elegans platform (Blau et al, 2014 ). This platform provides a Neural Network (NN) that replicates the complete Biological Nervous System (BNS) of the C. elegans and a Physics Engine (PE) that simulates the emerging physical behavior.…”

Section: Methodsmentioning

confidence: 99%

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

Mujika

Leškovský

Álvarez

et al. 2017

Front. Neuroinform.

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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 system. In this paper, we follow a different approach where we model a wide-range of different stimuli, with more flexible neural network configurations and simulations in mind. Moreover, we focus on the stimuli sensation by different types of sensory organs or various sensory principles of the neurons. As part of this work, most common stimuli involved in behavioral assays have been modeled. It includes models for mechanical, thermal, chemical, electrical and light stimuli, and for proprioception-related self-sensed information exchange with the neural network. The developed models have been implemented and tested with the hardware-based Si elegans simulation platform.

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Section: Methodsmentioning

confidence: 99%

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

Mujika

Leškovský

Álvarez

et al. 2017

Front. Neuroinform.

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“…According to rule 2B of the MIESE guidelines , all information needed for the correct implementation of the necessary simulation steps must be included through precise descriptions or references to unambiguous information sources. When it comes to projects such as OpenWorm (Szigeti et al, 2014) or Si elegans (Blau et al, 2014) that aim to simulate a complete life form, a behavioral input encoding is required. As an effort to standardize the C. elegans behavioral experiments input encoding, the following proposal is presented.…”

Section: Methodsmentioning

confidence: 99%

Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation

Epelde¹,

Mujika²,

Alvarez³

et al. 2015

Proceedings of the 3rd International Congress on Neurotechnology, Electronics and Informatics

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This paper discusses a Caenorhabditis elegans (C. elegans) nematode behavioral experiment input encoding. It proposes a common digital representation for behavioral studies with C. elegans. This work is a step forward towards the reproducibility and comparability of in silico simulations of the nematode with real-world experiments. The digital representation is divided into environmental and experimental configurations. The behavioral input is structured by duration-based behavioral experiment types at the top level (i.e. interaction at a specific time, interaction from t0-t1 and overall duration) and by interaction type (i.e. mechanotaxis, chemotaxis, thermotaxis, galvanotaxis and phototaxis) for each duration-based type. The environment configuration is composed of the identification of the worm's mutation type, worm crowding, initial location, configuration of the assay plate, and obstacle settings. Parameters are defined by an XML schema to ensure the interoperability with other simulation solutions. It is being implemented and tested in the context of the Si elegans project.

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“…The results presented in Section 3 were obtained by running experiments on the Si elegans open-access platform for the accurate emulation of the C. elegans nervous system [25]. This platform provides a sophisticated emulation environment, exploiting an advanced design environment where users can design their own custom neuron models, or use models from a model library, to run and visualise the results on a unique 3D Virtual Arena (VA).…”

Section: Accepted Manuscriptmentioning

confidence: 99%

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

et al. 2018

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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.

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The Si elegans Project – The Challenges and Prospects of Emulating Caenorhabditis elegans

Cited by 8 publications

References 1 publication

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

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

Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation

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

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