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

Data: 16.11.2015


Abstract

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 t 0  – t 1  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.

BIB_text

@Article {
title = {Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation},
pages = {115-120},
keywds = {

Behavioral Experiment Input Encoding, C, elegans, Complex Systems Simulation, in Silico Simulation


}
abstract = {

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 t 0  – t 1  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.


}
isbn = {978-989-758-161-8},
date = {2015-11-16},
year = {2015},
}
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