Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation
Authors: Andoni Mujika Amunarriz Roberto Álvarez Sánchez Alessandro de Mauro Finn Krewer Axel Blau
Date: 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
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},
}
