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

Abstract

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 neuronal networks to be generated incorporating varying levels of anatomical and physiological detail, which can be investigated and refined independently or linked to other tools developed in the OpenWorm modelling toolchain.This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.

Integrative biological simulation, neuropsychology, and AI safety

“…For the integrative simulation projects, we encourage interested researchers to consult the publications of the respective research groups to find concrete points of entry. For those attracted to expanding the repertoire of simple organisms that have such platforms, there are many commonalities in the necessary software infrastructure, with tools such as NEURON for simulating Hodgkin-Huxley type models, BluePyOpt for extracting kinetic parameters for experimental data, and NetPyNE/Bionet for specifying network models (Hines and Carnevale 1997;Van Geit et al 2016;Gratiy et al 2018). Aside from the connectome, an area where there are relevant differences between these organisms is in the gene expression of ion channels.…”

“…Moreover, insects share many neurochemical motivational systems with vertebrates and even higher mammals (Panksepp 1998). Proceeding up the evolutionary tree a little further, sophisticated brain centers involved in motor coordination, such as the basal ganglia, are known to be conserved across vertebrates (including zebrafish), and may have homologous structures in arthropods (Grillner and Robertson 2016). In other words, viewed as platforms for research into value-aligned AI systems, there may be clues even from invertebrates and simple vertebrates for how the insights from top-down, neuropsychology-based approaches may be used to design AI systems that possess far greater levels of transparency, intelligibility, and goal structure stability than we see in nature or in our current AI technologies.…”

Integrative biological simulation, neuropsychology, and AI safety

“…Coupling nervous system activity to drive a simulated body is a tractable approach with organisms such as C. elegans and Drosophila. In OpenWorm, for example, the Boyle-Cohen model of neuromuscular coupling allows for the output of connectome dynamics to drive the activation of body wall muscles and a simulated body (Boyle and Cohen 2008;Gleeson et al 2018;Palyanov, Khayrulin, and Larson 2018). Similar models are likely achievable with Drosophila as well.…”

OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

“…Indeed, researchers in the artificial intelligence community have posited that sensorimotor feedback may play a role in allowing future AI systems to learn from experience more efficiently than current data-hungry systems based on deep learning [ 16 ]. As such, we have unified a biomechanical model of C. elegans , Sibernetic [ 17 , 18 ], that incorporates interactions with a fluid or gel environment, with a modelling infrastructure for complex neuronal networks, c302 [ 19 ].…”