Geppetto: a reusable modular open platform for exploring neuroscience data and models. (10th September 2018)

• Record Type: Journal Article
• Authors: Cantarelli, Matteo; Marin, Boris; Quintana, Adrian; Earnshaw, Matt; Court, Robert; Gleeson, Padraig; Dura-Bernal, Salvador; Silver, R. Angus; Idili, Giovanni
• Is Part Of: Philosophical transactions. Volume 373:Number 1758(2018)
• Publication Date: 2018-09-10
• Subjects: computational neuroscience -- neuroinformatics -- computational biology -- modelling and simulation -- scientific software -- data visualization; Biology -- Periodicals; Science -- Periodicals; 570
• DOI: 10.1098/rstb.2017.0380
• Languages: English
• ISSNs: 0962-8436

Abstract

Abstract : Geppetto is an open-source platform that provides generic middleware infrastructure for building both online and desktop tools for visualizing neuroscience models and data and managing simulations. Geppetto underpins a number of neuroscience applications, including Open Source Brain (OSB), Virtual Fly Brain (VFB), NEURON-UI and NetPyNE-UI. OSB is used by researchers to create and visualize computational neuroscience models described in NeuroML and simulate them through the browser. VFB is the reference hub for Drosophila melanogaster neural anatomy and imaging data including neuropil, segmented neurons, microscopy stacks and gene expression pattern data. Geppetto is also being used to build a new user interface for NEURON, a widely used neuronal simulation environment, and for NetPyNE, a Python package for network modelling using NEURON. Geppetto defines domain agnostic abstractions used by all these applications to represent their models and data and offers a set of modules and components to integrate, visualize and control simulations in a highly accessible way. The platform comprises a backend which can connect to external data sources, model repositories and simulators together with a highly customizable frontend. This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.