| Title | Geppetto: an open source visualisation and simulation platform for neuroscience |
| Publication Type | Conference Paper |
| Year of Publication | 2017 |
| Authors | Cantarelli, M., Quintana A., Marin B., Earnshaw M., Gleeson P., Court R., McDougal R., R. Silver A., Dura-Bernal S., Larson S., Lytton W. W., & Idili G. |
| Conference Name | Computational Neuroscience Meeting (CNS 17') |
| Keywords | BMC, BMC Neuroscience 2017 |
| Abstract | Geppetto (geppetto.org) is an open-source web-based platform to explore and simulate neuroscience data and models. The platform, originally designed to support the simulation of a cell-level model of C. elegans as part of the OpenWorm project [1], has grown into a generic framework suitable for various neuroscience applications, offering out of the box solutions for data visualisation, integration and simulation. Geppetto is today used by Open Source Brain (opensourcebrain.org) (Fig. 1a), to explore and simulate computational neuroscience models described in NeuroML version 2 with a variety of simulators and by the Virtual Fly Brain (virtualflybrain.org) (Fig. 1b) to explore and visualise anatomy (including neuropil, segmented neurons and gene expression pattern data) and ontology knowledge base of Drosophila melanogaster. Geppetto is also being used to build a new experimental UI for the NEURON simulation environment [2, 3] (Fig. 1c) based on Python and Jupyter. WormSim (wormsim.org) (Fig. 1d) embeds Geppetto to let users explore dynamic mechanical and electrophysiological models of C. elegans produced by the OpenWorm project. Geppetto is capable of reading and visualising experimental data in the NWB format (nwb.org) to allow experimental and computational neuroscientists to share and compare data and models using a common platform. Geppetto is freely available, well documented and has an active user community. Interested potential users can try out the latest version of the platform at live.geppetto.org. |