- Poster presentation
- Open Access
Visualizing, editing and simulating neuronal models with the Open Source Brain 3D explorer
© Quintana et al. 2015
- Published: 18 December 2015
- Neuronal Model
- Complex Biological System
- Computational Neuroscience
- Multiple Brain Region
- Graphical Framework
Reproducibility, accessibility, standardization, and provenance tracking are some of the main challenges for the global scientific community today. In computational neuroscience, making models available in open and accessible formats is an important strategy for improving transparency and reusability of published models. The Open Source Brain initiative (OSB, http://www.opensourcebrain.org) is an online platform which aims to facilitate sharing and collaborative development of neuronal models. It provides a central location for models of multiple brain regions and species and a set of tools to analyze, edit, visualize and simulate them. While OSB can host models in any format, converting models to NeuroML (specifically v2.0, ) is actively encouraged as it allows OSB to access the internal dynamics of the model. NeuroML2 is a simulator independent model description language for computational neuroscience. It has been built on LEMS (Low Entropy Model Specification, ), a general purpose language developed to provide a machine readable way of expressing the structure and dynamics of physical models. These languages facilitate cross-simulator validation, which is a crucial factor in ensuring reproducibility and reusability of models.
This work has been primarily funded by the Wellcome Trust (101445/095667). BM is supported by the Brazilian agency CAPES (2257-13/0).
- Cannon RC, Gleeson P, Crook S, Ganapathy G, Marin B, Piasini E, Silver RA: LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML2. Frontiers in Neuroinformatics. 2014, 8: 79-PubMedPubMed CentralView ArticleGoogle Scholar
- Szigeti B, Gleeson P, Vella M, Khayrulin S, Palyanov A, Hokanson J, Currie M, Cantarelli M, Idili G, Larson S: OpenWorm: an open-science approach to modelling Caenorhabditis elegans. Front. Comput. Neurosci. 2014Google Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.