Journal:Arkheia: Data management and communication for open computational neuroscience
| Full article title | Arkheia: Data management and communication for open computational neuroscience |
|---|---|
| Journal | Frontiers in Neuroinformatics |
| Author(s) | Antolik, Ján; Davison, Andrew P. |
| Author affiliation(s) | Institut de la Vision, Centre National de la Recherche Scientifique |
| Primary contact | Email: antolikjan at gmail dot com |
| Editors | Valdes-Sosa, Pedro Antonio |
| Year published | 2018 |
| Volume and issue | 12 |
| Page(s) | 6 |
| DOI | 10.3389/fninf.2018.00006 |
| ISSN | 1662-5196 |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | https://www.frontiersin.org/articles/10.3389/fninf.2018.00006/full |
| Download | https://www.frontiersin.org/articles/10.3389/fninf.2018.00006/pdf (PDF) |
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Abstract
Two trends have been unfolding in computational neuroscience during the last decade. First, focus has shifted to increasingly complex and heterogeneous neural network models, with a concomitant increase in the level of collaboration within the field (whether direct or in the form of building on top of existing tools and results). Second, general trends in science have shifted toward more open communication, both internally, with other potential scientific collaborators, and externally, with the wider public. This multi-faceted development toward more integrative approaches and more intense communication within and outside of the field poses major new challenges for modelers, as currently there is a severe lack of tools to help with automatic communication and sharing of all aspects of a simulation workflow to the rest of the community. To address this important gap in the current computational modeling software infrastructure, here we introduce Arkheia, a web-based open science platform for computational models in systems neuroscience. It provides an automatic, interactive, graphical presentation of simulation results, experimental protocols, and interactive exploration of parameter searches in a browser-based application. Arkheia is focused on the automatic presentation of these resources with minimal manual input from users. Arkheia is written in a modular fashion, with a focus on future development of the platform. The platform is designed in an open manner, with a clearly defined and separated application programming interface (API) for database access, so that any project can write its own back-end, translating its data into the Arkheia database format. Arkheia is not a centralized platform, but it allows any user (or group of users) to set up their own repository, either for public access by the general population, or locally for internal use. Overall, Arkheia provides users with an automatic means to communicate information about not only their models but also individual simulation results and the entire experimental context in an approachable, graphical manner, thus facilitating the user's ability to collaborate in the field and outreach to a wider audience.
Keywords: computational modeling, workflow, publish, neuroscience, tool
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Notes
This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. The original article lists references alphabetically, but this version — by design — lists them in order of appearance. What were originally footnotes have been turned into inline external links.
