Arkheia: data management and communication for open computational neuroscience.
- 1FRE3693 Unité de Neuroscience, Information et Complexité (UNIC), France
- 2UMR7210 Institut de la Vision, France
Two trends have been unfolding in computational neuroscience during the last decade.
First, a shift of focus 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, a general trend in
science towards more open communication, both internally, with other potential scientific
collaborators, and externally, with the wider public. This multi-faceted development
towards more integrative approaches and more intense communication within and
outside of the field poses major new challenges for modellers, 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.
Arkheia is 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
web browser-based application. Arkheia is focused on 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 API for database access, so that any
project can write its own backend translating its data into the Arkheia database format.
Arkheia is not a centralized platform, but 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, tool, publishing system, Neuroscience
Received: 24 Oct 2017;
Accepted: 14 Feb 2018.
Edited by:Pedro A. Valdes-Sosa, Clinical Hospital of Chengdu Brain Science Institute, China
Reviewed by:Jan Grewe, Universität Tübingen, Germany
Leslie S. Smith, University of Stirling, United Kingdom
Copyright: © 2018 Antolík and Davison. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Mr. Ján Antolík, FRE3693 Unité de Neuroscience, Information et Complexité (UNIC), Gif-sur-Yvette, France, firstname.lastname@example.org