Standardised Representations of Network Structures
Anton Arkhipov, Allen Institute, USA
Tom Close, Monash University, Australia
Sharon Crook, Arizona State University, USA
Kael Dai, Allen Institute, USA
Andrew Davison, UNIC, CNRS, France
Lia Domide, Codemart, Romania & Aix-Marseille Université, France
Salvador Durá-Bernal, SUNY Downstate Medical Center, USA
Viktor Jirsa, Aix-Marseille Université, France
Padraig Gleeson, University College London, UK
Sacha van Albada, Jülich Research Centre, Germany
Marmaduke Woodman, Aix-Marseille Université, France
This SIG deals with the various tools and formats for creating and sharing representations of biological neuronal networks, and will work towards ensuring these are as interoperable and usable as possible for computational neuroscientists.
About this SIG
The motivation for this SIG is the ongoing development of complex data-driven models of neuronal networks, as well as the emergence of general purpose software packages and standardised formats to make it easier to build, specify and share such networks. To encourage researchers to use these common tools and formats (and ultimately create and disseminate higher quality models) we have gathered together developers creating these packages to share code and ideas, to encourage interoperability and have a forum for users and developers to find out about the state of the art and to contribute to a better ecosystem of tools and standards in this area.
Goals and Outcomes
The short-term goals focus on highlighting and promoting existing open source initiatives working with network representations. These include, but are not limited to:
- BMTK, The Brain Modeling Toolkit: github.com/AllenInstitute/bmtk
- NEST: nest-simulator.org
- NetPyNE: netpyne.org
- NeuroML: neuroml.org; github.com/NeuroML/NeuroMLlite
- NineML: nest-simulator.org
- PyNN: neuralensemble.org/PyNN
- Sonata: github.com/AllenInstitute/sonata
- TVB, The Virtual Brain: thevirtualbrain.org
Practical steps will include making sure these are compatible and interoperable where appropriate.
Longer term goals including working towards minimising overlap in functionality/scope, adding other open tools/formats to the interoperability framework and ensuring the use of these (particularly low-level declarative formats) are as transparent and as user-friendly as possible for the modeller.
Recent and upcoming activities
The SIG held its first meeting as a workshop, “Developing, standardising and sharing large-scale cortical network models”, at CNS 2018 in Seattle.
The purpose of this workshop was to highlight some of the initiatives currently underway to build detailed cortical models as well as those projects building the infrastructure to make it easier to develop, disseminate and compare the models. There was general agreement that it was useful for these initiatives to work together to make it easier for users to create detailed network models. An important aspect of all the work presented was that the code was open source and freely available for all. It was clear that all of these initiatives are still in active (sometimes early stages of) development and depend on input from the community and workshops to improve and become more usable.
Concrete steps which are planned going forward include:
- greater support for SONATA in NeuroMLlite, NetPyNE and PyNN
- investigation of areas of overlap in the NetPyNE format and NeuroMLlite and options for reuse of elements of the NetPyNE-UI in OSB
- getting the multi area cortical model into OSB and investigating options for mapping to NeuroML/NeuroMLlite/PyNN
Activities of the SIG will continue and the next online videoconference for the group is planned for September 2018.