Tools and Services

G-Node provides various services and tools to facilitate data access, data management, and data sharing.

Data Access

File Format for Neuroscientific Data

The Electrophysiology Task Force of the INCF Program on Standards for Data Sharing aims at developing standardized methods and models for storing electrophysiology and other neuroscience data together with their metadata in one common file format based on HDF5.
Starting from these efforts we developed a file format that uses highly generic models for experimental data and metadata, and defines standard schemata for HDF5 files representing these models (Stoewer et al 2014). Version 1.0 is available with libraries for C++ on Windows and Linux, as well as Python, Matlab and Java bindings.
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Neuroshare Tools

Neuroshare is a standard API to access data in proprietary formats, which is supported by many vendors. We develop a number of tools to facilitate data access through Neuroshare, such as

 

Data Objects for Neurophysiology

We are involved in the development of NEO, python objects for neurophysiology data that could serve as a common object model for neurophysiology.
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Data Annotation

In a collaboration with people from the Bernstein Center Munich we develop a standard metadata format for data annotation in electrophysiology, odML, which accounts for the variety of experimental approaches by providing flexibility in terms of the information that is stored (Grewe et al 2011).
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Terminologies for Electrophysiology
are part of the odML metadata approach. Using a common terminology facilitates data sharing and reproducibility of experiments. We invite the community to provide input and feedback.
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Data Management and Sharing

The G-Node data management platform is a service that lets you organize, annotate, and access your data through a web browser, which is a great way of ensuring access to your data wherever you are, and for sharing your data with your collaborators or the public.

Currently the infrastructure of this service is revised to utilize state-of-the-art technology for versioned data management and create compatibility with other developments in the field, such as DataLad (datalad.org).
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G-Node is a DOI Data Center and can provide Digital Object Identifiers for hosted datasets. If you want to have your data citable by a DOI, or if you have other specific data management or data sharing requirements that cannot be dealt with using our standard services, please contact us at info@g-node.org

 

Hosted Services and Collaborations

Cocomac 2

We support the continued development of Rolf Kötter's Database of Cortical Connectivity in the Macaque and host an new version of the database with improved features and an improved interface at cocomac.g-node.org (The original Cocomac database will continue to be available at cocomac.org)
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Spike Sorting Validation

In a collaboration with people from the Bernstein Center Berlin and the Norwegian INCF Node we are setting up a web site for the validation of spike sorting methods. This site provides benchmark datasets and automatically evaluates the sorting results uploaded by users who want to benchmark their spike sorting methods.
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Spyke-Viewer

This site provides extensions for Spyke-Vierwer, A data analysis platform for electrophysiology and neural simulation data, developed by Robert Pröpper at the Bernstein Center Berlin.
[more]

nuSPIC

A web interface to the NEST simulator, presented as a systems identification challenge. Developed by people from the Bernstein Center Freiburg.
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NeuroDebian mirror

G-Node is hosting a repository mirror for NeuroDebian, a turnkey software platform for neuroscience that is created by integrating research tools with the Debian operating system.
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Teaching and Training

G-Node runs and supports different training activities in Neuroinformatics, such as

  Short and Advanced Courses on Neural Data Analysis

and the course on

  Scientify Programming in Python.

We are also involved in the INCF activities to promote training in neuroinformatics.
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