This lecture covers structured data, databases, federating neuroscience-relevant databases, ontologies.
Since their introduction in 2016, the FAIR data principles have gained increasing recognition and adoption in global neuroscience. FAIR defines a set of high-level principles and practices for making digital objects, including data, software, and workflows, Findable, Accessible, Interoperable, and Reusable. But FAIR is not a specification; it leaves many of the specifics up to individual scientific disciplines to define. INCF has been leading the way in promoting, defining, and implementing FAIR data practices for neuroscience. We have been bringing together researchers, infrastructure providers, industry, and publishers through our programs and networks. In this session, we will hear some perspectives on FAIR neuroscience from some of these stakeholders who have been working to develop and use FAIR tools for neuroscience. We will engage in a discussion on questions such as: how is neuroscience doing with respect to FAIR? What have been the successes? What is currently very difficult? Where does neuroscience need to go?
This lecture covers FAIR atlases, from their background, their construction, and how they can be created in line with the FAIR principles.
This talk highlights a set of platform technologies, software, and data collections that close and shorten the feedback cycle in research.
An agent for reproducible neuroimaging
The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.
As models in neuroscience have become increasingly complex, it has become more difficult to share all aspects of models and model analysis, hindering model accessibility and reproducibility. In this session, we will discuss existing resources for promoting FAIR data and models in computational neuroscience, their impact on the field, and the remaining barriers. This lecture covers how to make modeling workflows FAIR by working through a practical example, dissecting the steps within the workflow, and detailing the tools and resources used at each step.
As models in neuroscience have become increasingly complex, it has become more difficult to share all aspects of models and model analysis, hindering model accessibility and reproducibility. In this session, we will discuss existing resources for promoting FAIR data and models in computational neuroscience, their impact on the field, and the remaining barriers. This lecture covers the structured validation process within computational neuroscience, including the tools, services, and methods involved in simulation and analysis.
The course is an introduction to the field of electrophysiology standards, infrastructure, and initiatives. This lecture discusses the FAIR principles as they apply to electrophysiology data and metadata, the building blocks for community tools and standards, platforms and grassroots initiatives, and the challenges therein.
This session provides users with an introduction to tools and resources that facilitate the implementation of FAIR in their research.
This session will include presentations of infrastructure that embrace the FAIR principles developed by members of the INCF Community.
This lecture provides an overview of The Virtual Brain Simulation Platform.
Demo of the BRIAN Simulator. BRIAN is a free, open source simulator for spiking neural networks. It is written in the Python programming language and is available on almost all platforms. We believe that a simulator should not only save the time of processors, but also the time of scientists. Brian is therefore designed to be easy to learn and use, highly flexible and easily extensible.
NeuroFedora is a volunteer driven initiative to provide a ready to use Fedora based Free/Open Source Software platform for neuroscience. We believe that similar to Free Software, science should be free for all to use, share, modify, and study. The use of Free Software also aids reproducibility, data sharing, and collaboration in the research community. By making the tools used in the scientific process easier to use, NeuroFedora aims to take a step to enable this ideal. The CompNeuro Fedora Lab was specially to enable computational neuroscience. It includes everything you will need to get your work done—modelling software, analysis tools, general productivity tools—all well integrated with the modern GNOME platform to give you a complete operating system.
neurolib is a computational framework for simulating coupled neural mass models written in Python. It helps you to easily load structural brain scan data to construct brain networks where each node is a neural mass representing a single brain area. This network model can be used to simulate whole-brain dynamics. neurolib provides a simulation and optimization framework which allows you to easily implement your own neural mass model, simulate fMRI BOLD activity, analyse the results and fit your model to empirical data.
GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users.
This video gives a short introduction to the EBRAINS data sharing platform, why it was developed, and how it contributes to open data sharing.
This video demonstrates how to find, access, and download data on EBRAINS.
Peer Herholz gives a tour of how popular virtualization tools like Docker and Singularity are playing a crucial role in improving reproducibility and enabling high-performance computing in neuroscience.
Today’s (neuro)scientific computing landscape depends more than ever on selecting, combining, and implementing a range of tools and technologies for each specific use case. For decades, neuroscience users have turned to MATLAB as an integration environment for pioneering & innovative small-scale studies. Tune in to learn how today’s MATLAB integrates with today’s powerful tools & technologies for larger-scale and next-generation neuroscience challenges.
This workshop will introduce reproducible workflows and a range of tools along the themes of organisation, documentation, analysis, and dissemination. After a brief introduction to the topic of reproducibility, the workshop will provide specific tips and tools useful in improving daily research workflows. The content will include modules such as data management, electronic lab notebooks, reproducible bioinformatics tools and methods, protocol and reagent sharing, data visualisation, and version control. All modules include interactive learning, real-time participation, and active knowledge sharing. The methods and tools introduced help researchers share work with their future self, their immediate colleagues, and the wider scientific community.