This lesson provides an overview of the current status in the field of neuroscientific ontologies, presenting examples of data organization and standards, particularly from neuroimaging and electrophysiology. 

This lesson continues from part one of the lecture Ontologies, Databases, and Standards, diving deeper into a description of ontologies and knowledg graphs. 

This lecture covers the NIDM data format within BIDS to make your datasets more searchable, and how to optimize your dataset searches.

This lecture covers positron emission tomography (PET) imaging and the Brain Imaging Data Structure (BIDS), and how they work together within the PET-BIDS standard to make neuroscience more open and FAIR.

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 lecture discusses how to standardize electrophysiology data organization to move towards being more FAIR.

The International Brain Initiative (IBI) is a consortium of the world’s major large-scale brain initiatives and other organizations with a vested interest in catalyzing and advancing neuroscience research through international collaboration and knowledge sharing. This workshop introduces the IBI, the efforts of the Data Standards and Sharing Working Group,  and keynote lectures on the impact of data standards and sharing on large-scale brain projects, as well as a discussion on prospects and needs for neural data sharing.

This is the third and final lecture of this course on neuroinformatics infrastructure for handling sensitive data. 

In this lecture, you will learn about virtual research environments (VREs) and their technical limitations, (i.e., a computing platform and the software stack behind it) and the security measures which should be considered during implementation. 

This lecture discusses the challenges of protecting hospital data.

This lecture discusses differential privacy and synthetic data in the context of medical data sharing in clinical neurosciences.

This talk presents state-of-the-art methods for ensuring data privacy with a particular focus on medical data sharing across multiple organizations.

In this talk the speakers will give a brief introduction of the Fenix Infrastructure and Service Offering, before focusing on Data Safety. The speaker will take the participants through the ETHZ-CSCS offering for EBRAINS and all the HBP Communities highlighting the Infrastructure role in a service implementation in respect of Security. Particular attention will be on showing what tools ETHZ-CSCS provides to a Portal/Service provider such as EBRAINS, MIP/HIP, TVB, NRP amongst others. Finally there will be given a quick glimpse into the future and the role that “multi-tenancy” will play.

This lecture explains the concept of federated analysis in the context of medical data, associated challenges. The lecture also presents an example of hospital federations via the Medical Informatics Platform.

This lesson continues with the second workshop on reproducible science, focusing on additional open source tools for researchers and data scientists, such as the R programming language for data science, as well as associated tools like RStudio and R Markdown. Additionally, users are introduced to Python and iPython notebooks, Google Colab, and are given hands-on tutorials on how to create a Binder environment, as well as various containers in Docker and Singularity.

This lesson contains both a lecture and a tutorial component. The lecture (0:00-20:03 of YouTube video) discusses both the need for intersectional approaches in healthcare as well as the impact of neglecting intersectionality in patient populations. The lecture is followed by a practical tutorial in both Python and R on how to assess intersectional bias in datasets. Links to relevant code and data are found below. 

This is a hands-on tutorial on PLINK, the open source whole genome association analysis toolset. The aims of this tutorial are to teach users how to perform basic quality control on genetic datasets, as well as to identify and understand GWAS summary statistics. 

This is a tutorial on using the open-source software PRSice to calculate a set of polygenic risk scores (PRS) for a study sample. Users will also learn how to read PRS into R, visualize distributions, and perform basic association analyses. 

This lesson is an overview of transcriptomics, from fundamental concepts of the central dogma and RNA sequencing at the single-cell level, to how genetic expression underlies diversity in cell phenotypes. 

This is a tutorial introducing participants to the basics of RNA-sequencing data and how to analyze its features using Seurat.