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Manipulate the default connectome provided with TVB to see how structural lesions effect brain dynamics. In this hands-on session you will insert lesions into the connectome within the TVB graphical user interface (GUI). Afterwards, the modified connectome will be used for simulations and the resulting activity will be analysed using functional connectivity.

Difficulty level: Beginner
Duration: 31:22
Speaker: : Paul Triebkorn

Research Resource Identifiers (RRIDs) are ID numbers assigned to help researchers cite key resources (e.g., antibodies, model organisms, and software projects) in biomedical literature to improve the transparency of research methods.

Difficulty level: Beginner
Duration: 1:01:36
Speaker: : Maryann Martone

This video gives a short introduction to the EBRAINS data sharing platform, why it was developed, and how it contributes to open data sharing.

Difficulty level: Beginner
Duration: 17:32
Speaker: : Ida Aasebø

This video explains what metadata is, why it is important, and how you can organize your metadata to increase the FAIRness of your data on EBRAINS.

Difficulty level: Beginner
Duration: 17:23
Speaker: : Ulrike Schlegel

This video introduces the importance of writing a Data Descriptor to accompany your dataset on EBRAINS. It gives concrete examples on what information to include and highlights how this makes your data more FAIR.

Difficulty level: Beginner
Duration: 9:48
Speaker: : Ingrid Reiten
Course:

KnowledgeSpace (KS) is a data discoverability portal and neuroscience encyclopedia that was developed to make it easier for the neuroscience community to find publicly available datasets that adhere to the FAIR Principles and to provide an integrated view of neuroscience concepts found in Wikipedia and NeuroLex linked with PubMed and 17 of the world's leading neuroscience repositories. In short, KS provides a single point of entry where reseaerchers can search for a neuroscience concept of interest and receive results that include: i. a description of the term found in Wikipedia/NeuroLex, ii. links to publicly available datasets related to the concept of interest, and iii. up-to-date references that support the concept of interests found in PubMed. APIs are available so that developers of other neuroscience research infrastructures can integrate KS components in their infrastructures. If your repository or your favorite repository is not indexed in KS, please contact us.

 

Difficulty level: Beginner
Duration: 6:14
Speaker: : Heather Topple

In this lesson, users will learn about the importance of proper citation of software resources and tools used in neuroscientific research. 

Difficulty level: Beginner
Duration: 58:00

The Allen Mouse Brain Atlas is a genome-wide, high-resolution atlas of gene expression throughout the adult mouse brain. This tutorial describes the basic search and navigation features of the Allen Mouse Brain Atlas.

Difficulty level: Beginner
Duration: 6:40

The Allen Developing Mouse Brain Atlas is a detailed atlas of gene expression across mouse brain development. This tutorial describes the basic search and navigation features of the Allen Developing Mouse Brain Atlas.

Difficulty level: Beginner
Duration: 6:35
Speaker: : Unknown

This tutorial demonstrates how to use the differential search feature of the Allen Mouse Brain Atlas to find gene markers for different regions of the brain, as well as to visualize this gene expression in three-dimensional space. Differential search is also available for the Allen Developing Mouse Brain Atlas and the Allen Human Brain Atlas.

Difficulty level: Beginner
Duration: 6:31
Speaker: : Unknown

This lecture covers visualizing extracellular neurotransmitter dynamics

Difficulty level: Beginner
Duration: 23:20

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.

Difficulty level: Beginner
Duration: 1:16:04

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. 

Difficulty level: Beginner
Duration: 52:26

In this hands-on session, you will learn how to explore and work with DataLad datasets, containers, and structures using Jupyter notebooks. 

Difficulty level: Beginner
Duration: 58:05

In this tutorial, you will learn the basic features of uploading and versioning your data within OpenNeuro.org.

Difficulty level: Beginner
Duration: 5:36
Speaker: : OpenNeuro

This tutorial shows how to share your data in OpenNeuro.org.

Difficulty level: Beginner
Duration: 1:22
Speaker: : OpenNeuro

Following the previous two tutorials on uploading and sharing data with OpenNeuro.org, this tutorial briefly covers how to run various analyses on your datasets.

Difficulty level: Beginner
Duration: 2:26
Speaker: : OpenNeuro
Course:

An introduction to data management, manipulation, visualization, and analysis for neuroscience. Students will learn scientific programming in Python, and use this to work with example data from areas such as cognitive-behavioral research, single-cell recording, EEG, and structural and functional MRI. Basic signal processing techniques including filtering are covered. The course includes a Jupyter Notebook and video tutorials.

 

Difficulty level: Beginner
Duration: 1:09:16
Speaker: : Aaron J. Newman

This video will document the process of uploading data into a brainlife project using ezBIDS.

Difficulty level: Beginner
Duration: 6:15
Speaker: :

This video will document the process of visualizing the provenance of each step performed to generate a data object on brainlife.

Difficulty level: Beginner
Duration: 0:21
Speaker: :