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Explore how to setup an epileptic seizure simulation with the TVB graphical user interface. This lesson will show you how to program the epileptor model in the brain network to simulate a epileptic seizure originating in the hippocampus. It will also show how to upload and view mouse connectivity data, as well as give a short introduction to the python script interface of TVB.

Difficulty level: Intermediate
Duration: 58:06
Speaker: : Paul Triebkorn

In this lesson you will learn how to simulate seizure events and epilepsy in The Virtual Brain. We will look at the paper On the Nature of Seizure Dynamics, which describes a new local model called the Epileptor, and apply this same model in The Virtual Brain. This is part 1 of 2 in a series explaining how to use the Epileptor. In this part, we focus on setting up the parameters.

Difficulty level: Beginner
Duration: 4:44
Speaker: : Paul Triebkorn

This short video walks you through the steps of publishing a dataset on brainlife, an open-source, free and secure reproducible neuroscience analysis platform.

Difficulty level: Beginner
Duration: 1:18
Speaker: :

This video shows how to use the brainlife.io interface to edit the participants' info file. This file is the ParticipantInfo.json file of the Brain Imaging Data Structure (BIDS).

Difficulty level: Beginner
Duration: 0:34
Speaker: :

This video will document the process of running an app on brainlife, from data staging to archiving of the final data outputs.

Difficulty level: Beginner
Duration: 3:43
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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
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This video will document the process of downloading and running the "reproduce.sh" script, which will automatically run all of the steps to generate a data object locally on a user's machine.

Difficulty level: Beginner
Duration: 3:44
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This video will document the process of creating a pipeline rule for batch processing on brainlife.

Difficulty level: Intermediate
Duration: 0:57
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This video will document the process of launching a Jupyter Notebook for group-level analyses directly from brainlife.

Difficulty level: Intermediate
Duration: 0:53
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This brief video walks you through the steps necessary when creating a project on brainlife.io. 

Difficulty level: Beginner
Duration: 1:45
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This brief video rus through how to make an accout on brainlife.io.

Difficulty level: Beginner
Duration: 0:30
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This video will document how to run a correlation analysis between the gray matter volume of two different structures using the output from brainlife app-freesurfer-stats.

Difficulty level: Beginner
Duration: 1:33
Speaker: :

This lecture introduces you to the basics of the Amazon Web Services public cloud. It covers the fundamentals of cloud computing and goes through both the motivations and processes involved in moving your research computing to the cloud.

Difficulty level: Intermediate
Duration: 3:09:12

As a part of NeuroHackademy 2020, this lecture delves into cloud computing, focusing on Amazon Web Services. 

Difficulty level: Beginner
Duration: 01:43:59

This talk presents an overview of CBRAIN, a web-based platform that allows neuroscientists to perform computationally intensive data analyses by connecting them to high-performance computing facilities across Canada and around the world.

Difficulty level: Beginner
Duration: 56:07
Speaker: : Shawn Brown

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 provides a quick tour of some data repositories and how to download and manipulate data from them.

Difficulty level: Beginner
Duration: 00:49:06
Speaker: : Sebastian Urchs
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 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
Course:

This lesson consists of a talk about the history and future of academic publishing and the need for transparency, as well as a live demo of an alpha version of NeuroLibre, a preprint server that goes beyond the PDF to complement research articles. This video was part of a virutal QBIN SciComm seminar.

Difficulty level: Beginner
Duration: 00:53:35