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This is the first of two workshops on reproducibility in science, during which participants are introduced to concepts of FAIR and open science. After discussing the definition of and need for FAIR science, participants are walked through tutorials on installing and using Github and Docker, the powerful, open-source tools for versioning and publishing code and software, respectively.

Difficulty level: Intermediate
Duration: 1:20:58

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. 

Difficulty level: Intermediate
Duration: 1:27:18
Speaker: : Dan Felsky

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. 

Difficulty level: Intermediate
Duration: 1:53:34
Speaker: : Dan Felsky

This tutorial introduces pipelines and methods to compute brain connectomes from fMRI data. With corresponding code and repositories, participants can follow along and learn how to programmatically preprocess, curate, and analyze functional and structural brain data to produce connectivity matrices. 

Difficulty level: Intermediate
Duration: 1:39:04

This is a tutorial on designing a Bayesian inference model to map belief trajectories, with emphasis on gaining familiarity with Hierarchical Gaussian Filters (HGFs).

 

This lesson corresponds to slides 65-90 of the PDF below. 

Difficulty level: Intermediate
Duration: 1:15:04
Speaker: : Daniel Hauke

This lecture goes into detailed description of how to process workflows in the virtual research environment (VRE), including approaches for standardization, metadata, containerization, and constructing and maintaining scientific pipelines. 

Difficulty level: Intermediate
Duration: 1:03:55
Speaker: : Patrik Bey

This lesson is the first of three hands-on tutorials as part of the workshop Research Workflows for Collaborative Neuroscience. This tutorial goes over how to visualize data with Scanpy, a scalable toolkit for analyzing single-cell gene expression. 

Difficulty level: Intermediate
Duration: 25:26

In this third and final hands-on tutorial from the Research Workflows for Collaborative Neuroscience workshop, you will learn about workflow orchestration using open source tools like DataJoint and Flyte. 

Difficulty level: Intermediate
Duration: 22:36
Speaker: : Daniel Xenes

This lecture describes how to build research workflows, including a demonstrate using DataJoint Elements to build data pipelines.

Difficulty level: Intermediate
Duration: 47:00
Speaker: : Dimitri Yatsenko

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

This tutorial covers the fundamentals of collaborating with Git and GitHub.

Difficulty level: Intermediate
Duration: 2:15:50
Speaker: : Elizabeth DuPre

This lesson provides an overview of Jupyter notebooks, Jupyter lab, and Binder, as well as their applications within the field of neuroimaging, particularly when it comes to the writing phase of your research. 

Difficulty level: Intermediate
Duration: 50:28
Speaker: : Elizabeth DuPre

Learn how to create a standard extracellular electrophysiology dataset in NWB using Python.

Difficulty level: Intermediate
Duration: 23:10
Speaker: : Ryan Ly

Learn how to create a standard calcium imaging dataset in NWB using Python.

Difficulty level: Intermediate
Duration: 31:04
Speaker: : Ryan Ly

In this tutorial, you will learn how to create a standard intracellular electrophysiology dataset in NWB using Python.

Difficulty level: Intermediate
Duration: 20:23
Speaker: : Pamela Baker

Learn how to create a standard intracellular electrophysiology dataset in NWB.

Difficulty level: Intermediate
Duration: 20:22
Speaker: : Pamela Baker

This lesson gives an overview of the Brainstorm package for analyzing extracellular electrophysiology, including preprocessing, spike sorting, trial alignment, and spectrotemporal decomposition.

Difficulty level: Intermediate
Duration: 47:47

This lesson provides an overview of the CaImAn package, as well as a demonstration of usage with NWB.

Difficulty level: Intermediate
Duration: 44:37

This lesson gives an overview of the SpikeInterface package, including demonstration of data loading, preprocessing, spike sorting, and comparison of spike sorters.

Difficulty level: Intermediate
Duration: 1:10:28
Speaker: : Alessio Buccino

In this lesson, users will learn about the NWBWidgets package, including coverage of different data types, and information for building custom widgets within this framework.

Difficulty level: Intermediate
Duration: 47:15
Speaker: : Ben Dichter