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.

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

This tutorial demonstrates how to perform cell-type deconvolution in order to estimate how proportions of cell-types in the brain change in response to various conditions. While these techniques may be useful in addressing a wide range of scientific questions, this tutorial will focus on the cellular changes associated with major depression (MDD). 

This is a tutorial on how to simulate neuronal spiking in brain microcircuit models, as well as how to analyze, plot, and visualize the corresponding data. 

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. 

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. 

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. 

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. 

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. 

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

This video will document the process of creating a pipeline rule for batch processing on brainlife.

This video will document the process of launching a Jupyter Notebook for group-level analyses directly from brainlife.

This lesson introduces the practical exercises which accompany the previous lessons on animal and human connectomes in the brain and nervous system. 

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.

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

This lecture and tutorial focuses on measuring human functional brain networks, as well as how to account for inherent variability within those networks. 

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. 

This lecture gives an overview of how to prepare and preprocess neuroimaging (EEG/MEG) data for use in TVB.