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

Difficulty level: Intermediate
Duration: 1:19:17
Speaker: : Sonny Chen

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). 

Difficulty level: Intermediate
Duration: 1:15:14
Speaker: : Keon Arbabi

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 provides an overview of how to conceptualize, design, implement, and maintain neuroscientific pipelines in via the cloud-based computational reproducibility platform Code Ocean. 

Difficulty level: Beginner
Duration: 17:01
Speaker: : David Feng

This lesson provides an overview of how to construct computational pipelines for neurophysiological data using DataJoint.

Difficulty level: Beginner
Duration: 17:37
Speaker: : Dimitri Yatsenko

This talk describes approaches to maintaining integrated workflows and data management schema, taking advantage of the many open source, collaborative platforms already existing.

Difficulty level: Beginner
Duration: 15:15
Speaker: : Erik C. Johnson

This hands-on tutorial walks you through DataJoint platform, highlighting features and schema which can be used to build robost neuroscientific pipelines. 

Difficulty level: Beginner
Duration: 26:06
Speaker: : Milagros Marin

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 lesson provides an introduction to the DataLad, a free and open source distributed data management system that keeps track of your data, creates structure, ensures reproducibility, supports collaboration, and integrates with widely used data infrastructure.

Difficulty level: Beginner
Duration: 22:56

This lesson introduces several open science tools like Docker and Apptainer which can be used to develop portable and reproducible software environments. 

Difficulty level: Beginner
Duration: 17:22
Speaker: : Joanes Grandjean

This lecture provides a detailed description of how to incorporate HED annotation into your neuroimaging data pipeline. 

Difficulty level: Beginner
Duration: 33:36
Speaker: : Dung Truong

This lecture covers a wide range of aspects regarding neuroinformatics and data governance, describing both their historical developments and current trajectories. Particular tools, platforms, and standards to make your research more FAIR are also discussed.

Difficulty level: Beginner
Duration: 54:58
Speaker: : Franco Pestilli

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

This lesson provides a short reel on who we are, what we're doing and why we're doing it.

Difficulty level: Beginner
Duration: 2:38
Speaker: :

In this webinar, educators currently implementing collaborative annotation in their classrooms discuss their experiences with collaborative annotation and using Hythothes.is and Canvas App.

Difficulty level: Beginner
Duration: 53:14
Speaker: : Jeremy Dean

This tutorial provides an overview of how to use the feature of Hypothes.is.

Difficulty level: Beginner
Duration: 09:30
Speaker: :

This lesson gives a brief overview of the Hypothes.is functionality from an end user's perspective.

Difficulty level: Beginner
Duration: 5:36
Speaker: : Heather Staines