This lesson provides an introduction to biologically detailed computational modelling of neural dynamics, including neuron membrane potential simulation and F-I curves.
In this lesson, users learn about the practical differences between MATLAB scripts and functions, as well as how to embed their neuronal simulation into a callable function.
This lesson teaches users how to generate a frequency-current (F-I) curve, which describes the function that relates the net synaptic current (I) flowing into a neuron to its firing rate (F).
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.
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 provides instruction on how to simulate brain tumors with TVB (reproducing publication: Marinazzo et al. 2020 Neuroimage). This tutorial comprises a didactic video, jupyter notebooks, and full data set for the construction of virtual brains from patients and health controls.
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.
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 provides an overview of how to conceptualize, design, implement, and maintain neuroscientific pipelines in via the cloud-based computational reproducibility platform Code Ocean.
In this workshop talk, you will receive a tour of the Code Ocean ScienceOps Platform, a centralized cloud workspace for all teams.
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 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.
JupyterHub is a simple, highly extensible, multi-user system for managing per-user Jupyter Notebook servers, designed for research groups or classes. This lecture covers deploying JupyterHub on a single server, as well as deploying with Docker using GitHub for authentication.