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 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 lesson is an overview of transcriptomics, from fundamental concepts of the central dogma and RNA sequencing at the single-cell level, to how genetic expression underlies diversity in cell phenotypes.
This lesson breaks down the principles of Bayesian inference and how it relates to cognitive processes and functions like learning and perception. It is then explained how cognitive models can be built using Bayesian statistics in order to investigate how our brains interface with their environment.
This lesson corresponds to slides 1-64 in the PDF below.
This lecture covers a lot of post-war developments in the science of the mind, focusing first on the cognitive revolution, and concluding with living machines.
While the previous lesson in the Neuro4ML course dealt with the mechanisms involved in individual synapses, this lesson discusses how synapses and their neurons' firing patterns may change over time.
This lesson delves into the human nervous system and the immense cellular, connectomic, and functional sophistication therein.
As the previous lesson of this course described how researchers acquire neural data, this lesson will discuss how to go about interpreting and analysing the data.
This lesson discusses a gripping neuroscientific question: why have neurons developed the discrete action potential, or spike, as a principle method of communication?
This lesson discusses both state-of-the-art detection and prevention schema in working with neurodegenerative diseases.
This lecture provides an overview of depression (epidemiology and course of the disorder), clinical presentation, somatic co-morbidity, and treatment options.
This lecture provides an introduction to the principal of anatomical organization of neural systems in the human brain and spinal cord that mediate sensation, integrate signals, and motivate behavior.
This lecture focuses on the comprehension of nociception and pain sensation, highlighting how the somatosensory system and different molecular partners are involved in nociception.
This lesson gives an introductory presentation on how data science can help with scientific reproducibility.
This lesson discusses FAIR principles and methods currently in development for assessing FAIRness.
This lecture provides an introduction to the Brain Imaging Data Structure (BIDS), a standard for organizing human neuroimaging datasets.
This lecture covers FAIR atlases, including their background and construction, as well as how they can be created in line with the FAIR principles.
This lecture covers how to make modeling workflows FAIR by working through a practical example, dissecting the steps within the workflow, and detailing the tools and resources used at each step.
This lecture discusses the FAIR principles as they apply to electrophysiology data and metadata, the building blocks for community tools and standards, platforms and grassroots initiatives, and the challenges therein.
This lecture contains an overview of electrophysiology data reuse within the EBRAINS ecosystem.