Journal Club 9:30-10:30

Daniel Russ - A Harmonized Atlas of Spinal Cord Cell Types and Their Computational Classification
Daniel E. Russ*, Ryan B. Patterson Cross*, Li Li, Stephanie C. Koch, Kaya J.E. Matson, Ariel J. Levine

Abstract - Single cell sequencing is transforming many fields of science but the vast amount of data it creates has the potential to both illuminate and obscure underlying biology. To harness the exciting potential of single cell data for the study of the mouse spinal cord, we have created a harmonized atlas of spinal cord transcriptomic cell types that unifies six independent and disparate studies into one common analysis. With the power of this large and diverse dataset, we reveal spinal cord cell type organization, validate a combinatorial set of markers for in-tissue spatial gene expression analysis, and optimize the computational classification of spinal cord cell types based on transcriptomic data. This work provides a comprehensive resource with unprecedented resolution of spinal cord cell types and charts a path forward for how to utilize transcriptomic data to expand our knowledge of spinal cord biology.

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Guest: Ariel Lavine - the neurobiology plasticity argument by a neurobiologist

Dr. Levine received an undergraduate degree in biology from Brandeis University in 2000, a Ph.D. from The Rockefeller University in 2008, and an M.D. from Cornell University in 2009. During her graduate research with Dr. Ali Brivanlou, she studied the role of TGF-β signaling during embryonic development. Dr. Levine did postdoctoral research with Dr. Samuel Pfaff at The Salk Institute, where she identified a novel population of spinal neurons that encode “motor synergies” – modular neural programs for simple movements that are thought to underlie a wide variety of common behaviors. She was an Associate Member of the Reeve Foundation Consortium and a Fellow of the George Hewitt Foundation. She joined NINDS in 2015 where her lab studies how the molecules, neurons, and circuits of the spinal cord mediate normal behavior and learn.

10:30-11:30 Hackaton

Traversing large files in Box, chunk by chunk

downloads:

https://developer.box.com/guides/downloads/get-url

uploads:

https://developer.box.com/guides/uploads/chunked

Web Components

... custom elements, shadow DOM etc - give it a try

class helloWorld extends HTMLElement {

connectedCallback() {

this.innerHTML = `<h3>Hello world at ${Date()}</h3>`;

}

}

customElements.define('hello-world', helloWorld);

BigQuery open session …

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Rendering manifests

example for Kundan: https://web4bio.github.io/webgen/presentationPoster

see manifest at https://github.com/web4bio/webgen/tree/master/presentationPoster

And another example, with interactive pages: https://github.com/jonasalmeida/presentations/blob/gh-pages/slides/presentations.json

rendered here: https://jonasalmeida.github.io/presentations/slides/culturgest.html

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