Rogue Scholar Posts

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Published in Jabberwocky Ecology

What impact did The Carpentries have on me? As a learner, it taught me most of my essential day-to-day computational tools. As an Instructor, it changed how I teach, allowing me to reach more students including those that need help the most. As an organiser, it taught me skills that are essential to collaborating and to managing teams. As a creator, it taught me how to hand off the work to the next leg in the never-ending relay race.

Published in GigaBlog

Marking the 10 th anniversary of the formulation of the FAIR principles, we have one of our GigaBlog Q&A’s with Peter-Bram ‘t Hoen, Alain van Gool, Anna Niehues and Casper de Visser from the Netherlands X-omics Initiative and Radboud University Medical Center in Nijmegen, authors of a new paper on publishing FAIR workflows.

Published in bjoern.brembs.blog
Author Björn Brembs

It was my freshman year, 1991. I was enthusiastic to finally be learning about biology, after being forced to waste a year in the German army’s compulsory service at the time. Little did I know that it was the same year a research paper was published that would guide the direction of my career to this day, more than 30 years later. Many of the links in this post will go to old web pages I created while learning about this research.

Published in Jabberwocky Ecology

After posting yesterday that we were ramping up the blog again, my RSS feed let me know that arguably the most impactful ecology blog of all time, Dynamic Ecology, was doing the same thing! We also heard from Terry McGlynn who has recently moved and renamed his really important blog, now a newsletter named Science For Everyone. And we heard from multiple other folks that they are in the process of spinning up new blogs/newsletters.

Published in Jabberwocky Ecology

We started Jabberwocky Ecology back in 2008 when blogs were becoming the dominant medium for informal (online) academic discussions. About the same time a handful of other ecology blogs got going and for a while the academic “blogosphere” was the hub for the sorts of things we now often talk about on other social media platforms.

Published in quantixed

I am having some fun running AlphaPulldown on a computing cluster. A requirement is to have input sequences in FASTA format. I found that I needed to get ~600 sequences. I had a list of the relevant Uniprot IDs. Surely getting the sequences for these proteins should be straightforward? Solution The Uniprot IDs can be converted – using the ID Mapping Tool on the Uniprot website – into any number of other IDs.

Published in quantixed

Bands have been known to declare “No Synths!” on their albums. This statement was a badge of pride indicating that the artists hadn’t used any modern trickery in their recordings. Today, the growing use of artificial intelligence (AI) and large language models (LLMs) in science has created a similar scenario. Advocates argue that these tools improve every aspect of science, including the publication process.

Published in Jabberwocky Ecology

We’re excited to announce the initial release of crown maps for 100 million trees in the National Ecological Observatory Network (NEON) with information on location, species identify, size, and alive/dead status. Using NEON’s remote sensing data we’ve been developing computer vision models to locate tree crowns for all individuals visible from above and classify those crowns to species (Weinstein et al. 2019, 2020, 2023; Marconi et al. 2022).