We just published a dataset of canopy tree maps for 100 million trees in the National Ecological Observatory Network (NEON) with information on location, species identify, size, and whether the tree is alive.

Welcome back to our next installment of: what the heck is happening with the Portal rodents? For those just tuning in, I might recommend reading our first two installments: Regime Shift Cometh? and Regime Shift Still Cometh? June in the Arizona desert can be a brutal time for conducting the Portal rodent trip.

The debate between Yann LeCun and Elon Musk, reported in Nature, questions whether science necessitates publishing results. My position is that science depends on how you produce your knowledge, not necessarily requiring publication. Only if you face the public, you need to publish about your work.

tl;dr : metrics-obsessed capitalism is the reason why we can’t have nice things – and watch @tante’s talk Back in Paris, I was semi-joking with friends about how the rate of technological innovations seem to have slowed down or come to a halt. The last “big” innovation that we could think about were smartphones, as carrying the internet permanently in our pockets was quite a change.

Back when I had optimistic views of my time, I vowed to do more blogging this year. Sadly, life had other plans. But I return with an update to an earlier post on the Portal rodent community. To recap, in April 2023, my student Pat Dumandan and I were afraid. Afraid that Chaetodipus penicillatus (the Desert pocket mouse) was about to undergo a population explosion.

Author Amir Aryani: (ORCID: 0000-0002-4259-9774) Definition A research collaboration network is a group of researchers, and practitioners, or both, working together on joint research activities. These networks often span across disciplines, geographic boundaries, and sectors, enabling participants to share resources, expertise, and data to address common research goals more effectively than they could individually.

Hot on the heals of the post on how to downsize microscopy movie files, let’s look at ways to shrink the size of a PDF file. There’s several ways to tackle this – suggestions came from this thread on Mastodon. Scenario: you have created a preprint/manuscript/proposal in PDF format.

What’s the best way to make a movie file from microscopy data? Maybe you need to generate a movie for the supplementary info for a paper, or insert one into your electronic lab notebook, or to show in a talk. The problem is that the requirements for each of those is different. This situation is compounded by the fact that there are so many options to make movie files and not much guidance on what is the best method.

This is a rather niche post, but the method can likely be adapted for other use cases. In the lab we have many different cell lines stored in liquid nitrogen. The arrangement is: the vials are in specific positions in a box (10 x 10) there are 13 boxes to a cane we have 5 canes Ideally, to retrieve the correct vial from the cell store requires a map.

Answering the question of what fraction of a journal’s papers were previously available as a preprint is quite difficult to do. The tricky part is matching preprints (from a number of different servers) with the published output from a journal.