Author: plydtanthera

Methods papers

When the best hit isn’t the right one: counting fungi from long reads with EMITS

Post provided by Aaron O’Brien · Centro de Biotecnología de Sistemas, Universidad Andrés Bello When a bioinformatics pipeline crashes, at least you know about it. The failures that worry me are the quiet ones: the run finishes, the species table looks plausible, but there are errors hiding inside the results. I’m Aaron O’Brien, a bioinformatician and software engineer at the Centro de Biotecnología de Sistemas … Continue reading When the best hit isn’t the right one: counting fungi from long reads with EMITS

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Practical Tools

It started with a paint tin: The story behind the VTMaxBox

Post provided by Juan C. Diaz-Ricaurte An unexpected beginning in the Cerrado Sometimes, scientific tools emerge from sophisticated laboratories and carefully planned engineering projects. Other times, they begin with an empty paint tin. Ours was definitely the second case. Back in 2018, while working on several research projects in the Brazilian Cerrado, we began discussing a question that would eventually become central to my PhD: … Continue reading It started with a paint tin: The story behind the VTMaxBox

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Ecology, Statistical methods, Theoretical methods

Defining species’ ranges in practice, not just in theory

Post provided by Alexa Fredston What is a range edge? Every ecologist and evolutionary biologist knows what the edges of species’ geographic ranges (also called distributions) mean, in theory. But I’ve learned that we have virtually no agreement on what they are in practice. Give ten researchers a dataset of a species’ occurrences and abundances over space and time to calculate where the range edges … Continue reading Defining species’ ranges in practice, not just in theory

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Ecology, Methods papers, Statistical methods

The Baby and the Teddy Bear: The Flash of Insight Behind the WAH-i Algorithm

Post Provided by Ravi Umadi On a sunny morning after heavy snowfall in the Bavarian winter, I stood by the door of an early train to Munich. Bright sunlight streamed through the glass and lit me up. I thought to myself: it was a good day. Moments later, the train screeched to a halt. The driver announced an unscheduled stop and possible disruptions due to … Continue reading The Baby and the Teddy Bear: The Flash of Insight Behind the WAH-i Algorithm

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Methods papers

Make insect metabarcoding quantitative? Challenge accepted.

Post provided by Ela Iwaszkiewicz-Eggebrecht The journey from scepticism to abundance estimates When I moved to Sweden in 2019 to start a postdoc, I entered a completely new research field. My background was in evolutionary biology, but I knew very little about DNA metabarcoding (identifying many species at once by sequencing barcode DNA from mixed samples). I was joining a project that was developing methods … Continue reading Make insect metabarcoding quantitative? Challenge accepted.

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Lab Methods

Reflecting on the past: developing hyperspectral reflectance spectroscopy for herbarium specimens

Post provided by Aaron Lee Complicated instruments and simple solutions It was an abnormally warm and balmy December in Minnesota, and Dr. Jeannine Cavender-Bares and I were in the lab. The lights were off, blinds were closed, and we had fashioned a makeshift stand to hold a large tungsten halogen lightbulb, angled perfectly to shine into the long fiber optic cable of a spectrometer connected … Continue reading Reflecting on the past: developing hyperspectral reflectance spectroscopy for herbarium specimens

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Ecology, Statistical methods, Theoretical methods

Hybrid Forest Models: integrating mechanistic knowledge and data

Post provided by Yannek Käber and Maximilian Pichler We met at YOMOS, a workshop for early-career researchers and young modelers in ecology supported by the German Society for Ecology, and we came at modeling from opposite ends. Yannek builds dynamic forest models, which are mechanistic models that integrate decades of ecological reasoning about how trees grow, compete, and die. Max builds machine learning models for … Continue reading Hybrid Forest Models: integrating mechanistic knowledge and data

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Ecology, Field Methods, Practical Tools

Goby gummies: the fish ‘lolly’ that provides a window to study predation underwater

Post provided by Christopher Hemingson Close your eyes and picture a predation event. Personally, I default to the Planet Earth series’ “Mountains” episode, in which a snow leopard acrobatically chases a mountain goat across near-vertical cliffs in an adrenaline-inducing pursuit. While iconic, predation sequences like this one generally represent the minority. More often than not, predation events occur on the order of split seconds – … Continue reading Goby gummies: the fish ‘lolly’ that provides a window to study predation underwater

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Code and Applications, Ecology

Processing visual survey data with sampley

Post provided by Jonathan Syme Picture this idyllic scene: You’re on a research vessel that is steadily making its way through the vast blue sea, surveying back and forth along a set of transect lines, its track recorded by a GPS. Through your binoculars, you see a column of spray, an arching back, a fluke that rises high above the water, then disappears. You call … Continue reading Processing visual survey data with sampley

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Ecology, Lab Methods, Methods papers

A longer read on microbes: Why bigger fragments matter in Earth’s harshest habitats

Post provided by Xi Peng When I first started analysing metagenomic data from cold seeps and hot springs, I didn’t expect to spend quite so much time staring at confusing lines of code and fragmented sequences. Yet these digital traces—broken fragments of DNA scattered across a matrix of microbial complexity—hold the fingerprints of life in Earth’s most extreme habitats. In this work, we developed an … Continue reading A longer read on microbes: Why bigger fragments matter in Earth’s harshest habitats

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