This is the third and final episode of our series on a giant metagenome assembly from Wisconsin’s Lake Mendota. In the last two episodes, we’ve covered the specialized software and supercomputers behind this project. But every part of this project depends on lakewater samples — so this episode is a look at how researchers get these specialized snapshots of a freshwater ecosystem. [Read More]
This series is the story of a giant metagenome assembly from Wisconsin’s Lake Mendota. In this episode: a look at the supercomputing that stitches together large datasets with the assembler program MetaHipMer2.
Oak Ridge National Lab is home to two supercomputers — Summit and Frontier — that process terabytes of data with MetaHipMer2. But nearby the JGI, a cluster called Dori is also capable of running smaller MetaHipMer assemblies — so we head there for a sense of what this supercomputing looks like.
Lake Mendota sits right next to the University of Wisconsin, Madison. And Trina McMahon’s lab has been sampling the microbes of that lake for over 20 years, to understand how the freshwater ecosystem works.
So a few years ago, when they set out to analyze 500 metagenomes, it was the biggest project the JGI had ever put together.
The next 3 episodes are the story behind that giant assembly from Lake Mendota. In this episode: the software evolution that made metagenome assemblies like this possible. [Read More]
To set up flexible, repeatable experiments on plants and microbes, Trent Northen’s group at Berkeley Lab created a fabricated ecosystem – an EcoFAB. These small plastic growth chambers let researchers around the world compare their work consistently. And EcoFABs also work well in the classroom. This episode, we visit Los Medanos College to see EcoFabs in action in Jill Bouchard’s BIO 21 lab course. [Read More]
To understand how organisms adapt to extreme environments, Marike Palmer and Brian Hedlund study organisms living in hot springs. Hear how their recent work revealed more about the history of the Chloroflexota phylum and a new way of moving: a tail-like flagella. [Read More]
A quick snippet on Antonio Camargo and Simon Roux, a few of the JGI researchers behind software that finds plasmids and viruses within microbial genomes. As mobile genetic elements like viruses spread their DNA, they can affect how microbes cycle nutrients and adapt to climate change. [Read More]
Meet researchers who have hiked, rafted and met local wildlife (a marmot!) as they’ve sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains. These lakes are isolated, but varied. They’re a great way to see how climate change affects freshwater ecosystems, and how those ecosystems work. [Read More]