Here’s a quick test running Dorado basecaller on ONT long read files in a Google Colab GPU instance, based on previous notes written by Miles Benton.

With the dusts of a hot and tumultuous September finally in tow, I decided to spent the month’s last few days at my friend Sebastian’s new place. His new lab is situated atop a hill overlooking a small pebble strewn Long Island beach side, surrounded by fresh air and lush greenery.

Our preprint addressing a fascinating Haloarchaeal genome discovery is right around the corner! There’s always a chance what we’re looking at is erroneous, but due diligence so far suggests otherwise. I’m really excited about the initial feedback- it looks like my first official publication could start off with a bang.

I’ve been away from this lab notebook for a little while – for good reasons. Pace of projects I’m involved in moved at breakneck speeds, and some of them being publication facing projects ended up enforcing a bit of self-imposed embargo for the stuff I’d normally write about.

Continuing on with the Halobacterium long-term culture observations. So out of the ‘unknown status’ cultures recorded on January 28th, 2020/Mar17 and 2020/Mar30 cultures remain questionable. I think Mar30 culture will end up picking up soon, but it could be safe at this stage to assume Mar17 culture is simply dead.

Before going further – Jan 27th was something of a momentous day. Our Deinococcus radiophilus genome submission finally became the representative genome on Genbank! Now I just need to get the preprint out there.

Note: This particular lab note is from an ongoing project in collaboration with a different lab. Please pardon some of the necessary vagueness.

Our warehouse lab has a new addition – a Thelio desktop computer from System76, fully decked out with 32 thread AMD Ryzen 9 5950X and 64GB of ECC RAM.

A quick note on minor housekeeping stuff for the unidentified Methylobacterium species we recovered from the East River (December 25th, 2021). Some of the culture plates started exhibiting anomalous growth patterns on the PPES-K plates.

Following is an early work-in-progress draft for an upcoming zine “Genome assembly for artists.” The content here is released under CC BY-NC-SA license. Normally I work with publicly accessible databases full of assembled genomes and other biological data, like the almost eponymous NCBI Genbank.

Quick note on what might be a second-to-last test of the HMW Deinococcus genome extraction. I set up a 24 hour ethanol precipitation reaction following the usual lysis step.