Interesting new things have been happening at the Binomica labs, and we’re updating our page to better directly deliver our new activities to anyone interested in us, or amateur research in general. Thanks to the inimitable Cris for the previous design, which had been the face of our research group for the last couple of years!
We hope to share detailed lab news and results of our researches so far in future posts dedicated to each specific topic – but for now here are a few housekeeping items:
If you’re new and would like to figure out what exactly we’re about, please check out the new About Us page – even if you already know us it might be worth a quick look. I believe we have a far clearer and focused message to share now.
We’re preparing for regularly scheduled, casual podcasts covering research items and thoughts. More news on this later.
The Deinococcus radiophilus sequencing paper close to two years in the making, tentatively titled “Draft genome assembly of Deinococcus radiophilus from single Nanopore flowcell hints at plasmids of prophage lineage: An amateur perspective” is almost bioarxiv and plos submission ready, and is going through a second round of formatting check for all the figures and tables. We’ll have our version of Deinococcus radiophilus genome ready to go on NCBI Genbank soon as well, and the quality is quite exceptional – almost incomparably better compared to the draft genome we started with. And all the improvement is based on processing the original data from the first flowcell. We have weeks and weeks of content and updates on this one for anyone interested.
We’ve semi-secretly been maintaining a likely mutant strain of Halobacteria NRC-1 in our lab for over a year now, along with a control culture. We’re currently preparing a genome extraction pipeline, with the aim of sequencing the mutant and the control using one Nanopore Flongle each. We already have a great pipeline for sequencing and assembly from our Deinococcus radiophilus experiment, but more insight on comparative genomic analysis would be necessary. Major updates on this project coming in later as well.
System76 sponsored us a fully decked out Thelio computer, with 64GB of RAM and Ryzen 16 core/32 thread number crunching power. We’re calling this one Inifuss, next to our Horadricube based on Xeon processors. We’ve done some interesting benchmarks on this machine, running scripts synthesizing each of the human chromosome based on the reference genome 38.
Numerous hardware projects are either underway or completed – some of the notable ones include completely analog spectrometer kit, room temperature rotating incubator that’s been running without a cinch continuously for about a year, DNA mutagenesis tool using photosensitive dye, and so on and so forth. We’re expecting major posts on each as well.
Our in-house plasmid, IDM (Infinite Discovery Machine) is version 5 going on 6 – and seems robust enough to handle almost anything we throw at it. Full description and discussions coming soon.
Our github page is alive and well, and contains designs for some of our lab equipment as well as some scripts to make your life easier. Please feel free to check out and provide feedback – we know we could use some improvements. https://github.com/Binomica-Labs/
We also have a directory page of open lab notebooks being maintained by independent researchers. Please contact us if you want your open lab notebook to be added to the list.
I think this is about it for today – tune in for more biology!