naturepoker

Amateur biologist at Binomica Labs. Studying Archaea from the Pangean era. Sequencing and assembling odds and ends.

#amateurbiology #microbiology #evolution #phylogeny #phylogenetics #phages #sequencing
#archaea #bioinformatics

My lab note: http://naturepoker.wordpress.com
Publications: https://orcid.org/0000-0002-6977-5440
Home page: https://naturepoker.github.io/
Our research group: https://binomicalabs.org/lab-notes-directory/

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Last Notes

2026-01-31 22:41:09 GMT

Experiments with vegemite continues. I picked up a small jar of honey at the tail end of today's farmer's market (sometimes there's a deep discount if they have leftovers & don't feel like lugging everything back upstate).
Thin layer of vegemite + honey on toast & strong black tea is the best combo so far!

2025-06-15 19:56:28 GMT

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ooh that's a long trip. This is my first long haul Amtrak so I don't know what to expect. Granted, I don't think the view on Lakeshore limited is as spectacular as the cross-continent ones

2025-06-15 19:42:27 GMT

Heading out to LA from NY by train. My home for the next 18 hours (to Chicago transfer). Always impressed by how roomy the seats are. #amtrak #train
https://cdn.masto.host/genomicsocial/media_attachments/files/114/689/084/308/496/450/original/bae366059c9cbbdf.jpg

2025-04-29 10:04:56 GMT

It looks like I need to manually untangle and thread my way through 100k bp worth of this 😬
https://cdn.masto.host/genomicsocial/media_attachments/files/114/420/680/969/113/687/original/79428070638f7e77.png

2025-04-28 15:43:39 GMT

Question for #archaea #microbiology #bioinformatics folks: I'm looking at a specific contig in an Archaeal genome with repeat elements that remain difficult to resolve even with 100~1000x coverage and minimum 10k read length.
Anyone else dealt with something similar? What could I even be looking at?

2025-04-20 11:39:50 GMT

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bummer 😞 I think I'll still have to get a corrections print out for future researcher's sake

2025-04-20 10:28:44 GMT

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Huh, scratch that, even the highest scoring 16S match is against whole another species. This bug seems to be completely mischaracterized in the repos.
I have no idea how to even propose a complete species level correction but that might be something I'll have to learn soon.

2025-04-20 10:16:24 GMT

For #microbiology and #taxonomy folks.
I have a microbial strain with 99.80% 16S identity match to closest known species, yet also shows 10% difference in ANI and over a megabase difference in genome length to the said species. Should this still be considered the same species based solely on 16S match?

2025-04-08 12:31:22 GMT

For #academia #biology
I started a part-time job at NYMC sequencing core past Oct. PI here (Ravi Sachidanandam) didn't pay me until late Jan, and is now arguing I shouldn't be paid for earlier period since I wasn't present full-time.
And now it looks like 'official' job contract only covers work from late November onward and he was just lying about backpay.
I don't even care about the money - but I would like to get a warning out there about this lab. What would be a good way for this?

2025-02-05 05:01:05 GMT

Received invitation to submit a review article to an established academic journal - it'll be on a topic adjacent to long read sequencing analysis and #Archaea
Not too bad for a warehouse worker sequencing out of an artists' studio, IMHO! I'm feeling pretty nervous though.
Any good resources out there for first-time review article writers?
#microbiology #bioinformatics #sequencing

2025-02-02 22:12:07 GMT

Silence from your usual silicon valley talking heads & forums on the latest going ons had been deafening.
Normally they have a take on everything under the sun.

2024-12-21 02:13:09 GMT

I gotta tell you, my fellow amateurs. Working with transcriptome, both on the bench and with data is a whole different can of paradigm shifting worms compared to the usual DNA assembly.
Can't wait to apply some long reads into the workflow soon!

2024-11-25 22:45:27 GMT

#bioinformatics folks, riddle me this. Had a weird chat with a lab's head scientist/bioinformatician.
He's claiming 150x2 illumina data (600m reads I think - so 90 gigabases?) is computationally impossible to do kmer screening for microbial/viral contamination (this is mRNA-seq data from a eukaryotic sample). I am VERY skeptical on his statement, but I only have exp with long reads in 5~9gb range.
What do you think?

2024-11-16 05:22:58 GMT

Quick question for #archaea folks - have you ever seen Halobacterial culture bottles produce extremely hard, round, dark-brown crystals within the liquid media at some point? I'm thinking some mineral slipped through in the media making, but am curious.

2024-08-30 07:23:06 GMT

I'm also on the new biocreatives index that's been making the rounds. Sweet!
Lots of interesting people on there open to freelance/contract work.
https://www.biocreativeindex.com/

2024-08-24 03:19:41 GMT

Assembling this linear chromosome is really kicking my behind. Working with long-long reads, I'm pretty sure the darn thing is series of 2x/3x/4x copies of operons held together by repeat sequences.
#bioinformatics #sequencing

2024-08-14 23:52:39 GMT

Another used bookstore find. Reminded me of when I first read E. O. Wilson's Consilience so many years ago. Considering where Gould stand on the spectrum, this ought to be an interesting read.
https://cdn.masto.host/genomicsocial/media_attachments/files/112/963/061/209/067/380/original/acc520f301b52772.jpg

2024-08-07 20:30:44 GMT

Reading through an interesting thread on latest conda shenanigans.
Conda TOS changed last year, and they're blocking IPs from larger nonprofit organizations (such as universities) with more than 200 connections/downloads. Connections will remain blocked until targeted organizations pay up.
#bioinformatics

2024-07-02 20:26:46 GMT

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yeah in the US these are mostly nonprofit organizations, and seems to often ask for scientists and researchers on volunteer basis. Very strange and likely unsustainable.

2024-07-02 20:18:35 GMT

I'm on bunch of citsci type mailing lists, and wow only jobs I've seen posted there for the last few of years were for directors and managers. Don't they also need at least an occasional researcher or two?