2026-07-15T04:28:46Z https://njump.me naturepoker https://njump.me/npub1wmp5tem6rsnh7x8naw6wrfvuf7qjw2nuhy25sp7cqyvqv6ja7mns2v5xus https://cdn.masto.host/genomicsocial/accounts/avatars/109/273/655/790/715/542/original/a29e7134a80fe533.png https://cdn.masto.host/genomicsocial/accounts/avatars/109/273/655/790/715/542/original/a29e7134a80fe533.png https://njump.me/nevent1qqsgh799k6wx92ptx8us5gprgjj82hxv5k96p095l3dche2ntn0kraqzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww4ucd8q Experiments with vegemite continues. I picked up a small jar of honey at the tail end of today&#39;s farmer&#39;s market (sometimes there&#39;s a deep discount if they have leftovers &amp; don&#39;t feel like lugging everything back upstate). <br/><br/>Thin layer of vegemite + honey on toast &amp; strong black tea is the best combo so far! 2026-01-31T22:41:09Z https://njump.me/nevent1qqsz5nn8cv20ryxx5gv85aaxwd5u8dlrprqzgj32vg7jp8u5mler9cgzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwweatn4h In reply to <a href='/nevent1qqs87g2c9m36dvrh0tjvhz2xgsdhrmn8grwjrzyarfakqcqyexuh37cwt6htg'>nevent1q…6htg</a><br/>_________________________<br/><br/>ooh that&#39;s a long trip. This is my first long haul Amtrak so I don&#39;t know what to expect. Granted, I don&#39;t think the view on Lakeshore limited is as spectacular as the cross-continent ones 2025-06-15T19:56:28Z https://njump.me/nevent1qqsfc52vc0x5hmccgheyjjx8fh5qfhlx4u5wyny0pzajgq032gzsrfszypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwu4g7nn 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<br/> <img src="https://cdn.masto.host/genomicsocial/media_attachments/files/114/689/084/308/496/450/original/bae366059c9cbbdf.jpg"> <br/> 2025-06-15T19:42:27Z https://njump.me/nevent1qqsgw72t4ytsn62r20kmjensw59qx0my0esqnsu4wrhej209de8x0hszypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwhw42re It looks like I need to manually untangle and thread my way through 100k bp worth of this 😬<br/> <img src="https://cdn.masto.host/genomicsocial/media_attachments/files/114/420/680/969/113/687/original/79428070638f7e77.png"> <br/> 2025-04-29T10:04:56Z https://njump.me/nevent1qqs2def5tmtpc7fkyh37pgga0k4vjp04aw3p50qp3c8yfur60ue993gzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwyfeps3 Question for #archaea #microbiology #bioinformatics folks: I&#39;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. <br/><br/>Anyone else dealt with something similar? What could I even be looking at? 2025-04-28T15:43:39Z https://njump.me/nevent1qqsy9ygq2tp78dnevawp4s3vtua775u8xmz94m4ja8ey09guqfjawuqzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww6mc4ms In reply to <a href='/nevent1qqsd3c8xn52shdzheruw7qfkj0jg79m3jw6u2mp3reudhmlzhf6vjqc0mhkma'>nevent1q…hkma</a><br/>_________________________<br/><br/>bummer 😞 I think I&#39;ll still have to get a corrections print out for future researcher&#39;s sake 2025-04-20T11:39:50Z https://njump.me/nevent1qqsxq6hat8e7pv5h3fvyyrg06rlxclk245gllvgwe9tl3x05wpg8xgqzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww0eyg2r In reply to <a href='/nevent1qqsv2tj68tfknsgmqct8g83ac05c73p7kz4fy9uw5mchx0f2s4ayphg0qxf9l'>nevent1q…xf9l</a><br/>_________________________<br/><br/>Huh, scratch that, even the highest scoring 16S match is against whole another species. This bug seems to be completely mischaracterized in the repos. <br/><br/>I have no idea how to even propose a complete species level correction but that might be something I&#39;ll have to learn soon. 2025-04-20T10:28:44Z https://njump.me/nevent1qqsv2tj68tfknsgmqct8g83ac05c73p7kz4fy9uw5mchx0f2s4ayphgzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwaq70u9 For #microbiology and #taxonomy folks. <br/><br/>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? 2025-04-20T10:16:24Z https://njump.me/nevent1qqswvqfedpts6cz5fv939nwyqzqrpw547r4vac8z7xdpqupnt54e0ugzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww7u3hqj For #academia #biology <br/><br/>I started a part-time job at NYMC sequencing core past Oct. PI here (Ravi Sachidanandam) didn&#39;t pay me until late Jan, and is now arguing I shouldn&#39;t be paid for earlier period since I wasn&#39;t present full-time. <br/><br/>And now it looks like &#39;official&#39; job contract only covers work from late November onward and he was just lying about backpay. <br/><br/>I don&#39;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? 2025-04-08T12:31:22Z https://njump.me/nevent1qqs8fppkvdnwyqmfpy393uqtllya8ucw8m09kmc0xhrgsmqsl4xjufczypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww3arkge Received invitation to submit a review article to an established academic journal - it&#39;ll be on a topic adjacent to long read sequencing analysis and #Archaea <br/><br/>Not too bad for a warehouse worker sequencing out of an artists&#39; studio, IMHO! I&#39;m feeling pretty nervous though.<br/><br/>Any good resources out there for first-time review article writers? <br/><br/>#microbiology #bioinformatics #sequencing 2025-02-05T05:01:05Z https://njump.me/nevent1qqs9zj82v5y0dtjlugjn4n2vqjmg9hswpajyjfjaj0qfcmljghsqqrszypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwzrdzp9 Silence from your usual silicon valley talking heads &amp; forums on the latest going ons had been deafening. <br/><br/>Normally they have a take on everything under the sun. 2025-02-02T22:12:07Z https://njump.me/nevent1qqs9t29cwqgp3cmxwrxxsxaszwuc8zd2dyd4mpg92rnlj0suww3p8rgzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww5f56gq 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. <br/><br/>Can&#39;t wait to apply some long reads into the workflow soon! 2024-12-21T02:13:09Z https://njump.me/nevent1qqs0k3mpuc376x8upajr9ynd9la2az3rzzm85vxr8wspycuss2wh9eqzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww4af8rr #bioinformatics folks, riddle me this. Had a weird chat with a lab&#39;s head scientist/bioinformatician. <br/><br/>He&#39;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.<br/><br/>What do you think? 2024-11-25T22:45:27Z https://njump.me/nevent1qqsq9lq56e6zdwen9xs78xwqadlx9e3fv3k9thk0p8zw4ky23h4xeeqzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwt8gnrx 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&#39;m thinking some mineral slipped through in the media making, but am curious. 2024-11-16T05:22:58Z https://njump.me/nevent1qqsttxtl63ax9ws3f90q5df7n95xaj35vxs769tgea8jtlxeunhm97szypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww9ftwxq I&#39;m also on the new biocreatives index that&#39;s been making the rounds. Sweet!<br/><br/>Lots of interesting people on there open to freelance/contract work. <br/><br/><a href="https://www.biocreativeindex.com/">https://www.biocreativeindex.com/</a> 2024-08-30T07:23:06Z https://njump.me/nevent1qqs0tvaqmkz6y8570v5wf0zrw3gmcs76jvpnzcgugfr8ad0pme2krrgzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwqrcv0d Assembling this linear chromosome is really kicking my behind. Working with long-long reads, I&#39;m pretty sure the darn thing is series of 2x/3x/4x copies of operons held together by repeat sequences. <br/><br/>#bioinformatics #sequencing 2024-08-24T03:19:41Z https://njump.me/nevent1qqsdsvz86xepre9gm2nujux6rw787e9as4hksum23cfkjjlc3ky8t7czypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwlm7uxa Another used bookstore find. Reminded me of when I first read E. O. Wilson&#39;s Consilience so many years ago. Considering where Gould stand on the spectrum, this ought to be an interesting read.<br/> <img src="https://cdn.masto.host/genomicsocial/media_attachments/files/112/963/061/209/067/380/original/acc520f301b52772.jpg"> <br/> 2024-08-14T23:52:39Z https://njump.me/nevent1qqsqmj5x74p3m40hgse09g9tq4kr6dtk2dz3mf50k0j5haunmtya35qzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww3w8wuz Reading through an interesting thread on latest conda shenanigans. <br/><br/>Conda TOS changed last year, and they&#39;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.<br/><br/>#bioinformatics 2024-08-07T20:30:44Z https://njump.me/nevent1qqst3fhukzmp3mz386auwpj84ynhg5vqje0nzjg3fvndwe35p9st60qzypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmww03ch62 In reply to <a href='/nevent1qqsyp0y73nudp8kw8k8zjj76scxf8qh8sgelzp9ucaulgnxvk329ppsknwawk'>nevent1q…wawk</a><br/>_________________________<br/><br/>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. 2024-07-02T20:26:46Z https://njump.me/nevent1qqsg90ppz4546t5yehc86qga29mdfasas2xxsrmz62408qg6dnjjyjszypmvx3080gwzwlcc704mfcd9n38czfe20ju32jq8mqq3spn2thmwwel5wyu I&#39;m on bunch of citsci type mailing lists, and wow only jobs I&#39;ve seen posted there for the last few of years were for directors and managers. Don&#39;t they also need at least an occasional researcher or two? 2024-07-02T20:18:35Z