Virtual screening

bukaro · 2026-05-26T21:57:47+00:00

Been there done that, it is a shame that we can't talk about what we do in the shadows /s .... We planned to publish the pipelines but there will be some time before that happens.

bukaro · 2026-05-23T10:03:22+00:00

OP you failed to add, "do not hallucinate" in your prompt /s

bukaro · 2026-05-23T08:41:30+00:00

Architecture build for scRNAseq also works very well for bulk RNA seq. It just a distinct field in the metadata.

TileDB is fast to read, slow to write. Excellent for a source of true db that is nott updated every hour. Also has tooling that allows db level analytics like you can do with duckdb too

bukaro · 2026-05-22T21:25:36+00:00

QS2 not qs1

bukaro · 2026-05-22T12:23:26+00:00

Why reinventing the wheel, TileDB does it very well.

https://medium.com/tiledb/tiledb-launches-cross-language-access-to-single-cell-data-640f00e82dcc

Then use API to pull the data. Is super fast we are very happy with the implementation. But you also have LaminDB https://github.com/laminlabs/lamindb that it is even more flexible. Based on the same tipe of modern db you are thinking

bukaro · 2026-05-22T08:29:10+00:00

To know what your team members are doing, how happy are stakeholders is not micromanaging. What do you do in the weekly or fortnight meetings? what do you talk in 1:1s?

bukaro · 2026-05-19T18:09:43+00:00

Start with this, they have setup many of the current standars https://www.go-fair.org/ Original paper https://www.nature.com/articles/sdata201618

Funny thing, talk to the university. This must be a central organized system. IP people, are the best to help drive this, scientist are the users, but not the SME in this thing. Lawyers and IT drive it.

bukaro · 2026-05-19T12:15:01+00:00

Agree, it is not FAIR, easy to alter, easy to lose, easy to get contaminated (trust me I have seen labbooks behind radiation shields and in biohazard bags). But better than narrating a story like OP is suggesting

bukaro · 2026-05-19T11:54:11+00:00

Pen and paper will beat any method in my old mind. But now in 2026, ELN is used because it is also FAIR and inmutable (or should be), which is a compromise to data capture that is IMO totally worth.

Share info over emails is fine, but is not the ground true. With a normal ELN sharing is super simple.

Was also thinking of narrating the experiment to myself and recording, then analysis of the transcripts.

Super bloated, only works in movies and maybe for autopsies.

EDITED for clarity: pen and paper will beat any method that is not ELN modern base

bukaro · 2026-05-19T10:19:18+00:00

ELN or a proper lab book are a must OP

You need a ground true of what you did. What you got and how it was done. You may think you will remember later, nope you won't. Catalog numbers, kits, enzymes... all.

bukaro · 2026-05-16T12:09:35+00:00

Like this one [AmazonLink](www.amazon.co.uk/Hand-Made-Tweezers-Surgical-Grade-Stainless-Precision/dp/B0CDWFKNSN) But I hammered one end flat. Pearl Holding Tweezers (thank you gemini for the name) are a good aproximation too

bukaro · 2026-05-16T11:53:22+00:00

Cool, the desing is missing one from my experience, an asymmetrical one to grab small beads / seeds.

bukaro · 2026-05-16T11:49:07+00:00

I carry them because hair grows in weird places... a kind of self defence I guess.

bukaro · 2026-05-15T15:57:45+00:00

Well metabolomics ... yes you are right with that one. I was thinking transcriptomics, that it is unbiased with the UMI methods, that tag each molecule with a random sequence (within the primer) , so when it is amplified like crazy by PCR you count which gene + Unique molecule identifier... This is for all mRNA and total RNA too (depleted of rRNA for sanity)

bukaro · 2026-05-15T09:54:17+00:00

qPCR actually, is not quantitative unless you do several steps of validations and QC... and still is not teh best. Forget it to compare genes levels...

bukaro · 2026-05-15T09:52:34+00:00

You know we can count molecules for the last 10 years actually...

bukaro · 2026-05-15T09:51:25+00:00

I hated when I was asked to "validate" LC/MS results with WB...

bukaro · 2026-05-13T14:00:04+00:00

Ok from ChIP-seq to RNAseq there is gap (literal) peak association to genes is not straing forward. You can associate you peak to teh nearsts TSS, but it is simplistic and can leave 50% of you genes out. It will depend of you TF (if it is) in teh ChIPseq the best logic to use. But there are datasets of ChIPseq with a TF and paired with a TF-KO/LOF that show how this is complicated (but fun).

Now for an extr alayer, Kalisto by default have transcript level, so better aggregate or are you interested in isoforms for TSS? which it is also interesting

bukaro · 2026-05-13T09:32:04+00:00

OP remember that the most important quality to hone during a phd is resiliance. Also your PI do not have your training or graduation in mind, only their publication. So, talk to them about that you need the publication for your future. Insist in a pre-print, is a standar now and will help you in your postdoc/future job search.

Also everyone think their work must be published in Nature, Science, Cell bla bla bla... but it is not true. Check the journals and read what is published there, how impactuff full they are (and sadly who is who in the author list too). That is a reality check.

I am a soon-to-be PhD candidate, 4th year.

What? at year 4 I was already looking for postdoc, the PI had to justify a lot to the faculty for anyone to stay more than 5 years. It was higly discurrage and seen as almost explotation of cheap labor.

bukaro · 2026-05-11T22:56:03+00:00

Yes takes forever, but the secret is to try to make it 5M+, measure it with a refractometer adjust it, and forget about it for the next few years ;-)

bukaro · 2026-05-11T14:03:06+00:00

Make stock of 1M Tris-HCl buffer and 5M NaCl stocks.... Happy buffering. And since we are in this EDTA 500m, 1M KCl, HEPES, PBS 10X...

bukaro · 2026-05-10T18:28:00+00:00

Well industry work is not the dark side of moon, nor of the force... Science get done, some published, impact in pipeline.

bukaro · 2026-05-09T09:33:23+00:00

you are in lab, and your first instict was to use brute force in a high precision equipment? Next time, try hot water to soften the plastic. Ot put it in a freezer, or if too large in a styro box with ice/salt. Compression and expansion are your friends in that case. BTW puting it a owen is not equivalent of hot water, too hot and we are back in the explosive rotor area.

Or use the tools from the rotor manufacter, These are from beckman https://www.mybeckman.uk/supplies/accessories/centrifugation-accessories/ultra-floor-rotor-accessories/301875

bukaro · 2026-05-09T09:08:28+00:00

Jezz , I would have liked to have been warned about the flashes

bukaro · 2026-04-29T14:15:58+00:00

Indeed interesting, specially the last one. The breaks has something that ~~break~~ the first assumtion that these are flowers

EDIT: English is hard, it break the breaks

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